WO2003035829A2 - Detection electrique d'adn basee sur un ensemble et mettant en application des sondes sous forme de nanoparticules - Google Patents

Detection electrique d'adn basee sur un ensemble et mettant en application des sondes sous forme de nanoparticules Download PDF

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Publication number
WO2003035829A2
WO2003035829A2 PCT/US2002/032088 US0232088W WO03035829A2 WO 2003035829 A2 WO2003035829 A2 WO 2003035829A2 US 0232088 W US0232088 W US 0232088W WO 03035829 A2 WO03035829 A2 WO 03035829A2
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WO
WIPO (PCT)
Prior art keywords
oligonucleotides
nanoparticles
nucleic acid
bound
sequence
Prior art date
Application number
PCT/US2002/032088
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English (en)
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WO2003035829A3 (fr
Inventor
So-Jung Park
Thomas A. Taton
Chad A. Mirkin
Robert L. Letsinger
Robert C. Mucic
James J. Storhoff
Robert Elghanian
Viswanadham Garimella
Zhi Li
Gang Lu
Original Assignee
Nanosphere, Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US10/008,978 external-priority patent/US6984491B2/en
Application filed by Nanosphere, Inc. filed Critical Nanosphere, Inc.
Priority to CA2463323A priority Critical patent/CA2463323C/fr
Priority to EP02799155A priority patent/EP1478774A4/fr
Priority to AU2002363062A priority patent/AU2002363062B2/en
Priority to JP2003538330A priority patent/JP4347049B2/ja
Publication of WO2003035829A2 publication Critical patent/WO2003035829A2/fr
Publication of WO2003035829A3 publication Critical patent/WO2003035829A3/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means

Definitions

  • 60/031,809 filed July 29, 1996; 60/176,409, filed January 13, 2000; 60/192699, filed March 28, 2000; 60/200,161, filed April 26, 2000; 60/213,906, filed June 26, 2000; 60/224*631, filed August 11, 2000; 60/254,392, filed December 8, 2000; 60/254,418, filed December 8, 2000; -60/255,235, filed December 11, 2000; 60/255,236, filed December 11, 2000; 60/282,640, filed April 9, 2001; and 60/327,864, filed October 8, 2001 is also claimed, the disclosures are inco ⁇ orated by reference.
  • the invention relates to methods of detecting analytes, including nucleic acids and proteins, whether natural or synthetic, and whether modified or unmodified.
  • the invention also relates to materials for detecting analytes, including nucleic acids and proteins, and methods of making those materials.
  • the invention further relates to methods of nanofabrication.
  • the invention relates to methods of separating a selected nucleic acid from other nucleic acids.
  • Colloidal gold-protein probes have found wide applications in i ⁇ ununocytochemistry [S. Garzon and M. Bendayan, "Colloidal Gold Probe: An Overview of its Applications in Viral Cytochemistry,” in “Immuno-Gold Electron Microscopy,” Ed. A. D. Hyatt and B. T. Eaton, CrC Press, Ann Arbor, MI (1993); J. E. Beesley, Colloidal Gold: A New Perspective for Cytochemical marking," Oxford University Press, Oxford, (1989)]. These probes have been prepared by adsorbing the antibodies onto the gold surface from an aqueous solution under carefully defined conditions.
  • the complexes produced in this manner are functional but suffer from several drawbacks: e.g., some of the protein desorbs on standing, liberating antibody into solution that competes with adsorbed antibodies for the antigen target; the activity is low since the amount adsorbed is low and some of the antibody denatures on adso ⁇ tion; and the protein-coated particles are prone to self aggregation, especially in solutions of high ionic strength.
  • An alternative means for preparing nanoparticle-protein probes has been described by J. E. Hainfeld, R. D. Leone, F. R. Furuya, and R. D. Powell (U.S. Patent 5,521,289, May 28, 1996, "Small Organometallic Probes").
  • this procedure involves reduction of a gold salt in an organic solvent containing a triarylphosphine or mercapto-alkyl derivative bearing a reactive substituent, X, to give small nanoparticles (50-70 gold atoms) carrying X substituents on linkers bound to the surface through Au-P or Au-S bonds. Subsequently the colloidal solution is treated with a protein bearing a substituent Y that reacts with X to link the protein covalently to the nanoparticle. Work with these nanoparticle is limited by the poor water solubility of many proteins, which limits the range of protein-nanoparticle conjugates that can be utilized effectively.
  • nanoparticles can be used in variety of detection formats that take advantage of their size dependent scattering, catalytic properties, abso ⁇ tion characteristics, and Raman-enhancing properties to develop systems that are substantially more sensitive and selective than their molecular fluorophore counte ⁇ arts (J. J. Storhoff, R. Elghanian, R. C. Mucic, C. A.
  • the invention provides methods of detecting nucleic acids.
  • the method comprises contacting a nucleic acid with a type of nanoparticles having oligonucleotides attached thereto (nanoparticle-oligonucleotide conjugates).
  • the nucleic acid has at least two portions, and the oligonucleotides on each nanoparticle have a sequence complementary to the sequences of at least two portions of the nucleic acid.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the nucleic acid.
  • the hybridization of the oligonucleotides on the nanoparticles, with the nucleic acid results in a detectable change.
  • the method comprises contacting a nucleic acid with at least two types of nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides on the first type of nanoparticles have a sequence complementary to a first portion of the sequence of the nucleic acid.
  • the oligonucleotides on the second type of nanoparticles have a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the method comprises providing a substrate having a first type of nanoparticles attached thereto.
  • the first type of nanoparticles has oligonucleotides attached thereto, and the oligonucleotides have a sequence complementary to a first portion of the sequence of a nucleic acid.
  • the substrate is contacted with the nucleic acid under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the nucleic acid.
  • a second type of nanoparticles having oligonucleotides attached thereto is provided.
  • the oligonucleotides have a sequence complementary to one or more other portions of the sequence of the nucleic acid, and the nucleic acid bound to the substrate is contacted with the second type of nanoparticle-oligonucleotide conjugates under conditions effective to allow hybridization of the oligonucleotides on the second type of nanoparticles with the nucleic acid.
  • a detectable change may be observable at this point.
  • the method may further comprise providing a binding oligonucleotide having a selected sequence having at least two portions, the first portion being complementary to at least a portion of the sequence of the oligonucleotides on the second type of nanoparticles.
  • the binding oligonucleotide is contacted with the second type of nanoparticle-oligonucleotide conjugates bound to the substrate under conditions effective to allow hybridization of the binding oligonucleotide to the oligonucleotides on the nanoparticles.
  • a third type of nanoparticles having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to the sequence of a second portion of the binding oligonucleotide is contacted with the binding oligonucleotide bound to the substrate under conditions effective to allow hybridization of the binding oligonucleotide to the oligonucleotides on the nanoparticles.
  • the detectable change produced by these hybridizations is observed.
  • the method comprises contacting a nucleic acid with a substrate having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to a first portion of the sequence of the nucleic acid.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the substrate with the nucleic acid.
  • the nucleic acid bound to the substrate is contacted with a first type of nanoparticles having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the nucleic acid.
  • the first type of nanoparticle- oligonucleotide conjugates bound to the substrate is contacted with a se ⁇ ond type of nanoparticles having oligonucleotides attached thereto, the oligonucleotides on the second type of nanoparticles having a sequence complementary to at least a portion of the sequence of the oligonucleotides on the first type of nanoparticles, the contacting taking place under conditions effective to allow hybridization of the oligonucleotides on the first and second types of nanoparticles. Finally, a detectable change produced by these hybridizations is observed.
  • the method comprises contacting a nucleic acid with a substrate having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to a first portion of the sequence of the nucleic acid.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the substrate with the nucleic acid.
  • the nucleic acid bound to the substrate is contacted with liposomes having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to a portion of the sequence of the nucleic acid.
  • This contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the liposomes with the nucleic acid.
  • the liposome-oligonucleotide conjugates bound to the substrate are contacted with a first type of nanoparticles having at least a first type of oligonucleotides attached thereto.
  • the first type of oligonucleotides have a hydrophobic group attached to the end not attached to the nanoparticles, and the contacting takes place under conditions effective to allow attachment of the oligonucleotides on the nanoparticles to the liposomes as a result of hydrophobic interactions. A detectable change may be observable at this point.
  • the method may further comprise contacting the first type of nanoparticle-oligonucleotide conjugates bound to the liposomes with a second type of nanoparticles having oligonucleotides attached thereto.
  • the first type of nanoparticles have a second type of oligonucleotides attached thereto which have a sequence complementary to at least a portion of the sequence of the oligonucleotides on the second type of nanoparticles, and the oligonucleotides on the second type of nanoparticles having a sequence complementary to at least a portion of the sequence of the second type of oligonucleotides on the first type of nanoparticles.
  • the method comprises contacting a nucleic acid to be detected with a substrate having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a first portion of the sequence of said nucleic acid
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the substrate with said nucleic acid.
  • said nucleic acid bound to the substrate is contacted with a type of nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a second portion of the sequence of said nucleic acid.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with said nucleic acid.
  • the substrate is contacted with silver stain to produce a detectable change, and the detectable change is observed.
  • the method comprises providing a substrate having a first type of nanoparticles attached thereto.
  • the nanoparticles have oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to a first portion of the sequence of a nucleic acid to be detected.
  • the nucleic acid is contacted with the nanoparticles attached to the substrate under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with said nucleic acid.
  • an aggregate probe comprising at least two types of nanoparticles having oligonucleotides attached thereto is provided.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to them. At least one of the types of nanoparticles of the aggregate probe have oligonucleotides attached thereto which have a sequence complementary to a second portion of the sequence of said nucleic acid. Finally, said nucleic acid bound to the substrate is contacted with the aggregate probe under conditions effective to allow hybridization of the oligonucleotides on the aggregate probe with said nucleic acid, and a detectable change is observed.
  • the method comprises providing a substrate having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a first portion of the sequence of a nucleic acid to be detected.
  • An aggregate probe comprising at least two types of nanoparticles having oligonucleotides attached thereto is provided.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to them.
  • At least one of the types of nanoparticles of the aggregate probe have oligonucleotides attached thereto which have a sequence complementary to a second portion of the sequence of said nucleic acid.
  • the nucleic acid, the substrate and the aggregate probe are contacted under conditions effective to allow hybridization of said nucleic acid with the oligonucleotides on the aggregate probe and with the oligonucleotides on the substrate, and a detectable change is observed.
  • the method comprises providing a substrate having oligonucleotides attached thereto.
  • An aggregate probe comprising at least two types of nanoparticles having oligonucleotides attached thereto is provided.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to them.
  • At least one of the types of nanoparticles of the aggregate probe have oligonucleotides attached thereto which have a sequence complementary to a first portion of the sequence of a nucleic acid to be detected.
  • a type of nanoparticles having at least two types of oligonucleotides attached thereto is provided
  • the first type of oligonucleotides has a sequence complementary to a second portion of the sequence of said nucleic acid
  • the second type of oligonucleotides has a sequence complementary to at least a portion of the sequence of the oligonucleotides attached to the substrate.
  • the nucleic acid, the aggregate probe, the nanoparticles and the substrate are contacted under conditions effective to allow hybridization of said nucleic acid with the oligonucleotides on the aggregate probe and on the nanoparticles and hybridization of the oligonucleotides on the nanoparticles with the oligonucleotides on the substrate, and a detectable change is observed.
  • the method comprises contacting a nucleic acid to be detected with a substrate having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a first portion of the sequence of said nucleic acid.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the substrate with said nucleic acid.
  • the nucleic acid bound to the substrate is contacted with liposomes having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to a portion of the sequence of said nucleic acid.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the liposomes with said nucleic acid.
  • An aggregate probe comprising at least two types of nanoparticles having oligonucleotides attached thereto is provided.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to them, at least one of the types of nanoparticles of the aggregate probe having oligonucleotides attached thereto which have a hydrophobic group attached to the end not attached to the nanoparticles.
  • the liposomes bound to the substrate are contacted with the aggregate probe under conditions effective to allow attachment of the oligonucleotides on the aggregate probe to the liposomes as a result of hydrophobic interactions, and a detectable change is observed.
  • the method comprises providing a substrate having oligonucleotides attached thereto.
  • the oligonucleotides having a sequence complementary to a first portion of the sequence of a nucleic acid to be detected.
  • a core probe comprising at least two types of nanoparticles is provided.
  • Each type of nanoparticles has oligonucleotides attached thereto which are complementary to the oligonucleotides on at least one of the other types of nanoparticles.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of the oligonucleotides attached to them.
  • a type of nanoparticles having two types of oligonucleotides attached thereto is provided.
  • the first type of oligonucleotides has a sequence complementary to a second portion of the sequence of said nucleic acid
  • the second type of oligonucleotides has a sequence complementary to a portion of the sequence of the oligonucleotides attached to at least one of the types of nanoparticles of the core probe.
  • the nucleic acid, the nanoparticles, the substrate and the core probe are contacted under conditions effective to allow hybridization of said nucleic acid with the oligonucleotides on the nanoparticles and with the oligonucleotides on the substrate and to allow hybridization of the oligonucleotides on the nanoparticles with the oligonucleotides on the core probe, and a detectable change is observed.
  • Another embodiment of the method comprises providing a substrate having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to a first portion of the sequence of a nucleic acid to be detected.
  • a core probe comprising at least two types of nanoparticles is provided.
  • Each type of nanoparticles has oligonucleotides attached thereto which are complementary to the oligonucleotides on at least one other type of nanoparticles.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of the oligonucleotides attached to them.
  • a type of linking oligonucleotides comprising a sequence complementary to a second portion of the sequence of said nucleic acid and a sequence complementary to a portion of the sequence of the oligonucleotides attached to at least one of the types of nanoparticles of the core probe is provided.
  • the nucleic acid, the linking oligonucleotides, the substrate and the core probe are contacted under conditions effective to allow hybridization of said nucleic acid with the linking oligonucleotides and with the oligonucleotides on the substrate and to allow hybridization of the oligonucleotides on the linking oligonucleotides with the oligonucleotides on the core probe, and a detectable change is observed.
  • the method comprises providing nanoparticles having oligonucleotides attached thereto and providing one or more types of binding oligonucleotides.
  • Each of the binding oligonucleotides has two portions. The sequence of one portion is complementary to the sequence of one of the portions of the nucleic acid, and the sequence of the other portion is complementary to the sequence of the oligonucleotides on the nanoparticles.
  • the nanoparticle- oligonucleotide conjugates and the binding oligonucleotides are contacted under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the binding oligonucleotides.
  • the nucleic acid and the binding oligonucleotides are contacted under conditions effective to allow hybridization of the binding oligonucleotides with the nucleic acid. Then, a detectable change is observed.
  • the nanoparticle-oligonucleotide conjugates may be contacted with the binding oligonucleotides prior to being contacted with the nucleic acid, or all three may be contacted simultaneously.
  • the method comprises contacting a nucleic acid with at least two types of particles having oligonucleotides attached thereto.
  • the oligonucleotides on the first type of particles have a sequence complementary to a first portion of the sequence of the nucleic acid and have energy donor molecules on the ends not attached to the particles.
  • the oligonucleotides on the second type of particles have a sequence complementary to a second portion of the sequence of the nucleic acid and have energy acceptor molecules on the ends not attached to the particles.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the particles with the nucleic acid, and a detectable change brought about by this hybridization is observed.
  • the energy donor and acceptor molecules may be fluorescent molecules.
  • the method comprises providing a type of microspheres having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a first portion of the sequence of the nucleic acid and are labeled with a fluorescent molecule.
  • a type of nanoparticles having oligonucleotides attached thereto and which produce a detectable change is also provided. These oligonucleotides have a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the nucleic acid is contacted with the microspheres and the nanoparticles under conditions effective to allow hybridization of the oligonucleotides on the latex microspheres and on the nanoparticles with the nucleic acid. Then, changes in fluorescence, another detectable change, or both are observed.
  • the method comprises providing a first type of metallic or semiconductor nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a first portion of the sequence of the nucleic acid and are labeled with a fluorescent molecule.
  • a second type of metallic or semiconductor nanoparticles having oligonucleotides attached thereto is also provided. These oligonucleotides have a sequence complementary to a second portion of the sequence of the nucleic acid and are also labeled with a fluorescent molecule.
  • the nucleic acid is contacted with the two types of nanoparticles under conditions effective to allow hybridization of the oligonucleotides on the two types of nanoparticles with the nucleic acid. Then, changes in fluorescence are observed.
  • the method comprises providing a type of particle having oligonucleotides attached thereto.
  • the oligonucleotides have a first portion and a second portion, both portions being complementary to portions of the sequence of the nucleic acid.
  • a type of probe oligonucleotides comprising a first portion and a second portion is also provided.
  • the first portion has a sequence complementary to the first portion of the oligonucleotides attached to the particles, and both portions are complementary to portions of the sequence of the nucleic acid.
  • the probe oligonucleotides are also labeled with a reporter molecule at one end.
  • the particles and the probe oligonucleotides are contacted under conditions effective to allow for hybridization of the oligonucleotides on the particles with the probe oligonucleotides to produce a satellite probe.
  • the satellite probe is contacted with the nucleic acid under conditions effective to provide for hybridization of the nucleic acid with the probe oligonucleotides.
  • the particles are removed and the reporter molecule detected.
  • a nucleic acid is detected by contacting the nucleic acid with a substrate having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a first portion of the sequence of the nucleic acid.
  • the oligonucleotides are located between a pair of electrodes located on the substrate.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the substrate with the nucleic acid.
  • the nucleic acid bound to the substrate is contacted with a type of nanoparticles.
  • the nanoparticles are made of a material which can conduct electricity.
  • the nanoparticles will have one or more types of oligonucleotides attached to them, at least one of the types of oligonucleotides having a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the nucleic acid. If the nucleic acid is present, a change in conductivity can be detected.
  • the substrate will have a plurality of pairs of electrodes located on it in an array to allow for the detection of multiple portions of a single nucleic acid, the detection of multiple different nucleic acids, or both. Each of the pairs of electrodes in the array will have a type of oligonucleotides attached to the substrate between the two electrodes.
  • the invention further provides a method of detecting a nucleic acid wherein the method is performed on a substrate.
  • the method comprises detecting the presence, quantity or both, of the nucleic acid with an optical scanner.
  • the invention further provides kits for detecting nucleic acids.
  • the kit comprises at least one container, the container holding at least two types of nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides on the first type of nanoparticles have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the oligonucleotides on the second type of nanoparticles have a sequence complementary to the sequence of a second portion of the nucleic acid.
  • the kit may comprise at least two containers.
  • the first container holds nanoparticles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the second container holds nanoparticles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a second portion of the nucleic acid.
  • the kit comprises at least one container.
  • the container holds metallic or semiconductor nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to portion of a nucleic acid and have fluorescent molecules attached to the ends of the oligonucleotides not attached to the nanoparticles.
  • the kit comprises a substrate, the substrate having attached thereto nanoparticles, the nanoparticles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the kit also includes a first container holding nanoparticles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a second portion of the nucleic acid.
  • the kit further includes a second container holding a binding oligonucleotide having a selected sequence having at least two portions, the first portion being complementary to at least a portion of the sequence of the oligonucleotides on the nanoparticles in the first container.
  • the kit also includes a third container holding nanoparticles having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to the sequence of a second portion of the binding oligonucleotide.
  • the kit comprises a substrate having oligonucleotides attached thereto which have a sequence complementary to the sequence of a first portion of a nucleic acid, a first container holding nanoparticles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a second portion of the nucleic acid, and a second container holding nanoparticles having oligonucleotides attached thereto which have a sequence complementary to at least a portion of the oligonucleotides attached to the nanoparticles in the first container.
  • the kit comprises a substrate, a first container holding nanoparticles, a second container holding a first type of oligonucleotides having a sequence complementary to the sequence of a first portion of a nucleic acid, a third container holding a second type of oligonucleotides having a sequence complementary to the sequence of a second portion of the nucleic acid, and a fourth container holding a third type of oligonucleotides having a sequence complementary to at least a portion of the sequence of the second type of oligonucleotides.
  • the kit comprises a substrate having oligonucleotides attached thereto which have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the kit also includes a first container holding liposomes having oligonucleotides attached thereto which have a sequence complementary to the sequence of a second portion of the nucleic acid and a second container holding nanoparticles having at least a first type of oligonucleotides attached thereto, the first type of oligonucleotides having a hydrophobic group attached to the end not attached to the nanoparticles so that the nanoparticles can be attached to the liposomes by hydrophobic interactions.
  • the kit may further comprise a third container holding a second type of nanoparticles having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to at least a portion of the sequence of a second type of oligonucleotides attached to the first type of nanoparticles.
  • the second type of oligonucleotides attached to the first type of nanoparticles have a sequence complementary to the sequence of the oligonucleotides on the second type of nanoparticles.
  • the kit comprises a substrate having nanoparticles attached to it.
  • the nanoparticles have oligonucleotides attached to them which have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the kit also includes a first container holding an aggregate probe.
  • the aggregated probe comprises at least two types of nanoparticles having oligonucleotides attached to them.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to each of them.
  • At least one of the types of nanoparticles of the aggregate probe has oligonucleotides attached to it which have a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the kit comprises a substrate having oligonucleotides attached to it.
  • the oligonucleotides have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the kit further includes a-first container holding an aggregate probe.
  • the aggregate probe comprises at least two types of nanoparticles having oligonucleotides attached to them.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to each of them.
  • At least one of the types of nanoparticles of the aggregate probe has oligonucleotides attached thereto which have a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the kit comprises a substrate having oligonucleotides attached to it and a first container holding an aggregate probe.
  • the aggregate probe comprises at least two types of nanoparticles having oligonucleotides attached to them.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to each of them.
  • At least one of the types of nanoparticles of the aggregate probe has oligonucleotides attached to it which have a sequence complementary to a first portion of the sequence of the nucleic acid.
  • the kit also includes a second container holding nanoparticles.
  • the nanoparticles have at least two types of oligonucleotides attached to them.
  • the first type of oligonucleotides has a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the second type of oligonucleotides has a sequence complementary to at least a portion of the sequence of the oligonucleotides attached to the substrate.
  • the kit comprises a substrate which has oligonucleotides attached to it.
  • the oligonucleotides have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the kit also comprises a first container holding liposomes having oligonucleotides attached to them.
  • the oligonucleotides have a sequence complementary to the sequence of a second portion of the nucleic acid.
  • the kit further includes a second container holding an aggregate probe comprising at least two types of nanoparticles having oligonucleotides attached to them.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to each of them.
  • At least one of the types of nanoparticles of the aggregate probe has oligonucleotides attached to it which have a hydrophobic groups attached to the ends not attached to the nanoparticles.
  • the kit may comprise a first container holding nanoparticles having oligonucleotides attached thereto.
  • the kit also includes one or more additional containers, each container holding a binding oligonucleotide.
  • Each binding oligonucleotide has a first portion which has a sequence complementary to at least a portion of the sequence of oligonucleotides on the nanoparticles and a second portion which has a sequence complementary to the sequence of a portion of a nucleic acid to be detected.
  • the sequences of the second portions of the binding oligonucleotides may be different as long as each sequence is complementary to a portion of the sequence of the nucleic acid to be detected.
  • the kit comprises a container holding one type of nanoparticles having oligonucleotides attached thereto and one or more types of binding oligonucleotides.
  • Each of the types of binding oligonucleotides has a sequence comprising at least two portions. The first portion is complementary to the sequence of the ohgonucleotides on the nanoparticles, whereby the binding oligonucleotides are hybridized to the oligonucleotides on the nanoparticles in the container(s). The second portion is complementary to the sequence of a portion of the nucleic acid.
  • kits may comprise one or two containers holding-two types of particles.
  • the first type of particles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the oligonucleotides are labeled with an energy donor on the ends not attached to the particles.
  • the second type of particles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a second portion of a nucleic acid.
  • the oligonucleotides are labeled with an energy acceptor on the ends not attached to the particles.
  • the energy donors and acceptors may be fluorescent molecules.
  • the kit comprises a first container holding nanoparticles having oligonucleotides attached thereto.
  • the kit also includes one or more additional containers, each container holding binding oligonucleotides.
  • Each binding oligonucleotide has a first portion which has a sequence complementary to at least a portion of the sequence of oligonucleotides on the nanoparticles and a second portion which has a sequence complementary to the sequence of a portion of a nucleic acid to be detected.
  • the sequences of the second portions of the binding oligonucleotides may be different as long as each sequence is complementary to a portion of the sequence of the nucleic acid to be detected.
  • the kit comprises a container holding one type of nanoparticles having oligonucleotides attached thereto and one or more types of binding oligonucleotides.
  • Each of the types of binding oligonucleotides has a sequence comprising at least two portions. The first portion is complementary to the sequence of the oligonucleotides on the nanoparticles, whereby the binding oligonucleotides are hybridized to the oligonucleotides on the nanoparticles in the container(s). The second portion is complementary to the sequence of a portion of the nucleic acid.
  • the kit comprises at least three containers.
  • the first container holds nanoparticles.
  • the second container holds a first oligonucleotide having a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the third container holds a second oligonucleotide having a sequence complementary to the sequence of a second portion of the nucleic acid.
  • the kit may further comprise a fourth container holding a binding oligonucleotide having a selected sequence having at least two portions, the first portion being complementary to at least a portion of the sequence of the second oligonucleotide, and a fifth container holding an oligonucleotide having a sequence complementary to the sequence of a second portion of the binding oligonucleotide.
  • the kit comprises one or two containers, the container(s) holding two types of particles.
  • the first type of particles having oligonucleotides attached thereto that have a sequence complementary to a first portion of the sequence of a nucleic acid and have energy donor molecules attached to the ends not attached to the nanoparticles.
  • the second type of particles having oligonucleotides attached thereto that have a sequence complementary to a second portion of the sequence of a nucleic acid and have energy acceptor molecules attached to the ends not attached to the nanoparticles.
  • the energy donors and acceptors may be fluorescent molecules.
  • the kit comprises a first container holding a type of microspheres having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a first portion of the sequence of a nucleic acid and are labeled with a fluorescent molecule.
  • the kit also comprises a second container holding a type of nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the kit comprises a first container holding a first type of metallic or semiconductor nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a first portion of the sequence of a nucleic acid and are labeled with a fluorescent molecule.
  • the kit also comprises a second container holding a second type of metallic or semiconductor nanoparticles having oligonucleotides attached thereto. These oligonucleotides have a sequence complementary to a second portion of the sequence of a nucleic acid and are labeled with a fluorescent molecule.
  • the kit comprises a container holding an aggregate probe.
  • the aggregate probe comprises at least two types of nanoparticles having oligonucleotides attached to them.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to each of them.
  • At least one of the types of nanoparticles of the aggregate probe has oligonucleotides attached to it which have a sequence complementary to a portion of the sequence of a nucleic acid.
  • the kit comprises a container holding an aggregate probe.
  • the aggregate probe comprises at least two types of nanoparticles having oligonucleotides attached to them.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to each of them.
  • At least one of the types of nanoparticles of the aggregate probe has oligonucleotides attached to it which have a hydrophobic group attached to the end not attached to the nanoparticles.
  • the kit comprises a container holding a satellite probe.
  • the satellite probe comprises a particle having attached thereto oligonucleotides.
  • the oligonucleotides have a first portion and a second portion, both portions having sequences complementary to portions of the sequence of a nucleic acid.
  • the satellite probe also comprises probe oligonucleotides hybridized to the oligonucleotides attached to the nanoparticles.
  • the probe oligonucleotides have a first portion and a second portion.
  • the first portion has a sequence complementary to the sequence of the first portion of the oligonucleotides attached to the particles, and both portions have sequences complementary to portions of the sequence of the nucleic acid.
  • the probe oligonucleotides also have a reporter molecule attached to one end.
  • the kit comprising a container holding a core probe, the core probe comprising at least two types of nanoparticles having oligonucleotides attached thereto, the nanoparticles of the core probe being bound to each other as a result of the hybridization of some of the oligonucleotides attached to them.
  • the kit comprises a substrate having attached to it at least one pair of electrodes with oligonucleotides attached to the substrate between the electrodes.
  • the oligonucleotides have a sequence complementary to a first portion of the sequence of a nucleic acid to be detected.
  • the invention also provides the satellite probe, an aggregate probe and a core probe.
  • the invention further provides a substrate having nanoparticles attached thereto.
  • the nanoparticles may have oligonucleotides attached thereto which have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the invention also provides a metallic or semiconductor nanoparticle having oligonucleotides attached thereto.
  • the oligonucleotides are labeled with fluorescent molecules at the ends not attached to the nanoparticle.
  • the invention further provides a method of nanofabrication. The method comprises providing at least one type of linking oligonucleotide having a selected sequence, the sequence of each type of linking oligonucleotide having at least two portions.
  • the method further comprises providing one or more types of nanoparticles having oligonucleotides attached thereto, the oligonucleotides on each type of nanoparticles having a sequence complementary to a portion of the sequence of a linking oligonucleotide.
  • the linking oligonucleotides and nanoparticles are contacted under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles to the linking oligonucleotides so that a desired nanomaterials or nanostructure is formed.
  • the invention provides another method of nanofabrication.
  • This method comprises providing at least two types of nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides on the first type of nanoparticles have a sequence complementary to that of the oligonucleotides on the second type of nanoparticles.
  • the oligonucleotides on the second type of nanoparticles have a sequence complementary to that of the oligonucleotides on the first type of nanoparticle-oligonucleotide conjugates.
  • the first and second types of nanoparticles are contacted under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles to each other so that a desired nanomaterials or nanostructure is formed.
  • the invention further provides nanomaterials or nanostructures composed of nanoparticles having oligonucleotides attached thereto, the nanoparticles being held together by oligonucleotide connectors.
  • the invention also provides a composition comprising at least two types of nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides on the first type of nanoparticles have a sequence complementary to the sequence of a first portion of a nucleic acid or a linking oligonucleotide.
  • the oligonucleotides on the second type of nanoparticles have a sequence complementary to the sequence of a second portion of the nucleic acid or linking oligonucleotide.
  • the invention further provides an assembly of containers comprising a first container holding nanoparticles having oligonucleotides attached thereto, and a second container holding nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides attached to the nanoparticles in the first container have a sequence complementary to that of the oligonucleotides attached to the nanoparticles in the second container.
  • the oligonucleotides attached to the nanoparticles in the second container have a sequence complementary to that of the oligonucleotides attached to the nanoparticles in the first container.
  • the invention also provides a nanoparticle having a plurality of different oligonucleotides attached to it.
  • the invention further provides a method of separating a selected nucleic acid having at least two portions from other nucleic acids.
  • the method comprises providing one or more types of nanoparticles having oligonucleotides attached thereto, the oligonucleotides on each of the types of nanoparticles having a sequence complementary to the sequence of one of the portions of the selected nucleic acid.
  • the selected nucleic acid and other nucleic acids are contacted with the nanoparticles under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the selected nucleic acid so that the nanoparticles hybridized to the selected nucleic acid aggregate and precipitate.
  • the invention provides methods of making unique nanoparticle- oligonucleotide conjugates.
  • the first such method comprises binding oligonucleotides to charged nanoparticles to produce stable nanoparticle- oligonucleotide conjugates.
  • oligonucleotides having covalently bound thereto a moiety comprising a functional group which can bind to the nanoparticles are contacted with the nanoparticles in water for a time sufficient to allow at least some of the oligonucleotides to bind to the nanoparticles by means of the functional groups.
  • at least one salt is added to the water to form a salt solution.
  • the ionic strength of the salt solution must be sufficient to overcome at least partially the electrostatic repulsion of the oligonucleotides from each other and, either the electrostatic attraction of the negatively-charged oligonucleotides for positively- charged nanoparticles, or the electrostatic repulsion of the negatively-charged oligonucleotides from negatively-charged nanoparticles.
  • the oligonucleotides and nanoparticles are incubated in the salt solution for an additional period of time sufficient to allow sufficient additional oligonucleotides to bind to the nanoparticles to produce the stable nanoparticle-oligonucleotide conjugates.
  • the invention also includes the stable nanoparticle-oligonucleotide conjugates, methods of using the conjugates to detect and separate nucleic acids, kits comprising the conjugates, methods of nanofabrication using the conjugates, and nanomaterials and nanostructures comprising the conjugates.
  • the invention provides another method of binding oligonucleotides to nanoparticles to produce nanoparticle-oligonucleotide conjugates.
  • the method comprises providing oligonucleotides, the oligonucleotides comprising a type of recognition oligonucleotides and a type of diluent oligonucleotides.
  • the oligonucleotides and the nanoparticles are contacted under conditions effective to allow at least some of each of the types of oligonucleotides to bind to the nanoparticles to produce the conjugates.
  • the invention also includes the nanoparticle- oligonucleotide conjugates produced by this method, methods of using the conjugates to detect and separate nucleic acids, kits comprising the conjugates, methods of nanofabrication using the conjugates, and nanomaterials and nanostructures comprising the conjugates.
  • Recognition oligonucleotides are oligonucleotides which comprise a sequence complementary to at least a portion of the sequence of a nucleic acid or oligonucleotide target.
  • “Diluent oligonucleotides” may have any sequence which does not interfere with the ability of the recognition oligonucleotides to be bound to the nanoparticles or to bind to their targets.
  • the invention provides yet another method of binding oligonucleotides to nanoparticles to produce nanoparticle-oligonucleotide conjugates.
  • the method comprises providing oligonucleotides, the oligonucleotides comprising at least one type of recognition oligonucleotides.
  • the recognition oligonucleotides comprise a recognition portion and a spacer portion.
  • the recognition portion of the recognition oligonucleotides has a sequence complementary to at least one portion of the sequence of a nucleic acid or oligonucleotide target.
  • the spacer portion of the . recognition oligonucleotide is designed so that it can bind to the nanoparticles.
  • the recognition portion is spaced away from the surface of the nanoparticles and is more accessible for hybridization with its target.
  • the oligonucleotides, including the recognition oligonucleotides, and the nanoparticles are contacted under conditions effective allow at least some of the recognition oligonucleotides to bind to the nanoparticles.
  • the invention also includes the nanoparticle-oligonucleotide conjugates produced by this method, methods of using the conjugates to detect and separate nucleic acids, kits comprising the conjugates, methods of nanofabrication using the conjugates, and nanomaterials and nanostructures comprising the conjugates.
  • the invention comprises a method of attaching oligonucleotides to nanoparticles by means of a linker comprising a cyclic disulfide.
  • Suitable cyclic disulfides have 5 or 6 atoms in their rings, including the two sulfur atoms. Suitable cyclic disulfides are available commercially. The reduced form of the cyclic disulfides can also be used.
  • the linker further comprises a hydrocarbon moiety attached to the cyclic disulfide. Suitable hydrocarbons are available commercially, and are attached to the cyclic disulfides, e.g., as described in the Appendix. Preferably the hydrocarbon moiety is a steroid residue.
  • the linkers are attached to the oligonucleotides and the oligonucleotide-linkers are attached to nanoparticles as described herein.
  • the present invention also relates to novel nanoparticle probes that exploit specific binding interactions such as antibody-antigen binding, methods for preparing and using the same, and kits including such probes.
  • the invention provides a method for detecting an analyte comprising contacting the analyte with a nanoparticle conjugate having oligonucleotides bound thereto. At least a portion of the oligonucleotides attached to the nanoparticles are bound, as a result of hybridization, to second oligonucleotides having bound thereto a specific binding complement of said analyte.
  • the contacting takes place under conditions effective to allow specific binding interactions between the analyte and specific binding complement bound to the nanoparticle conjugate. A detectable change may be observed as a result of the specific binding interaction between the analyte and the probe.
  • the method for detecting an analyte comprises providing contacting the analyte with a nanoparticle conjugate having oligonucleotides bound thereto. At least a portion of the oligonucleotides attached to the nanoparticles are bound, as a result of hybridization, to a first portion of a linker oligonucleotide. The second portion of the linker oligonucleotide is bound, as a result of hybridization, to oligonucleotides having bound thereto a specific binding complement of said analyte.
  • the contacting takes place under conditions effective to allow specific binding interaction between the analyte and the nanoparticle conjugate and a detectable change may be. observed.
  • the method for detecting an analyte comprising providing an analyte having a first oligonucleotide bound thereto, and contacting the oligonucleotide bound to the analyte with a first type of nanoparticles having oligonucleotides bound thereto.
  • the contacting occurs under conditions effective to allow hybridization between the oligonucleotides bound to the analyte with the oligonucleotides attached to the first type of nanoparticles to form a nanoparticle analyte conjugate.
  • the method further comprising contacting the nanoparticle analyte conjugate with a second type of nanoparticle conjugate having oligonucleotides bound thereto.
  • At least a portion of the oligonucleotides bound to the second type of nanoparticle are bound, as a result of hybridization, to oligonucleotides having bound thereto a specific binding complement of said analyte.
  • the oligonucleotide bound to the analyte has a sequence that is complementary to at least a portion of the oligonucleotides bound to the first type of nanoparticles.
  • the method for detecting an analyte comprises providing an analyte having an oligonucleotide bound thereto, a linker oligonucleotide having two portions, and a first type of nanoparticle have oligonucleotides attached thereto.
  • the oligonucleotide bound to the analyte has a sequence that is complementary to the first portion of the sequence of the linker oligonucleotide.
  • At least a portion of the oligonucleotides bound to the first type of nanoparticles have a sequence that is complementary to a second portion of the linker oligonucleotide.
  • the oligonucleotide bound to the analyte, the oligonucleotide bound to the nanoparticle and the linker oligonucleotide are contacted under conditions effective to allow hybridization between the linker oligonucleotide with the oligonucleotide bound to the analyte and the oligonucleotides bound to the first type of nanoparticles to form a nanoparticle analyte conjugate.
  • the method further comprises contacting the analyte conjugate with a second type of nanoparticle conjugate having oligonucleotides bound thereto, a least a portion of the oligonucleotides bound to the second type of nanoparticle are bound, as a result of hybridization, to oligonucleotides having bound thereto a specific binding complement of said analyte.
  • the contacting takes place under conditions effective to allow specific binding interaction between the nanoparticle analyte conjugate and the specific binding complement second type of nanoparticle. A detectable change may be observed as a result of the specific bind interaction.
  • the method for detecting an analyte comprises providing a support having an analyte bound thereto.
  • the method further comprises contacting the analyte bound to the support to a nanoparticle conjugate having oligonucleotides bound thereto, a least a portion of the oligonucleotides are bound, as a result of hybridization, to second oligonucleotides having bound thereto a specific binding complement of said analyte.
  • the contacting takes place under conditions effective to allow specific binding interactions between the analyte and specific binding complement bound to the nanoparticle conjugate. A detectable change may be observable at this point.
  • the method for detecting an analyte comprises providing a support having a oligonucleotides bound thereto and an analyte having an oligonucleotide bound thereto, the oligonucleotide bound to the analyte has a sequence that is complementary to the linker oligonucleotides bound to the support.
  • the method further comprises contacting the oligonucleotides bound to the support with the olumbleucleotide bound to the analyte under conditions effective to allow hybridization between the oligonucleotides bound to the support and the oligonucleotides bound to the analytes.
  • a type of nanoparticle conjugate having oligonucleotides bound thereto is provided. At least a portion of the oligonucleotides bound to the nanoparticle are bound, as a result of hybridization, to second oligonucleotides having bound thereto a specific binding complement of said analyte. Finally, the analyte bound to the support and the specific binding complement bound to the nanoparticle conjugate are contacted under conditions effective to allow for specific binding interactions between the analyte bound to the support and the specific binding complement bound to the nanoparticle, and a detectable change is observed.
  • the method for detecting an analyte comprises providing a support having oligonucleotides bound thereto and a linker oligonucleotide, the sequence of the linker oligonucleotide having at least two portions.
  • the oligonucleotides bound to the support have a sequence that is complementary to the first portion of the linker oligonucleotide.
  • the oligonucleotide bound to the support is then contacted with the linker oligonucleotide under conditions effective to allow hybridization between the oligonucleotides bound to the support with the first portion of the linker oligonucleotide.
  • an analyte having an oligonucleotide bound thereto is provided.
  • the oligonucleotide bound to the analyte has a sequence that is complementary to the second portion of the linker oligonucleotides.
  • the linker oligonucleotide bound to the support is then contacted with the oligonucleotide bound to the analyte under conditions effective to allow hybridization between the oligonucleotide bound to the analyte and the second portion of the linker oligonucleotide.
  • a type of nanoparticle conjugate having oligonucleotides bound thereto is provided.
  • At least a portion of the oligonucleotides bound to the nanoparticle conjugate are bound, as a result of hybridization, to oligonucleotides having bound thereto a specific binding complement of said analyte.
  • the analyte bound to the support is then contacted with the nanoparticle conjugate under conditions effective to allow specific binding interaction between the analyte bound to the support and the specific binding complement bound to the nanoparticle and detectable change is observed.
  • the method for detecting an analyte comprises contacting a support having oligonucleotides bound thereto with oligonucleotide bound to an analyte, the sequence of the oligonucleotide bound to the analyte is complementary to the sequence of the oligonucleotides bound the the support.
  • the contacting occurs on under conditions effective to allow hybridization between the oligonucleotides bound to the support with the oligonucleotides bound to the analyte.
  • a type of nanoparticle conjugate having oligonucleotides attached thereto is provided.
  • At least a portion of the oligonucleotides attached to the nanoparticle are bound, as a result of hybridization, to a first portion of a linker oligonucleotide.
  • a second portion of the linker oligonucleotide is further bound, as a result of hybridization, to an oligonucleotide having a oligonucleotide having bound thereto a specific binding complement of said analyte.
  • the analyte bound to the support is then contacted with the nanoparticle conjugate under conditions effective to allow specific binding interactions between the analyte bound to the support and the specific binding complement bound to the nanoparticle. Then, a detectable change is observed.
  • the method for detecting an analyte comprises providing a support having an analyte bound thereto.
  • the support is contacted with an aggregate probe comprising at least two types of nanoparticles having oligonucleotides bound thereto.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to them.
  • At least one of the types of nanoparticles of the aggregate probe have oligonucleotides attached thereto which bound, as a result of hybridization, to second oligonucleotides having bound thereto a specific binding complement of said analyte.
  • the contacting takes place under conditions effective to allow specific binding interactions between the analyte bound to the support and specific binding complement bound to the aggregate probe. A detectable change may be observable at this point.
  • the method for detecting an analyte comprises contacting a support having oligonucleotides bound thereto with an analyte having an oligonucleotide bound thereto.
  • the oligonucleotide bound to the analyte has a sequence that is complementary to the sequence of the oligonucleotides bound to the support.
  • the contacting occurs under conditions effective to allow hybridization of the oligonucleotides bound to the analyte with the oligonucleotides bound to the support.
  • an aggregate probe comprising at least two types of nanoparticles having oligonucleotides bound thereto is provided.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to them. At least one of the types of nanoparticles of the aggregate probe have some oligonucleotides attached thereto which are bound, as a result of hybridization, to second oligonucleotides having bound thereto a specific binding complement of said analyte.
  • the contacting takes place under conditions effective to allow specific binding interactions between the analyte bound to the support and specific binding complement bound to the aggregate probe. Then, a detectable change is observed..
  • the method for detecting an analyte comprises providing contacting a support having a oligonucleotides bound thereto with linker oligonucleotides, the sequence of the second linker oligonucleotide having at least two portions.
  • the contacting occurs under conditions effective to allow hybridization between the oligonucleotides bound to the support and the first portion of the linker oligonucleotide.
  • an analyte having an oligonucleotide bound thereto is provided.
  • the oligonucleotide bound to the analyte has a sequence that is complementary with the second portion of the linker oligonucleotide.
  • the linker oligonucleotide bound to the support is then contacted with the oligonucleotide bound to the analyte under conditions effective to allow hybridization between the second portion of the linker oligonucleotide bound to the support and the oligonucleotide bound to the analyte.
  • an aggregate probe comprising at least two types of nanoparticles having oligonucleotides bound thereto is provided. The nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to them.
  • At least one of the types of nanoparticles of the aggregate probe have some oligonucleotides attached thereto which bound, as a result of hybridization, to second oligonucleotides having bound thereto a specific binding complement of said analyte.
  • the analyte bound to the support is then contacted with the aggregate probe under conditions effective to allow specific binding interactions between the analyte bound to the support and specific binding complement bound to the aggregate probe.
  • a detectable change may be observable at this point.
  • the method for detecting an analyte comprises contacting a support having oligonucleotides bound thereto with an oligonucleotide having analyte bound thereto, the oligonucleotide has a sequence that is complementary to the sequence of the oligonucleotide bound to the support.
  • the contacting occurs under conditions effective to allow hybridization of the oligonucleotides bound to the analyte with the oligonucleotides bound to the support.
  • an aggregate probe comprising at least two types of nanoparticles having oligonucleotides bound thereto is provided.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to them. At least one of the types of nanoparticles of the aggregate probe have some oligonucleotides attached thereto which bound to a first portion of a linker oligonucleotide as a result of hybridization. A second portion of the second linker oligonucleotide is bound, as a result of hybridization, to a oligonucleotide having bound thereto a specific binding complement of said analyte. Then, the analyte bound to the support is contacted with the aggregate probe under conditions effective to allow specific binding interactions between the analyte bound to the support and specific binding complement bound to the aggregate probe. A detectable change is then observed.
  • the method for detecting an analyte comprises contacting a support having an analyte bound thereto with a nanoparticle conjugate having oligonucleotides bound thereto, at least some of the oligonucleotides attached to the nanoparticle are bound, as a result of hybridization, to second oligonucleotides having bound thereto a specific binding complement of said analyte.
  • the contacting takes place under conditions effective to allow specific binding interactions between the analyte bound to the support and specific binding complement bound to the nanoparticle conjugate.
  • the substate is contacted with silver stain to produce a detectable change, and the detectable change is observed.
  • the method for detecting an analyte comprises contacting a polyvalent analyte with a nanoparticle probe having oligonucleotides bound thereto. At least some of the oligonucleotides attached to the nanoparticle are bound to a first portion of a reporter oligonucleotide as a result of hybridization. A second portion of the reporter oligonucleotide is bound, as a result of hybridization, to an oligonucleotide having bound thereto a specific binding complement to the analyte.
  • the contacting takes place under conditions effective to allow specific binding interactions between the analyte and the nanoparticle probe and to aggregation of the nanoparticles.
  • the invention also provides a method for detecting a nucleic acid comprising providing (i) a nucleic acid, (ii) one or more types of nanoparticles having oligonucleotides bound thereto, and (iii) a complex comprising streptavidin or avidin bound, by specific binding interaction, to two or more biotin molecules each having oligonucleotides bound thereto.
  • the sequence of the nucleic acid has at least two portions.
  • the oligonucleotides bound to the nanoparticles have a sequence that is complementary to a first portion of the nucleic acid while the oligonucleotides bound to biotin have a sequence that is complementary to a second portion of the nucleic acid.
  • the nucleic acid is contacted with the nanoparticle conjugate and complex under conditions effective to allow hybridization of the nanoparticles, the complex and the nucleic acid. A detectable change resulting from the subsequent aggregation ⁇ is observed.
  • a method for detecting a nucleic acid comprising providing (i) a nucleic acid, (ii) one or more types of nanoparticles having oligonucleotides bound thereto, (iii) oligonucleotides have biotin bound thereto; and (iv) streptavidin or avidin.
  • the sequence of the nucleic acid has at least two portions.
  • the oligonucleotides bound to the nanoparticles have a sequence that is complementary to a first portion of the nucleic acid while the oligonucleotides bound to biotin have a sequence that is complementary to a second portion of the nucleic acid.
  • the nucleic acid is contacted with the nanoparticle conjugate and oligonucleotide bound to biotin under conditions effective to allow hybridization between the nucleic acid with the oligonucleotides attached to the nanoparticles and the oligonucleotides attached to the biotin.
  • the resulting biotin complex is then contacted with streptavidin or avidin. A detectable change resulting from the subsequent aggregation is observed.
  • the method for detecting a nucleic acid comprises contacting a first type of nanoparticle have oligonucleotides attached thereto with the nucleic acid.
  • the sequence of the nucleic acid has at least two portions. At least some of the oligonucleotides attached to the nanoparticles have a sequence that is complementary to the first portion of the nucleic acid.
  • the contacting occurs under conditions effective to allow hybridization between the oligonucleotides attached to the nanoparticle and the first portion of the nucleic acid.
  • an oligonucleotide having a sbp member, e.g., biotin, bound thereto is provided.
  • the sequence of the oligonucleotide bound to the sbp member has a sequence that is complementary to the second portion of the sequence of the nucleic acid.
  • the oligonucleotide bound to the sbp member is then contacted to the nucleic acid bound to the first type of nanoparticle under conditions effective to allow hybridization between the oligonucleotide bound to the sbp member and the second portion of the nucleic acid. Then, a second type of nanoparticle conjugate having oligonucleotides bound thereto is provided.
  • At least a portion of the oligonucleotides bound to the second type of nanoparticle are bound, as a result of hybridization, to oligonucleotides having bound thereto a specific binding complement of said analyte (e.g., streptavidin or avidin).
  • a specific binding complement of said analyte e.g., streptavidin or avidin.
  • the contacting takes place under conditions effective to allow specific binding interaction between the sbp member (e.g., biotin) bound to the first type of nanoparticle and the sbp complement (e.g., streptavidin or avidin) bound to the second type of nanoparticle.
  • a detectable change may result.
  • the method for detecting a nucleic acid comprises contacting a support having oligonucleotides bound thereto with a nucleic acid, the sequence of the nucleic acid having at least two portions.
  • the oligonucleotides bound to the support have a sequence that is complementary to the first portion of the nucleic acid.
  • the contacting occurs under conditions effective to allow hybridization between the oligonucleotides bound to the support with the first portion of the nucleic acid.
  • an oligonucleotide having a sbp member e.g., biotin
  • the nucleic acid bound to the support is then contacted with the oligonucleotide bound to the sbp member under conditions effective to allow hybridization between the oligonucleotide bound to the sbp member and the second portion of the nucleic acid.
  • a type of nanoparticle conjugate having oligonucleotides bound thereto is provided. At least a portion of the oligonucleotides bound to the nanoparticle conjugate are bound, as a result of hybridization, to oligonucleotides having bound thereto a specific binding complement (e.g., streptavidin or avidin) of said sbp member.
  • the sbp member bound to the support is then contacted with the nanoparticle conjugate under conditions effective to allow specific binding interaction between the sbp member bound to the support and the specific binding complement bound to the nanoparticle and a detectable change is observed.
  • the method for detecting a nucleic acid comprises contacting a nucleic acid with a nanoparticle conjugate having oligonucleotides attached thereto.
  • the sequence of the nucleic acid has at least two portions. At least some of the oligonucleotides attached to the nanoparticles have a sequence that is complementary to the first portion of the nucleic acid.
  • the contacting occurs under conditions effective to allow hybridization of the oligonucleotides attached to the nanoparticles with the first portion of the nucleic acid.
  • an oligonucleotide having sbp member e.g., streptavidin
  • the oligonucleotide have an sbp member bound thereto has a sequence that is complementary to the second portion of the nucleic acid.
  • the oligonucleotide having the sbp member is then contacted with the nucleic acid bound to the nanoparticle under conditions effective to allow hybridization between the oligonucleotide having the sbp member and the nucleic acid.
  • a support having bound thereto a specific binding complement (e.g., biotin) to the sbp member is provided.
  • the support is then contacted with the sbp member bound to the nanoparticle under conditions effective to allow specific binding interactions to occur between the sbp member and the sb complement bound to the support.
  • a detectable event can be observed.
  • the method for detecting a nucleic acid comprises providing contacting the nucleic acid with a support having oligonucleotides bound thereto.
  • the sequence of the nucleic acid has at least two portions and oligonucleotide bound the the support has a sequence that is complementary to the first portion of the nucleic acid.
  • the contacting occurs under conditions effective to allow hybridization between the oligonucleotides bound to the support and the first portion of the nucleic acid.
  • an oligonucleotide having a sbp member e.g., biotin
  • the nucleic acid bound to the support is then contacted with the oligonucleotide bound to the sbp member under conditions effective to allow hybridization between the second portion of the nucleic acid bound to the support and the oligonucleotide bound to the sbp member.
  • an aggregate probe comprising at least two types of nanoparticles having oligonucleotides bound thereto is provided. The nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to them.
  • At least one of the types of nanoparticles of the aggregate probe have some oligonucleotides attached thereto which bound, as a result of hybridization, to second oligonucleotides having bound thereto a specific binding complement (e.g., streptavidin) of said sbp member.
  • the sbp member bound to the support is then contacted with the aggregate probe under conditions effective to allow specific binding interactions between the sbp member bound to the support and specific binding complement bound to the aggregate probe.
  • a detectable change may be observable at this point.
  • the method for detecting a nucleic acid comprises contacting a nucleic acid with an aggregate probe comprising at least two types of nanoparticles having oligonucleotides bound thereto is provided.
  • the nucleic acid has two portions.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to them.
  • At least one of the types of nanoparticles of the aggregate probe have some oligonucleotides attached thereto which bound to a first portion of the nucleic acid as a result of hybridization.
  • an oligonucleotide having sbp member e.g., streptavidin
  • the oligonucleotide have an sbp member bound thereto has a sequence that is complementary to the second portion of the nucleic acid.
  • the oligonucleotide having the sbp member is then contacted with the nucleic acid bound to the aggregate probe under conditions effective to allow hybridization between the oligonucleotide having the sbp member and the nucleic acid attached to the probe.
  • a support having bound thereto a specific binding complement (e.g., biotin) to the sbp member is provided.
  • the support is then contacted with the sbp member bound to the aggregate probe under conditions effective to allow specific binding interactions to occur between the sbp member bound to the aggregate probe and the sb complement bound to the support.
  • a detectable event can be observed.
  • the invention further provides a nanoparticle-oligonucleotide-sbp member conjugate (nanoparticle sbp conjugate) and compositions containing the same.
  • the nanoparticle sbp conjugate comprise nanoparticles having oligonucleotides bound thereto, at least a portion of the oligonucleotides are hybridized to a first oligonucleotide having a specific binding pair (sbp) member covalently linked thereto.
  • the oligonucleotides attached to the nanoparticles have at a sequence that is complementary to at least a portion of the first oligonucleotides.
  • the invention also provides a method for preparing a nanoprobe sbp conjugate comprising providing a nanoparticle conjugate having oligonucleotides bound thereto and a oligonucleotides having a sbp member bound thereto, and contacting the oligonucleotides attached to the nanoparticle conjugate with the oligonucleotides bound to the sbp member. At least a portion of the oligonucleotides bound to the nanoparticles have a sequence that is complementary to the sequence of the oligonucleotides bound to the sbp member. The contacting occurs under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the first oligonucleotide.
  • kits for detecting an analyte includes at least one container.
  • the container holds nanoparticle sbp conjugates comprising nanoparticles having oligonucleotides bound thereto, at least a portion of the oligonucleotides are hybridized to a first oligonucleotide having a specific binding pair (sbp) member covalently linked thereto.
  • the oligonucleotides attached to the nanoparticles have at a sequence that is complementary to at least a portion of the first oligonucleotides.
  • the kit may also include a substrate for observing a detectable change.
  • the kit in another embodiment, includes at least two containers.
  • the first container includes nanoparticles having oligonucleotides bound thereto. At least a portion of the oligonucleotides have a sequence that is complementary to a portion of a first oligonucleotide.
  • the second container includes first oligonucleotides having an sbp member covalently bound thereto.
  • the kit may also include a substrate for observing a detectable change.
  • the kit includes at least two containers.
  • the first container includes nanoparticles having oligonucleotides bound thereto.
  • the second container includes first oligonucleotides having a moiety that can be used to covalently link an sbp member.
  • the kit may also include a substrate for observing a detectable change.
  • the kit includes at least three containers.
  • the first container includes nanoparticles having oligonucleotides bound thereto.
  • the second container contains a linker oligonucleotide having at least two portions.
  • the third container includes first oligonucleotides having a moiety that can be used to covalently link an sbp member.
  • the oligonucleotides have a sequence that is complementary to a first portion of a linker oligonucleotide.
  • the first oligonucleotides have a sequence that is complementary to at least a second portion of the linker oligonucleotides.
  • the kit may also include a substrate for observing a detectable change.
  • the invention further provides a method of nanofabrication. The method comprises providing at least one type of linking oligonucleotide having a selected sequence, the sequence of each type of linking oligonucleotide having at least two portions.
  • the method further comprises providing one or more types of nanoparticles having oligonucleotides attached thereto, the oligonucleotides on each type of nanoparticles having a sequence complementary to a first portion of the sequence of a linking oligonucleotide.
  • the method further comprises providing a complex comprised of strepavidin or avidin bound to two or more biotin molecules, each having a first oligonucleotide bound thereto, the first oligonucleotide having a sequence complementary to a second portion of the sequence of the linking oligonucleotide.
  • the linking oligonucleotides, complex, and nanoparticles are contacted under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles and the first oligonucleotides bound to the biotin to the linking oligonucleotides so that a desired nanomaterials or nanostructure is formed.
  • the invention provides another method of nanofabrication.
  • This method comprises providing (a) at least two types of nanoparticles having oligonucleotides attached thereto; (b) at least one type of linking oligonucleotide having a selected sequence, the sequence of each type of linking oligonucleotide having at least two portions; and (c) a complex comprised of strepavidin or avidin bound to two or more biotin molecules, each having a first oligonucleotide bound thereto.
  • the oligonucleotides on the first type of nanoparticles have a sequence complementary to that of the oligonucleotides on the second type of nanoparticles and a sequence that is complementary to the first portion of the sequence of the linking oligonucleotides.
  • the oligonucleotides on the second type of nanoparticles have a sequence complementary to that of the oligonucleotides on the first type of nanoparticle- oligonucleotide conjugates and a sequence that is complementary to the second portion of the sequence of the linking oligonucleotide.
  • the first and second types of nanoparticles, the linking oligonucleotides, and the complex are contacted under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles to each other and to the linking oligonucleotide and the hybridization of the oligonucleotides of the complexes to the linking oligonucleotides so that a desired nanomaterials or nanostructure is formed.
  • the invention further provides yet another method of nanofabrication.
  • the method comprises providing (a) at least one type of linking oligonucleotide having a selected sequence, the sequence of each type of linking oligonucleotide having at least two portions; (b) one or more types of nanoparticles having oligonucleotides attached thereto, the oligonucleotides on each type of nanoparticles having a sequence complementary to a first portion of the sequence of a linking oligonucleotide; (c) biotin having a first oligonucleotide bound thereto, the first oligonucleotide having a sequence complementary to a second portion of the sequence of the linking oligonucleotide; and (d) strepavidin or avidin.
  • the linking oligonucleotides, biotin conjugate, and nanoparticles are contacted under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles and the first oligonucleotides bound to the biotin to the linking oligonucleotides. Then, the resulting complex is contacting with streptavidin or avidin under conditions effective to allow specific binding interaction between biotin and streptavidin or avidin so that a desired nanomaterials or nanostructure is formed.
  • the invention further provides nanomaterials or nanostructures composed of nanoparticles having oligonucleotides attached thereto, the nanoparticles being held together by oligonucleotide connectors and sbp interactions.
  • the invention further provides a method of separating a selected target nucleic acid having at least two portions from other nucleic acids.
  • the method comprises providing (a) one or more types of nanoparticles having oligonucleotides attached thereto, the oligonucleotides on each of the types of nanoparticles having a sequence complementary to the sequence of the first portion of the selected nucleic acid; (b) a complex comprised of strepavidin or avidin bound to two or more biotin molecules, each having a first oligonucleotide bound thereto, the first oligonucleotide having a sequence complementary to the sequence of the second portion of the selected nucleic acid.
  • the selected nucleic acid and other nucleic acids are contacted with the nanoparticles under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles and the first oligonucleotides of the complex with the selected nucleic acid so that the nanoparticles and complex hybridized to the selected nucleic acid aggregate and precipitate.
  • the invention further provides a method of separating a selected target nucleic acid having at least two portions from other nucleic acids.
  • the method comprises providing (a) one or more types of nanoparticles having oligonucleotides attached thereto, the oligonucleotides on each of the types of nanoparticles having a sequence complementary to the sequence of the first portion of the selected nucleic acid; (b) biotin having a first oligonucleotide bound thereto, the first oligonucleotide having a sequence complementary to the sequence of the second portion of the selected nucleic acid; and (c) strepavidin or avidin.
  • the selected nucleic acid and other nucleic acids are contacted with the nanoparticles and biotin construct under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles and the first oligonucleotides of the biotin construct with the selected nucleic acid. Then, the resulting complex is contacted with streptavidin or avidin under conditions effective to allow specific binding interactions between the biotin and streptavidin or avidin and subsequent aggregation and precipation of the resulting selected nucleic acid complex.
  • the invention also provides a method to actively move and concentrate nanoparticle probes bound to a biomolecules to and from an electrode surface containing captured target molecules or a set of nanoparticle probes bound to captured target in solution to a surface of interest.
  • Another object of the invention is to provide a method for accelerating movement of a nanoparticle to an electrode surface comprising providing a nanoparticle bound to a charged first member of a specific binding pair and an electrode surface including a second member of a specific binding pair; contacting the nanoparticle and the surface under conditions effective to allow binding between the first and the second members of the specific binding pair; and subjecting the nanoparticle to an electrical field so as to accelerate movement of the nanoparticle to the surface and facilitate binding between the first and second members of the binding pair.
  • the specific binding pairs include an antibody/antigen and receptor/ligand.
  • Yet another object of the invention is to provide a method of detecting a nucleic acid bound to an electrode surface, the nucleic acid having at least two portions, comprising: providing one or more types of nanoparticles having oligonucleotides attached thereto, the oligonucleotides on each of the types of nanoparticles having a sequence complementary to the sequence of one of the portions of the nucleic acid; contacting the nucleic acid and the nanoparticles under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the nucleic acid; subjecting the nanoparticle to an electrical field so as to accelerate movement of the nanoparticle to the surface; and observing a detectable change brought about by hybridization of the oligonucleotides on the nanoparticles with the nucleic acid.
  • Yet another object of the invention is to provide a method of detecting nucleic acid bound to a surface, the nucleic acid having at least two portions comprising: contacting the nucleic acid with at least two types of nanoparticles having oligonucleotides attached thereto, the oligonucleotides on the first type of nanoparticles having a sequence complementary to a first portion of the sequence of the nucleic acid, the oligonucleotides on the second type of nanoparticles having a sequence complementary to a second portion of the sequence of the nucleic acid, the contacting taking place under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the nucleic acid; subjecting the nanoparticle to an electrical field so as to accelerate movement of the nanoparticle to the surface; and observing a detectable change brought about by hybridization of the oligonucleotides on the nanoparticles with the nucleic acid.
  • Contacting conditions may include freezing and thawing, and
  • the invention further provides a method for multicolor labeling and imaging of DNA arrays using different sized oligonucleotide-functionalized nanoparticle probes is described. Because different sized (e.g., 50 nm and 100 nm diameter) gold nanoparticles scatter light of different colors (due to their different surface plasmon resonances), they can be used to label different DNA targets hybridized to the same array. Using an evanescent waveguide technique which only detects particles bound at the array surface and not those suspended in solution above the array, sequence information and melting profiles can be obtained from nanoparticle-labeled arrays in real time as targets are melted away from array elements with increasing temperature.
  • different sized gold nanoparticles scatter light of different colors (due to their different surface plasmon resonances)
  • sequence information and melting profiles can be obtained from nanoparticle-labeled arrays in real time as targets are melted away from array elements with increasing temperature.
  • a method of detecting nucleic acid in a sample, the nucleic acid having at least two portions, is provided. .
  • the method comprises: (a) providing a substrate having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to a first portion of the sequence of a nucleic acid to be detected; (b) providing a scattered light detectable nanoparticle probe having oligonucleotides attached thereto, the oligonucleotides bound to the nanoparticle probe having a sequence complementary to a second portion of the sequence of said nucleic acid wherein the oligonucleotides are attached to the nanoparticles in a stepwise ageing process comprising (i) contacting the oligonucleotides with the nanoparticles in a first aqueous solution for a period of time sufficient to allow some of the oligonucleotides to bind to the nanoparticles; (ii) adding at least one salt to the aqueous solution to create a second aqueous solution; and (iii) contacting the oligonucleotides and nanop
  • a method of detecting two or more nucleic acids in a sample, each nucleic acid having at least two portions comprises: (a) providing a substrate having two or more types of oligonucleotides attached thereto, each type of oligonucleotides attached to a different place on the substrate and each type of oligonucleotides having sequences complementary to a first portion of the sequences of one of nucleic acids to be detected; (b) providing two or more types of scattered light detectable nanoparticle probes, each type of nanoparticle probes having the oligonucleotides bound thereto, the oligonucleotides bound to each type of probe have a sequence that are complementary to a second portion of the sequence of one of said nucleic acids to be detected, wherein the oligonucleotides are attached to the nanoparticles in a stepwise ageing process comprising (i) contacting the oligonucleotides with
  • the invention also provides a method for increasing the selectivity of nucleic acid detection by exploiting the salt concentration dependent hybridization behavior of the nanoparticle conjugates of the invention.
  • the unusual salt-dependence of the melting properties of the nanoparticle oligonucleotide conjugates can be used to eliminate thermal stringency washes for mismatch discrimination, a significant step towards the development of a hand-held DNA detection system. Accordingly, in one embodiment of the invention, a method for detecting a nucleic acid is provided.
  • the method comprises providing a substrate having oligonucleotides bound thereto, the oligonucleotides bound to the substrate have a sequence that is complementary to a first portion of a sequence of a nucleic acid; providing labels, such as nanoparticles, having oligonucleotides bound thereto, at least some of the oligonucleotides having a sequence that is complementary to the sequence of a second portion of the nucleic acid; contacting the substrate, nucleic acid, and labels, the contacting taking place under conditions effective to allow hybridization between the oligonucleotides bound to the substrate with the nucleic acids and between the nucleic acid and the oligonucleotide bound to the label so as to form a test substrate having labels complexed thereto; contacting the test substrate with an aqueous salt solution having a salt concentration effective to substantially remove non-specifically bound labels; and observing a detectable change.
  • the method for detecting a nucleic acid having at least two portions comprises (a) contacting a nucleic acid with a substrate having oligonucleotides attached thereto, the oligonucleotides being located between a pair of electrodes, the oligonucleotides having a sequence complementary to a first portion of the sequence of said nucleic acid, the contacting taking place under conditions effective to allow hybridization of the oligonucleotides on the substrate with said nucleic acid; (b) contacting said nucleic acid bound to the substrate with a first type of labels such as nanoparticles, the labels being made of a material which can conduct electricity, the labels having one or more types of oligonucleotides attached thereto, at least one of the types of oligonucleotides having a sequence complementary to a second portion of the sequence of said nucleic acid, the contacting taking place under conditions effective to allow hybridization of the oligonucleotides on the labels with said
  • a "type of oligonucleotides” refers to a plurality of oligonucleotide molecules having the same sequence.
  • a "type of nanoparticles, conjugates, particles, latex microspheres, etc. having oligonucleotides attached thereto refers to a plurality of that item having the same type(s) of oligonucleotides attached to them.
  • Nanoparticles having oligonucleotides attached thereto are also sometimes referred to as “nanoparticle-oligonucleotide conjugates” or, in the case of the detection methods of the invention, “nanoparticle-oligonucleotide probes," “nanoparticle probes,” or just “probes.”
  • analyte refers to the compound or composition to be detected, including drugs, metabolites, pesticides, pollutants, and the like. .
  • the analyte can be comprised of a member of a specific binding pair (sbp) and may be a ligand, which is monovalent (monoepitopic) or polyvalent (polyepitopic), usually antigenic or haptenic, and is a single compound or plurality of compounds which share at least one common epitopic or determinant site.
  • the analyte can be a part of a cell such as bacteria or a cell bearing a blood group antigen such as A, B, D, etc., or an HLA antigen or a microorganism, e.g., bacterium, fungus, protozoan, or virus.
  • the polyvalent ligand analytes will normally be poly(amino acids), i.e., polypeptides and proteins, polysaccharides, nucleic acids, and combinations thereof. Such combinations include components of bacteria, viruses, chromosomes, genes, mitochondria, nuclei, cell membranes and the like.
  • the polyepitopic ligand analytes to which the subject invention can be applied will have a molecular weight of at least about 5,000, more usually at least about 10,000.
  • the poly(amino acid) category the poly(amino acids) of interest will generally be from about 5,000 to 5,000,000 molecular weight, more usually from about 20,000 to 1,000,000 molecular weight; among the hormones of interest, the molecular weights will usually range from about 5,000 to 60,000 molecular weight.
  • proteins may be considered as to the family of proteins having similar structural features, proteins having particular biological functions, proteins related to specific microorganisms, particularly disease causing microorganisms, etc. Such proteins include, for example, immunoglobulins, cytokines, enzymes, hormones, cancer antigens, nutritional markers, tissue specific antigens, etc.
  • the types of proteins, blood clotting factors, protein hormones, antigenic polysaccharides, microorganisms and other pathogens of interest in the present invention are specifically disclosed in U.S. Pat. No. 4,650,770, the disclosure of which is inco ⁇ orated by reference herein in its entirety.
  • the monoepitopic ligand analytes will generally be from about 100 to 2,000 molecular weight, more usually from 125 to 1,000 molecular weight.
  • the analyte may be a molecule found directly in a sample such as a body fluid from a host. The sample can be examined directly or may be pretreated to render the analyte more readily detectible.
  • the analyte of interest may be determined by detecting an agent probative of the analyte of interest such as a specific binding pair member complementary to the analyte of interest, whose presence will be detected only when the analyte of interest is present in a sample.
  • the agent probative of the analyte becomes the analyte that is detected in an assay.
  • the body fluid can be, for example, urine, blood, plasma, serum, saliva, semen, stool, sputum, cerebral spinal fluid, tears, mucus, and the like.
  • sbp member refers to one of two different molecules, having an area on the surface or in a cavity which specifically binds to and is thereby defined as complementary with a particular spatial and polar organization of the other molecule.
  • the members of the specific binding pair are referred to as ligand and receptor (antiligand).
  • ligand and receptor antiligand
  • ligand refers to any organic compound for which a receptor naturally exists or can be prepared.
  • ligand also includes ligand analogs, which are modified ligands, usually an organic radical or analyte analog, usually of a molecular weight greater than 100, which can compete with the analogous ligand for a receptor, the modification providing means to join the ligand analog to another molecule.
  • the ligand analog will usually differ from the ligand by more than replacement of a hydrogen with a bond which links the ligand analog to a hub or label, but need not.
  • the ligand analog can bind to the receptor in a manner similar to the ligand.
  • the analog could be, for example, an antibody directed against the idiotype of an antibody to the ligand.
  • receptor refers to any compound or composition capable of recognizing a particular spatial and polar organization of a molecule, e.g., epitopic or determinant site.
  • Illustrative receptors include naturally occurring receptors, e.g., thyroxine binding globulin, antibodies, enzymes, Fab fragments, lectins, nucleic acids, avidin, protein A, barstar, complement component Clq, and the like.
  • Avidin is intended to include egg white avidin and biotin binding proteins from other sources, such as streptavidin.
  • specific binding refers to the specific recognition of one of two different molecules for the other compared to substantially less recognition of other molecules. Generally, the molecules have areas on their surfaces or in cavities giving rise to specific recognition between the two molecules. Exemplary of specific binding are antibody-antigen interactions, enzyme-substrate interactions, polynucleotide interactions, and so forth.
  • non-specific binding refers to the non-covalent binding between molecules that is relatively independent of specific surface structures. Non-specific binding may result from several factors including hydrophobic interactions between molecules.
  • antibody refers to an immunoglobulin which specifically binds to and is thereby defined as complementary with a particular spatial and polar organization of another molecule.
  • the antibody can be monoclonal or polyclonal and can be prepared by techniques that are well known in the art such as immunization of a host and collection of sera (polyclonal) or by preparing continuous hybrid cell lines and collecting the secreted protein (monoclonal), or by cloning and expressing nucleotide sequences or mutagenized versions thereof coding at least for the amino acid sequences required for specific binding of natural antibodies.
  • Antibodies may include a complete immunoglobulin or fragment thereof, which immunoglobulins include the various classes and isotypes, such as IgA, IgD, IgE, IgGl, IgG2a, IgG2b and IgG3, IgM, etc. Fragments thereof may include Fab, Fv and F(ab').sub.2, Fab 1 , and the like.
  • aggregates, polymers, and conjugates of immunoglobulins or their fragments can be used where appropriate so long as binding affinity, for a particular molecule is maintained.
  • Figure 1 Schematic diagram illustrating the formation of nanoparticle ' aggregates by combining nanoparticles having complementary oligonucleotides attached to them, the nanoparticles being held together in the aggregates as a result of the hybridization of the complementary oligonucleotides.
  • X represents any covalent anchor (such as -S(CH 2 ) 3 OP(O)(O " )-, where S is joined to a gold nanoparticle).
  • oligonucleotide is shown to be attached to each particle but, in fact, each particle has several oligonucleotides attached to it.
  • the relative sizes of the gold nanoparticles and the oligonucleotides are not drawn to scale.
  • Figure 2 Schematic diagram illustrating a system for detecting nucleic acid using nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides on the two nanoparticles have sequences complementary to two different portions of the single-stranded DNA shown. As a consequence, they hybridize to the DNA producing detectable changes (forming aggregates and producing a color change).
  • Figure 3 Schematic diagram of a variation of the system shown in Figure 2.
  • the oligonucleotides on the two nanoparticles have sequences complementary to two different portions of the single-stranded DNA shown which are separated by a third portion which is not complementary to the oligonucleotides on the nanoparticles.
  • an optional filler oligonucleotide which can be used to hybridize with the noncomplementary portion of the single-stranded DNA.
  • Figure 4 Schematic diagram illustrating reversible aggregation of nanoparticles having oligonucleotides attached thereto as a result of hybridization and de-hybridization with a linking oligonucleotide.
  • the illustrated linking oligonucleotide is a double-stranded DNA having overhanging termini (sticky ends) which are complementary to the oligonucleotides attached to the nanoparticles.
  • Figure 5 Schematic diagram illustrating the formation of nanoparticle aggregates by combining nanoparticles having oligonucleotides attached thereto with linking oligonucleotides having sequences complementary to the oligonucleotides attached to the nanoparticles.
  • FIG. 6 Cuvettes containing two types of gold colloids, each having a different oligonucleotide attached thereto and a linking double-stranded oligonucleotide with sticky ends complementary to the oligonucleotides attached to the nanoparticles (see Figure 4).
  • Cuvette A at 80 ° C, which is above the Tm of the linking DNA; de-hybridized (thermally denatured). The color is dark red.
  • Cuvette B after cooling to room temperature, which is below the Tm of the linking DNA; hybridization has taken place, and the nanoparticles have aggregated, but the aggregates have not precipitated. The color is pu ⁇ le.
  • Cuvette C after several hours at room temperature, the aggregated nanoparticles have settled to the bottom of the cuvette. The solution is clear, and the precipitate is pinkish gray. Heating B or C will result in A.
  • Figure 7 A graph of absorbance versus wavelength in nm showing changes in absorbance when gold nanoparticles having oligonucleotides attached thereto aggregate due to hybridization with linking oligonucleotides upon lowering of the temperature, as illustrated in Figure 4.
  • Figure 8 A is a graph of change in absorbance versus temperature/time for the system illustrated in Figure 4.
  • gold nanoparticles having oligonucleotides attached thereto aggregate due to hybridization with linking oligonucleotides (see Figure 4).
  • high temperature 80°C
  • the nanoparticles are de-hybridized. Changing the temperature over time shows that this is a reversible process.
  • Figure 8B is a graph of change in absorbance versus temperature/time performed in the same manner using an aqueous solution of unmodified gold nanoparticles. The reversible changes seen in Figure 8A are not observed.
  • Figures 9A-B Transmission Electron Microscope (TEM) images.
  • Figure 9A is a TEM image of aggregated gold nanoparticles held together by hybridization of the oligonucleotides on the gold nanoparticles with linking oligonucleotides.
  • Figure 9B is a TEM image of a two-dimensional aggregate showing the ordering of the linked nanoparticles.
  • Figure 10 Schematic diagram illustrating the formation of thermally-stable triple-stranded oligonucleotide connectors between nanoparticles having the pyrimidme:purine:pyrimidine motif. Such triple-stranded connectors are stiffer than double-stranded connectors.
  • one nanoparticle has an oligonucleotide attached to it which is composed of all purines, and the other nanoparticle has an oligonucleotide attached to it which is composed of all pyrimidines.
  • the third oligonucleotide for forming the triple-stranded connector (not attached to a nanoparticle) is composed of pyrimidines.
  • Figure 11 Schematic diagram illustrating the formation of nanoparticle aggregates by combining nanoparticles having complementary oligonucleotides attached to them, the nanoparticles being held together in the aggregates as, a result of the hybridization of the complementary oligonucleotides.
  • the circles represent the nanoparticles
  • the formulas are oligonucleotide sequences
  • s is the thio-alkyl linker. The multiple oligonucleotides on the two types of nanoparticles can hybridize to each other, leading to the formation of an aggregate structure.
  • Figures 12A-F Schematic diagrams illustrating systems for detecting nucleic acid using nanoparticles having oligonucleotides attached thereto. Oligonucleotide- nanoparticle conjugates 1 and 2 and single-stranded oligonucleotide targets 3, 4, 5, 6 and 7 are illustrated. The circles represent the nanoparticles, the formulas are oligonucleotide sequences, and the dotted and dashed lines represent connecting links of nucleotide.
  • Figures 13 A-B Schematic diagrams illustrating systems for detecting DNA (analyte DNA) using nanoparticles and a transparent substrate.
  • Figures 14A-B Figure 14A is a graph of absorbance versus wavelength in nm showing changes in absorbance when gold nanoparticles having oligonucleotides attached thereto (one population of which is in solution and one population of which is attached to a transparent substrate as illustrated in Figure 13B) aggregate due to hybridization with linking oligonucleotides.
  • Figure 14B a graph of change in absorbance for the hybridized system referred to in Figure 14A as the temperature is increased (melted).
  • Figures 15A-G Schematic diagrams illustrating systems for detecting nucleic acid using nanoparticles having oligonucleotides attached thereto.
  • Oligonucleotide- nanoparticle conjugates 1 and 2 and single-stranded oligonucleotide targets 3, 4, 5, 6, 7 and 8 are illustrated.
  • the circles represent the nanoparticles, the formulas are oligonucleotide sequences, and S represents the thio-alkyl linker.
  • Figures 16A-C Schematic diagrams illustrating systems for detecting nucleic acid using nanoparticles having oligonucleotides attached thereto. Oligonucleotide- nanoparticle conjugates 1 and 2, single-stranded oligonucleotide targets of different lengths, and filler oligonucleotides of different lengths are illustrated. The circles represent the nanoparticles, the formulas are oligonucleotide sequences, and S represents the thio-alkyl linker.
  • Figures 17A-E Schematic diagrams illustrating nanoparticle-oligonucleotide conjugates and systems for detecting nucleic acid using nanoparticles having oligonucleotides attached thereto.
  • the circles represent the nanoparticles
  • the straight lines represent oligonucleotide chains (bases not shown)
  • two closely-spaced parallel lines represent duplex segments
  • the small letters indicate specific nucleotide sequences (a is complementary to a', b is complementary to b', etc.).
  • Figure 18 Schematic diagram illustrating a system for detecting nucleic acid using liposomes (large double circle), nanoparticles (small open circles) and a transparent substrate.
  • the filled-in squares represent cholesteryl groups, the squiggles represent oligonucleotides, and the ladders represent double-stranded (hybridized) oligonucleotides.
  • Figure 19A is a graph of absorbance versus wavelength in nm showing changes in absorbance when gold nanoparticle-oligonucleotide conjugates assemble in multiple layers on a transparent substrate as illustrated in Figure 13 A.
  • Figure 19B is a graph of change in absorbance for the hybridized system referred to in Figure 19A as the temperature is increased (melted).
  • Figures 20A-B Illustrations of schemes using fluorescent-labeled oligonucleotides attached to metallic or semiconductor quenching nanoparticles (Figure 20A) or to non-metallic, non-semiconductor particles (Figure 20B).
  • Figure 21 Schematic diagram illustrating a system for detecting target nucleic acid using gold nanoparticles having oligonucleotides attached thereto and latex microspheres having fluorescently-labeled oligonucleotides attached thereto. The small, closed, dark circles represent the nanoparticles, the large, open circles represent the latex microspheres, and the large oval represents a microporous membrane.
  • Figure 22 Schematic diagram illustrating a system for detecting target nucleic acid using two types of fluorescently-labeled oligonucleotide-nanoparticle conjugates.
  • the closed circles represent the nanoparticles , , and the large oval represents a microporous membrane.
  • FIG. 23 Sequences of materials utilized in an assay for Anthrax Protective Antigen (see Example 12).
  • Figure 24 Schematic diagram illustrating a system for detecting target nucleic acid using a "satellite probe” which comprises magnetic nanoparticles (dark spheres) having oligonucleotides (straight lines) attached to them, probe oligonucleotides (straight lines) hybridized to the oligonucleotides attached to the nanoparticles, the probe oligonucleotides being labeled with a reporter group (open rectangular box).
  • A, B, C, A', B', and C represent specific nucleotide sequences, with A, B and C being complementary to A', B' and C, respectively.
  • Figures 25 A-B Schematic diagrams illustrating systems for detecting DNA using nanoparticles and a transparent substrate. In these figures, a, b and c refer to different oligonucleotide sequences, and a', b' and c' refer to oligonucleotide sequences complementary to a, b and c,
  • Figure 26 Schematic diagram illustrating systems for forming assemblies of CdSe/ZnS core/shell quantum dots (QD).
  • Figures 27A-D Figure 27A shows fluorescence spectra comparing dispersed and aggregated QDs, with an excitation at 400 nm. The samples were prepared identically, except for the addition of complementary "linker” DNA to one and an equal volume and concentration of non-complementary DNA to the other.
  • Figure 27B shows UV- Visible spectra of QD/QD assemblies at different temperatures before, during and after "melting”.
  • Figure 27C shows high resolution TEM image of a portion of a hybrid gold/QD assembly. The lattice fringes of the QDs, which resemble finge ⁇ rints, appear near each gold nanoparticle.
  • Figure 27D shows UN- .
  • Figures 28A-E Schematic diagrams illustrating the preparation of core probes, aggregate probes and systems for detecting D ⁇ A using these probes.
  • a, b, c and d refer to different oligonucleotide sequences
  • a', b', c' and d' refer to oligonucleotide sequences complementary to a, b, c and d, respectively.
  • Figure 29 Graph of fractional displacement of oligonucleotides by mercaptoethanol from nanoparticles (closed circles) or gold thin films (open squares) to which the oligonucleotides had been attached.
  • Figure 30 Graph of surface coverages of recognition oligonucleotides on nanoparticles obtained for different ratios of recognition: diluent oligonucleotides used in the preparation of the nanoparticle-oligonucleotide conjugates.
  • Figure 31 Graph of surface coverages of hybridized complementary oligonucleotides versus different surface coverages of recognition oligonucleotides on nanoparticles.
  • Figure 32 Schematic diagram illustrating system for detecting a target D ⁇ A in a four-element array on a substrate using nanoparticle-oligonucleotide conjugates and amplification with silver staining.
  • Figure 33 Images obtained with a flatbed scanner of 7 mm x 13 mm oligonucleotide-functionalized float glass slides.
  • A Slide before hybridization of D ⁇ A target and gold nanoparticle-oligonucleotide indicator conjugate.
  • B Slide A after hybridization of 10 nM target D ⁇ A and 5 nM nanoparticle-oligonucleotide indicator conjugate. A pink color was imparted by attached, red 13 nm diameter gold nanoparticles.
  • C Slide B after exposure to silver amplification solution for 5 minutes.
  • D Same as (A).
  • E Slide D after hybridization of 100 pM target and 5 nM nanoparticle-oligonucleotide indicator conjugate.
  • Figures 35 A-B Graphs of percent hybridized label versus temperature showing dissociation of fluorophore-labeled ( Figure 35 A) and nanoparticle-labeled ( Figure 35B) targets from an oligonucleotide-functionalized glass surface. Measurements were made by measuring fluorescence ( Figure 35 A) or absorbance ( Figure 35B) of dissociated label in the solution above the glass surface.
  • the lines labeled "b” show the dissociation curves for perfectly matched oligonucleotides on the glass, and the lines labeled "r”show curves for mismatched oligonucleotides (a one-base mismatch) on the glass.
  • Figures 36 A-B Images of model oligonucleotide arrays challenged with synthetic target and fluorescent-labeled (Figure 36A) or nanoparticle-labeled ( Figure 36B) nanoparticle-oligonucleotide conjugate probes.
  • C, A, T, and G represent spots (elements) on the array where a single base change has been made in the oligonucleotide attached to the substrate to give a perfect match with the target (base A) or a single base mismatch (base C, T or G in place of the perfect match with base A).
  • the greyscale ratio for elements C:A:T:G is 9:37:9: 11 for Figure 36A and 3:62:7:34 for Figure 36B.
  • Figure 37 Schematic diagram illustrating system for forming aggregates (A) or layers (B) of nanoparticles (a and b) linked by a linking nucleic acid (3).
  • Figure 38A UV-visible spectra of alternating layers of gold nanoparticles a and b (see Figure 37) hybridized to an oligonucleotide-functionalized glass microscope slide via the complementary linker 3.
  • Figure 38B Graph of absorbance for nanoparticle assemblies (see Figure 38 A) at ⁇ max with increasing numbers of layers.
  • Figure 39A Figure 39A: FE-SEM of one layer of oligonucleotide- functionalized gold nanoparticles cohybridized with DNA linker to an oligonucleotide-functionalized, conductive indium-tin-oxide (ITO) slide (prepared in the same way as oligonucleotide-funcationalized glass slide).
  • ITO conductive indium-tin-oxide
  • Figure 39B FE-SEM image of two layers of nanoparticles on the ITO slide.
  • FIG 39C Absorbance at 260 nm (A 26 o) showing dissociation of a 0.5 ⁇ M solution of the oligonucleotide duplex (1 + 2 + 3; see Figure 37, A) to single strands in 0.3 M NaCl, 10 mM phosphate buffer solution (pH 7).
  • Figures 39D-F Absorbance at 260 nm (A2 60 ) showing dissociation of 1 layer (Figure 39D), 4 layers (Figure 39E) and 10 layers (Figure 39F) of oligonucleotide- functionalized gold nanoparticles from glass slides immersed in 0.3 MNaCl, 10 mM phosphate buffer solution. Melting profiles were obtained by measuring the decreasing abso ⁇ tion at 520 nm (A 520 ) through the slides with increasing temperature. In each of Figures 39D-F, the insets show the first derivatives of the measured dissociation curves. FWHM of these curves were (Figure 39C inset) 13.2 °C, ( Figure 39D inset) 5.6 °C, ( Figure 39E inset) 3.2 °C, and (Figure 39F inset) 2.9 °C.
  • Figure 40 Schematic diagram illustrating system used to measure the electrical properties of gold nanoparticle assemblies linked by DNA. For simplicity, only one hybridization event is drawn.
  • Figure 41 Schematic diagram illustrating a method of detecting nucleic acid using gold electrodes and gold nanoparticles.
  • Figure 42 Schematic diagram illustrating the structures of a cyclic disulfide 1, including the preferred compound 1, having a steroid moiety for use in linking oligonucleotides to nanoparticles.
  • the steroid disulfide molecule was obtained by condensation of 4,5-dihydroxy-l,2-dithiane with epiandrosterone.
  • Gold nanoparticle- oligonucleotide conjugates were prepared using oligonucleotides modified with the steroid disulfide exhibit greater stability towards DTT relative to those nanoparticles- oligonucleotides that employ oligonucleotide-mercaptohexyl linkers for their preparation.
  • Figure 43 Schematic diagram for the synthesis and formulas for the steroid cyclic disulfide anchor group.
  • Figure 44 Schematic diagram illustrating cyclic disulfides of formulas 2 for use in preparing oligonucleotide-cyclic disulfide linkers as described in Example 24, and same related cyclic disulfides for use as anchor groups.
  • Figure 45 Schematic diagram illustrating the structures described in Example 25.
  • Figure 45(a) illustrates the structures of 5'-monothiol-modified oligonucleotide 5, a 35-base 5 '-steroid disulfide oligomer 6 and Trembler phosphoramide 7 and 5-tri- mercaptoalkyl oligonucleotide 8.
  • Figure 46 Schematic diagram illustrating the chemistry of making a novel tri- thiol oligonucleotide.
  • Figure 47 Schematic representation of high density oligonucleotide nanoparticle conjugate I, oligonucleotide protein conjugate 1, a nanoparticle- oligonucleotide-protein conjugate II, and probe-target complex III.
  • the oligonucleotide conjugate 1 has a sequence that is complementary to the oligonucleotide bound to conjugate I.
  • Probe II is a representative probe for proteins.
  • Complex III results from the specific binding interaction between the protein target and the protein bound to probe II.
  • Figure 48 Schematic representation of the application of Probe II in detecting a specific protein in an array of different proteins immobilized on a glass surface.
  • the gold nanoparticles can be recognized visually or by silver staining. Fluorescent nanoparticles can be recognized by their fluorescence.
  • the glass plate shows three different proteins immobilized on the surface, one of which binds to the protein in Probe II.
  • step 1 the plate is exposed to a solution containing Probe II.
  • unbound Probe II is washed away.
  • step, 3 the presence of bound nanoparticles (IV) at the site occupied by the first protein in the series is observed.
  • Figure 49 Schematic representation of nanoparticle-oligonucleotide-receptor probes (IF) and applications in detecting a specific target in an array of substances immobilized on a smooth surface.
  • the recognition receptor unit (specific binding complement to target) is designated A and the target, B.
  • Figure 50 Schematic representation of (a) nanoparticle-oligonucleotide- receptor probe (II) showing that the oligonucleotide linked to the receptor (R) is complementary to the oligonucleotide bound to the nanoparticle and that the nanoparticle conjugate is bound by hybridization to the oligonucleotide bound to the receptor and (b) nanoparticle-oligonucleotide-receptor probe (II) showing that the oligonucleotide linked to the receptor (R) is bound, as a result of hybridization, to a first portion of the linking oligonucleotide and the oligonucleotides bound to the nanoparticle are bound, as a result of hybridization, to a second portion of the linking oligonucleotide.
  • oligonucleotide-protein conjugate is shown bound to the oligonucleotide-nanoparticle conjugate; the actual number may be greater.
  • Figure 51 Schematic representation of the application of a probe ( Figure 50(b), in (a) detecting a specific target, e.g., drug or protein, in an array of different drug or proteins immobilized on a glass surface and (b) detecting a specific target in a cell having an mixture of different molecules.
  • the probe can also be used in a spot test where the analyte, e.g., protein or drug, has multiple binding sites.
  • Figure 52 Schematic representation of a 3-dimensional gold nanoparticle- streptavidin assembly or aggregate formed as a result of (a) the hybridization of a complex of streptavidin bound to biotin molecules having bound thereto an oligonucleotide 1, nanoparticle oligonucleotide conjugates 2 and a target nucleic acid 3; (b) a gold nanoparticle assembly from by the hybridization of oligonucleotides of one type of nanoparticle with a second type of nanoparticle; and (c) a gold nanoparticle assembly by the hybridization of a complex of avidin specifically bound to four biotin molecules, each molecule bound to an oligonucleotide that has a sequence that is complementary to the oligonucleotides bound to the nanoparticle. In all three cases, the colors of the solutions changed from red to pu ⁇ le or blue-gray upon aggregate formation.
  • Figure 53 Photograph illustrating the nonspecific binding test (Example 27) of the inventive gold nanoparticle/oligonucleotide/streptavidin conjugate (left) a a commercial gold colloid/streptavidin conjugate (right).
  • the commercial conjugate showed a gray spot, indicating that the conjugate sticks to the glass surface while the inventive conjugate showed no significant silver stain.
  • Figure 54 Schematic diagram of a gold nanoparticle-oligonucleotide- streptavidin conjugate binding to a biotin bound to surface.
  • the biotin is linked to an oligonucleotide having a sequence that is complemenary to an oligonucleotide bound to the surface of the support and oligonucleotide-biotin conjugate is hybridized to the oligonucleotide bound to the surface.
  • Figure 55 Schematic diagram of a protein detection method using a linker as a DNA reporter for protein.
  • a nanoparticle-oligonucleotide-biotin conjugate having the reporter DNA bound thereto forms a 3-D nanoparticle assembly on addition of streptavidin.
  • the aggregate is then isolated, and subjected to dehybridization to release nanoparticle-oligonucletide conjugates, a complex of streptavidin bound to biotin molecules having oligonucleotides bound thereto, and the reporter.
  • the protein is detected by the identification of the reporter DNA by conventional means, including the use of a DNA chip.
  • Figure 56 Schematic diagram showing the preparation of a gold nanoparticle- oligonucleotide-streptavidin conjugate (Example 26) from (a) streptavidin bound to a single biotin linked to a oligonucleotide, the oligonucleotide bound to the biotin is further bound, as a result of hybridization, to a first portion of a linker oligonucleotide and (b) a gold nanoparticle having oligonucleotides bound thereto, the oligonucleotides bound to the nanoparticles have a sequence that is complementary to a second portion of the linker oligonucleotide.
  • FIG 57 Transmission electron microscopy (TfiM) images (Example 28) showing (a) formation of aggregates upon heating a solution of streptavidin- oligonucleotide conjugate (1-STV), 13 nm gold particles (2-Au) and linker DNA (3) to 53 C and (b)particles within the aggregates retain their physical shape prior to and after annealing, show no particle fusion and further demonstrate stabilizing influence of the surface oligonucleotide layer.
  • TfiM Transmission electron microscopy
  • Figure 58 Melting curves (a) as a function of temperature (b) function of wavelength confirm that streptavidin-nanoparticle aggregates are formed by DNA hybridization interactions, not nonspecific interactions, and that the process is reversible. See Example 28.
  • Figure 59 Small Angle X-ray Scattering diffraction patterns showing various inte ⁇ article distances of various aggregates as described in Example 28.
  • Figure 60 Illustration of ITO electrode setup as described in Example 29.
  • Figure 61 The DNA sequences of the array capture strands, the oligonucleotide-functionalized nanoparticle labels, and the targets to be detected were designed to cohybridize in a three-component sandwhich assay.
  • Figure 62 Microscope images of model DNA arrays functionalized with oligonucleotide sequences c (left) and d (right) and incubated with a solution of 50 nm diameter Au nanoparticles functionalized with sequence a (10 nM), 100 nm diameter Au nanoparticles functionalized with sequence b (3.5 nM), and oligonucleotide target(s) a'c' and/or b'd' (200 nM).
  • 11 (A) Array and nanoparticles hybridized with both targets a'c' and b'd'.
  • B Array and nanoparticles hybridized with only target b 'd'.
  • C Array and nanoparticles hybridized with only target a'c'.
  • Figure 64 Illustration of a slide assembly mounted in a fiber optic illuminator (Darklite Illuminator, Micro Video Instruments, Avon, MA) on an inverted microscope (Axiovert 100A, Carl Zeiss, Jena, Germany) for imaging. Illumination was provided by a 200 W halogen source (Fiber-Lite PL-750, Dolan-Jenner, Lawrence, MA) set to 40/o intensity and allowed to equilibrate for at least 15 min before imaging. Images were captured with a Penguin 600 CL digital camera (Pixera, Los Gatos, CA). See Example 30.
  • Figure 65 Illustration of a slide was mounted on an inverted microscope equipped with a controlled temperature stage mount (BS60, Instec Inc., Boulder Co) and a miniature magnetic stirrer (Telemodul Mini, H+P Labortechnik, Kunststoff, Germany) as shown in Figure 65 A (top view) and S2B (side view). The assembly was subjected to a temperature ramp from 25 °C to 75 °C at a rate of 0.5°C/min with a 3 min hold at each temperature. Images were captured as described above, and analyzed using image processing software (Adobe Photoshop 5.0, Adobe Systems, San Jose, CA). See Example 31.
  • Figure 66 Green curve: Visible spectra of light scattered from glass slides functionalized with oligonucleotide sequence c and incubated with a solution of 50 nm diameter Au nanoparticles functionalized with sequence a (lO nM) and oligonucleotide target a'c' (200 nM). (Details of the hybridization procedure and data collection are given in Examples 30 and 31) Orange curve: Visible spectra of light scattered from glass slides functionalized with oligonucleotide sequence d and incubated with a solution of 100 nm diameter Au nanoparticles functionalized with sequence b (3.5 nM) and oligonucleotide target b'd' (200 nM).
  • Figure 67 Dependence of scattered light intensity with respect to target oligonucleotide concentration, for arrays spotted with oligonucleotide sequence c and incubated with a solution of 50 nm diameter Au nanoparticles functionalized with sequence a (10 nM) and oligonucleotide target a'c'. Intensity values were determined by analysis of microscope images taken at each target concentration, described in Examples 30 and 31. Each graph point represents the average measured intensity at four array spots.
  • Figure 68 Detection scheme illustrating (A) selective binding event between a capture oligonucleotide strand located between two electrodes and a target oligonucleotide in solution.
  • the target oligonucleotide has contiguous recognition elements, which are complementary to the capture strand and a nanoparticle probe, respectively. Therefore, when the device with the pair of electrodes is immersed in a solution containing the appropriate probe and target, particles fill the gap. In principle, capacitance or conductivity measurements can be made to determine the number of particles and, therefore, target molecules that fill the gap.
  • the sensitivity of the device can be dramatically increased by exposing the active component of the device to a silver stain, e.g., solution of Ag(I) and hydroquinone (photographic developing solution);
  • a silver stain e.g., solution of Ag(I) and hydroquinone (photographic developing solution);
  • microelectrodes 60 nm Au on 5nm Ti
  • 20 ⁇ m gaps were prepared by standard photolithography on a Si wafer with 1000 angstrom coating of SiO 2 as described in Example 32; and
  • C the sequences of capture, target, and probe DNA strands in the experiment described in Example 32.
  • Figure 69 (A) Resistance of the electrode gaps measured as a function of increasing silver enhancing time.
  • B Resistance of the electrode gaps as a function of enhancing time.
  • Figure 70 FE-SEM images of the nanoparticle probes on an ITO-coated glass surface: (A) before silver deposition, (B) after a 3 minute treatment with the enhancing solution, (C) after 6 minute treatment with the enhancer solution, and (D) after 9 minute treatment with silver enhancer solution.
  • ITO-coated glass substrates (Delta Technologies, Stillwater, MN) were modified with complementary capture DNA strands, and the target DNA and oligonucleotide-modified nanoparticles were assembled on the substrates following the same procedure used for DNA detection.
  • FIG 71 An FE-SEM image of the edge of a DNA spot after the nanoparticle assembly and silver deposition process.
  • the substrate has been treated with a higher concentration of nanoparticles (10 nM), which includes nonspecific binding of nanoparticles on the area where there is no capture DNA strands (below arrow). Note that there is no significant silver deposition below the arrow, even though there is a fair amount of nonspecifically bound nanoparticles.
  • Nanoparticles useful in the practice of the invention include metal (e.g., gold, silver, copper and platinum), semiconductor (e.g., CdSe, CdS, and CdS or CdSe coated with ZnS) and magnetic (e.g., ferromagnetite) colloidal materials.
  • metal e.g., gold, silver, copper and platinum
  • semiconductor e.g., CdSe, CdS, and CdS or CdSe coated with ZnS
  • magnetic e.g., ferromagnetite
  • nanoparticles useful in the practice of the invention include ZnS, ZnO, TiO 2 , Agl, AgBr, Hgl 2 , PbS, PbSe, ZnTe, CdTe, In 2 S 3 , In 2 Se 3 , Cd 3 P 2 , Cd 3 As 2 , InAs, and GaAs.
  • the size of the nanoparticles is preferably from about 5 nm to about 150 nm (mean diameter), more preferably from about 5 to about 50 nm, most .preferably from about 10 to about 30 nm.
  • the nanoparticles may also be rods.
  • Suitable nanoparticles are also commercially available from, e.g., Ted Pella, Inc. (gold), Amersham Co ⁇ oration (gold) and Nanoprobes, Inc. (gold).
  • Gold nanoparticles Presently preferred for use in detecting nucleic acids are gold nanoparticles.
  • Gold colloidal particles have high extinction coefficients for the bands that give rise to their beautiful colors. These intense colors change with particle size, concentration, inte ⁇ article distance, and extent of aggregation and shape (geometry) of the aggregates, making these materials particularly attractive for colorimetric assays. For instance, hybridization of oligonucleotides attached to gold nanoparticles with oligonucleotides and nucleic acids results in an immediate color change visible to the naked eye (see, e.g, the Examples).
  • Gold nanoparticles are also presently preferred for use in nanofabrication for the same reasons given above and because of their stability, ease of imaging by electron microscopy, and well-characterized modification with thiol functionalities (see below).
  • semiconductor nanoparticles are also preferred for use in nanofabrication because of their unique electronic and luminescent properties.
  • the nanoparticles, the oligonucleotides or both are functionalized in order to attach the oligonucleotides to the nanoparticles.
  • Such methods are known in the art. For instance, oligonucleotides functionalized with alkanethiols at their 3 '-termini or 5'-termini readily attach to gold nanoparticles. See Whitesides, Proceedings of the Robert A. Welch Foundation 39th Conference On Chemical Research Nanophase Chemistry, Houston, TX, pages 109-121 (1995). See also, Mucic et al. Chem.
  • Oligonucleotides terminated with a 5' thionucleoside or a 3' thionucleoside may also be used for attaching oligonucleotides to solid surfaces.
  • Oligonucleotides functionalized with a cyclic disulfide are within the scope of this invention.
  • the cyclic disulfides preferably have 5 or 6 atoms in their rings, including the two sulfur atoms. Suitable cyclic disulfides are available commercially or may be synthesized by known procedures. The reduced form of the cyclic disulfides can also be used.
  • the linker further comprises a hydrocarbon moiety attached to the cyclic disulfide.
  • Suitable hydrocarbons are available commercially, and are attached to the cyclic disulfides
  • the hydrocarbon moiety is a steroid residue.
  • Oligonucleotide-nanoparticle conjugates prepared using linkers comprising a steroid residue attached to a cyclic disulfide have unexpectedly been found to be remarkably stable to thiols (e.g., dithiothreitol used in polymerase chain reaction (PCR) solutions) as compared to conjugates prepared using alkanethiols or acyclic disulfides as the linker. Indeed, the oligonucleotide-nanoparticle conjugates of the invention have been found to be 300 times more stable. This unexpected stability is likely due to the fact that each oligonucleotide is anchored to a nanoparticle through two sulfur atoms, rather than a single sulfur atom.
  • thiols e.g., dithiothreitol used in polymerase chain reaction (PCR) solutions
  • PCR polymerase chain reaction
  • the two sulfur atoms of the cyclic disulfide should preferably be close enough together so that both of the sulfur atoms can attach simultaneously to the nanoparticle. Most preferably, the two sulfur atoms are adjacent each other. Also, the hydrocarbon moiety should be large so as to present a large hydrophobic surface screening the surfaces of the nanoparticles.
  • oligonucleotide-cyclic nanoparticle conjugates that employ cyclic disulfide linkers may be used as probes in diagnostic assays for detecting nucleic acids or in methods of nanofabrication as described herein.
  • conjugates according to the present invention have unexpectedly been found to improve the sensitivity of diagnostic assays in which they are used.
  • assays employing oligonucleotide-nanoparticle conjugates prepared using linkers comprising a steroid residue attached to a cyclic disulfide have been found to be about 10 times more sensitive than assays employing conjugates prepared using alkanethiols or acyclic disulfides as the linker.
  • oligonucleotide-nanoparticle conjugates of the invention to thiols described above allows them to be used directly in PCR solutions.
  • oligonucleotide-nanoparticle conjugates of the invention added as probes to a DNA target to be amplified by PCR can be carried through the 30 or 40 heating-cooling cycles of the PCR and are still able to detect the amplicons without opening the tubes. Opening the sample tubes for addition of probes after PCR can cause serious problems through contamination of the equipment to be used for subsequent tests.
  • kits comprising a container holding a type of oligonucleotide-cyclic disulfide linkers of the invention or a container holding a type of oligonucleotide-nanoparticle conjugates of the invention.
  • the kits may also contain other reagents and items useful for detecting nucleic acids or for nanofabrication.
  • Each nanoparticle will have a plurality of oligonucleotides attached to it.
  • each nanoparticle-oligonucleotide conjugate can bind to a plurality of oligonucleotides or nucleic acids having the complementary sequence.
  • Oligonucleotides of defined sequences are used for a variety of pu ⁇ oses in the practice of the invention. Methods of making oligonucleotides of a predetermined sequence are well-known. See, e.g., Sambrook et al, Molecular Cloning: A Laboratory Manual (2nd ed. 1989) andF. Eckstein (ed.) Oligonucleotides and Analogues, 1st Ed. (Oxford University Press, New York, 1991). Solid-phase synthesis methods are preferred for both oligoribonucleotides nd oligodeoxyribonucleotides (the well-known methods of synthesizing DNA are also useful for synthesizing RNA). Oligoribonucleotides and oligodeoxyribonucleotides can also be prepared enzymatically.
  • the invention provides methods of detecting nucleic acids. Any type of nucleic acid may be detected, and the methods may be used, e.g., for the diagnosis of disease and in sequencing of nucleic acids.
  • nucleic acids that can be detected by the methods of the invention include genes (e.g., a gene associated with a particular disease), viral RNA and DNA, bacterial DNA, fungal DNA, cDNA, mRNA, RNA and DNA fragments, oligonucleotides, synthetic oligonucleotides, modified oligonucleotides, single-stranded and double-stranded nucleic acids, natural and synthetic nucleic acids, etc.
  • examples of the uses of the methods of detecting nucleic acids include: the diagnosis and/or monitoring of viral diseases (e.g., human immunodeficiency virus, hepatitis viruses, he ⁇ es viruses, cytomegalovirus, and Epstein-Barr virus), bacterial diseases (e.g., tuberculosis, Lyme disease, H.
  • viral diseases e.g., human immunodeficiency virus, hepatitis viruses, he ⁇ es viruses, cytomegalovirus, and Epstein-Barr virus
  • bacterial diseases e.g., tuberculosis, Lyme disease, H.
  • pylori Escherichia coli infections, Legionella infections, Mycoplasma infections, Salmonella infections
  • sexually transmitted diseases e.g., gonorrhea
  • inherited disorders e.g., cystic fibrosis, Duchene muscular dystrophy, phenylketonuria, sickle cell anemia
  • cancers e.g., genes associated with the development of cancer
  • the methods of detecting nucleic acids based on observing a color change with the naked eye are cheap, fast, simple, robust (the reagents are stable), do not require specialized or expensive equipment, and little or no instrumentation is required. This makes them particularly suitable for use in, e.g., research and analytical laboratories in DNA sequencing, in the field to detect the presence of specific pathogens, in the doctor's office for quick identification of an infection to assist in prescribing a drug for treatment, and in homes and health centers for inexpensive first-line screening.
  • the nucleic acid to be detected may be isolated by known methods, or may be detected directly in cells, tissue samples, biological fluids (e.g., saliva, urine, blood, serum), solutions containing PCR components, solutions containing large excesses of oligonucleotides or high molecular weight DNA, and other samples, as also known in the art. See, e.g., Sambrook et al, Molecular Cloning: A Laboratory Manual (2nd ed. 1989) and B.D. Hames and SJ. Higgins, Eds., Gene Probes 1 (IRL Press, New York, 1995). Methods of preparing nucleic acids for detection with hybridizing probes are well known in the art.
  • nucleic acid is present in small amounts, it may be applied by methods known in the art. See, e.g., Sambrook et al, Molecular Cloning: A Laboratory Manual (2nd ed. 1989) and B.D. Hames and S J. Higgins, Eds., Gene Probes 1 (IRL Press, New York, 1995). Preferred is polymerase chain reaction (PCR) amplification.
  • PCR polymerase chain reaction
  • One method according to the invention for detecting nucleic acid comprises contacting a nucleic acid with one or more types of nanoparticles having oligonucleotides attached thereto.
  • the nucleic acid to be detected has at least two portions.
  • the lengths of these portions and the distance(s), if any, between them are chosen so that when the oligonucleotides on the nanoparticles hybridize to the nucleic acid, a detectable change occurs. These lengths and distances can be determined empirically and will depend on the type of particle used and its size and the type of electrolyte which will be present in solutions used in the assay (as is known in the art, certain electrolytes affect the conformation of nucleic acids).
  • the portions of the nucleic acid to which the oligonucleotides on the nanoparticles are to bind must be chosen so that they contain sufficient unique sequence so that detection of the nucleic acid will be specific. Guidelines for doing so are well known in the art.
  • nucleic acids may contain repeating sequences close enough to each other so that only one type of oligonucleotide-nanoparticle conjugate need be used, this will be a rare occurrence.
  • the chosen portions of the nucleic acid will have different sequences and will be contacted with nanoparticles carrying two or more different oligonucleotides, preferably attached to different nanoparticles.
  • An example of a system for the detection of nucleic acid is illustrated in Figure 2. As can be seen, a first oligonucleotide attached to a first nanoparticle has a sequence complementary to a first portion of the target sequence in the single-stranded DNA.
  • a second oligonucleotide attached to a second nanoparticle has a sequence complementary to a second portion of the target sequence in the DNA. Additional portions of the DNA could be targeted with corresponding nanoparticles. See Figure 17. Targeting several portions of a nucleic acid increases the magnitude of the detectable change.
  • the contacting of the nanoparticle-oligonucleotide conjugates with the nucleic acid takes place under conditions effective for hybridization of the oligonucleotides on the nanoparticles with the target sequence(s) of the nucleic acid.
  • hybridization conditions are well known in the art and can readily be optimized for the particular system employed. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual (2nd ed. 1989).
  • Preferably stringent hybridization conditions are employed.
  • Faster hybridization can be obtained by freezing and thawing a solution containing the nucleic acid to be detected and the nanoparticle-oligonucleotide conjugates.
  • the solution may be frozen in any convenient manner, such as placing it in a dry ice-alcohol bath for a sufficient time for the solution to freeze, (generally about 1 minute for 100 :L of solution).
  • the solution must be thawed at a temperature below the thermal denaturation temperature, which can conveniently be room temperature for most combinations of nanoparticle-oligonucleotide conjugates and nucleic acids.
  • the hybridization is complete, and the detectable change may be observed, after thawing the solution.
  • the rate of hybridization can also be increased by warming the solution containing the nucleic acid to be detected and the nanoparticle-oligonucleotide conjugates to a temperature below the dissociation temperature (Tm) for the complex formed between the oligonucleotides on the nanoparticles and the target nucleic acid.
  • rapid hybridization can be achieved by heating above the dissociation temperature (Tm) and allowing the solution to cool.
  • the rate of hybridization can also be increased by increasing the salt concentration (e.g. , from 0.1 M to 0.3 M NaCl).
  • the detectable change that occurs upon hybridization of the oligonucleotides on the nanoparticles to the nucleic acid may be a color change, the formation of aggregates of the nanoparticles, or the precipitation of the aggregated nanoparticles.
  • the color changes can be observed with the naked eye or spectroscopically.
  • the formation of aggregates of the nanoparticles can be observed by electron microscopy or by nephelometry.
  • the precipitation of the aggregated nanoparticles can be observed with the naked eye or microscopically.
  • Particularly preferred is a color change observable with the naked eye.
  • the observation of a color change with the naked eye can be made more readily against a background of a contrasting color.
  • the observation of a color change is facilitated by spotting a sample of the hybridization solution on a solid white surface (such as silica or alumina TLC plates, filter paper, cellulose nitrate membranes, and nylon membranes, preferably a C-18 silica TLC plate) and allowing the spot to dry. Initially, the spot retains the color of the hybridization solution (which ranges from pink/red, in the absence of hybridization, to pu ⁇ lish-red/pu ⁇ le, if there has been hybridization).
  • a solid white surface such as silica or alumina TLC plates, filter paper, cellulose nitrate membranes, and nylon membranes, preferably a C-18 silica TLC plate
  • a blue spot develops if the nanoparticle-oligonucleotide conjugates had been linked by hybridization with the target nucleic acid prior to spotting.
  • the spot In the absence of hybridization (e.g., because no target nucleic acid is present), the spot is pink.
  • the blue and the pink spots are stable and do not change on subsequent cooling or heating or over time. They provide a convenient permanent record of the test. No other steps (such as a separation of hybridized and unhybridized nanoparticle-oligonucleotide conjugates) are necessary to observe the color change.
  • An alternate method for easily visualizing the assay results is to spot a sample of nanoparticle probes hybridized to a target nucleic acid on a glass fiber filter (e.g., Borosilicate Microfiber Filter, 0.7 micron pore size, grade FG75, for use with gold nanoparticles 13 nm in size), while drawing the liquid through the filter. Subsequent rinsing with water washes the excess, non-hybridized probes through the filter, leaving behind an observable spot comprising the aggregates generated by hybridization of the nanoparticle probes with the target nucleic acid (retained because these aggregates are larger than the pores of the filter).
  • This technique may provide for greater sensitivity, since an excess of nanoparticle probes can be used.
  • the nanoparticle probes stick to many other solid surfaces that have been tried (silica slides, reverse-phase plates, and nylon, nitrocellulose, cellulose and other membranes), and these surfaces cannot be used.
  • An important aspect of the detection system illustrated in Figure 2 is that obtaining a detectable change depends on cooperative hybridization of two different oligonucleotides to a given target sequence in the nucleic acid. Mismatches in either of the two oligonucleotides will destabilize the inte ⁇ article connection. It is well known that a mismatch in base pairing has a much greater destabilizing effect on the binding of a short oligonucleotide probe than on the binding of a long oligonucleotide probe.
  • the advantage of the system illustrated in Figure 2 is that it utilizes the base discrimination associated with a long target sequence and probe (eighteen base-pairs in the example illustrated in Figure 2), yet has the sensitivity characteristic of a short oligonucleotide probe (nine base-pairs in the example illustrated in Figure 2).
  • the target sequence of the nucleic acid may be contiguous, as in Figure 2, or the two portions of the target sequence may be separated by a third portion which is not complementary to the oligonucleotides on the nanoparticles, as illustrated in Figure 3.
  • a filler oligonucleotide which is free in solution and which has a sequence complementary to that of this third portion (see Figure 3).
  • the filler oligonucleotide hybridizes with the third portion of the nucleic acid, a double-stranded segment is created, thereby altering the average distance between the nanoparticles and, consequently, the color.
  • the system illustrated in Figure 3 may increase the sensitivity of the detection method.
  • Some embodiments of the method of detecting nucleic acid utilize a substrate.
  • the detectable change (the signal) can be amplified and the sensitivity of the assay increased.
  • Suitable substrates include transparent solid surfaces (e.g., glass, quartz, plastics and other polymers), opaque solid surface (e.g., white solid surfaces, such as TLC silica plates, filter paper, glass fiber filters, cellulose nitrate membranes, nylon membranes), and conducting solid surfaces (e.g., indium-tin-oxide (ITO)).
  • transparent solid surfaces e.g., glass, quartz, plastics and other polymers
  • opaque solid surface e.g., white solid surfaces, such as TLC silica plates, filter paper, glass fiber filters, cellulose nitrate membranes, nylon membranes
  • conducting solid surfaces e.g., indium-tin-oxide (ITO)
  • the substrate can be any shape or thickness, but generally will be flat and thin.
  • transparent substrates such as glass (e.g., glass slides) or plastics (e.g., wells of microtiter plates).
  • oligonucleotides are attached to the substrate.
  • the oligonucleotides can be attached to the substrates as described in, e.g., Chrisey et al., Nucleic Acids Res., 24, 3031-3039 (1996); Chrisey et al., Nucleic Acids Res., 24, 3040-3047 (1996); Mucic et al., Chem. Commun., 555 (1996); Zimmermann and Cox, Nucleic Acids Res., 22, 492 (1994); Bottomley et al., J. Vac. Sci. Technol. A, 10, 591 (1992); and Hegner et al., FEBSLett., 336, 452 (1993).
  • the oligonucleotides attached to the substrate have a sequence complementary to a first portion of the sequence of a nucleic acid to be detected.
  • the nucleic acid is contacted with the substrate under conditions effective to allow hybridization of the oligonucleotides on the substrate with the nucleic acid. In this manner the nucleic acid becomes bound to the substrate. Any unbound nucleic acid is preferably washed from the substrate before adding nanoparticle-oligonucleotide conjugates.
  • the nucleic acid bound to the substrate is contacted with a first type of nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a second portion of the sequence of the nucleic acid, and the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the nucleic acid.
  • the first type of nanoparticles become bound to the substrate.
  • the substrate is washed to remove any unbound nanoparticle-oligonucleotide conjugates and nucleic acid.
  • the oligonucleotides on the first type of nanoparticles may all have the same sequence or may have different sequences that hybridize with different portions of the nucleic acid to be detected.
  • each nanoparticle may have all of the different oligonucleotides attached to it or, preferably, the different oligonucleotides are attached to different nanoparticles.
  • Figure 17 illustrates the use of nanoparticle-oligonucleotide conjugates designed to hybridize to multiple portions of a nucleic acid.
  • the oligonucleotides on each of the first type of nanoparticles may have a plurality of different sequences, at least one of which must hybridize with a portion of the nucleic acid to be detected (see Figure 25B).
  • the first type of nanoparticle-oligonucleotide conjugates bound to the substrate is contacted with a second type of nanoparticles having oligonucleotides attached thereto.
  • These oligonucleotides have a sequence complementary to at least a portion of the sequence(s) of the oligonucleotides attached to the first type of nanoparticles, and the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the first type of nanoparticles with those on the second type of nanoparticles.
  • the substrate is preferably washed to remove any unbound nanoparticle-oligonucleotide conjugates.
  • each of the first type of nanoparticles has multiple oligonucleotides (having the same or different sequences) attached to it, each of the first type of nanoparticle- oligonucleotide conjugates can hybridize to a plurality of the second type of nanoparticle-oligonucleotide conjugates.
  • the first type of nanoparticle- oligonucleotide conjugates may be hybridized to more than one portion of the nucleic acid to be detected.
  • the amplification provided by the multiple hybridizations may make the change detectable for the first time or may increase the magnitude of the detectable change. This amplification increases the sensitivity of the assay, allowing for detection of small amounts of nucleic acid.
  • additional layers of nanoparticles can be built up by successive additions of the first and second types of nanoparticle-oligonucleotide conjugates. In this way, the number of nanoparticles immobilized per molecule of target nucleic acid can be further increased with a corresponding increase in intensity of the signal.
  • nanoparticles bearing oligonucleotides that would serve to bind the nanoparticles together as a consequence of hybridization with binding oligonucleotides could be used.
  • FIG. 25B Another example of this method of detecting nucleic acid is illustrated in Figure 25B.
  • the combination of hybridizations produces dark areas where nanoparticle aggregates are linked to the substrate by analyte DNA which can be observed with the naked eye.
  • nanoparticles are attached to the substrate.
  • Nanoparticles can be attached to substrates as described in, e.g., Grabar et al., Analyt. Chem., 67, 73-743 (1995); Bethell et al., J. Electroanal. Chem., 409, 137 (1996); Bar et al., Langmuir, 12, 1172 (1996); Colvin et al., J. Am. Chem. Soc, 114, 5221 (1992).
  • oligonucleotides are attached to the nanoparticles. This may be accomplished in the same manner described above for the attachment of oligonucleotides to nanoparticles in solution.
  • the oligonucleotides attached to the nanoparticles have a sequence complementary to a first portion of the sequence of a nucleic acid.
  • the substrate is contacted with the nucleic acid under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the nucleic acid. In this manner the nucleic acid becomes bound to the substrate. Unbound nucleic acid is preferably washed from the substrate prior to adding further nanoparticle- oligonucleotide conjugates.
  • a second type of nanoparticles having oligonucleotides attached thereto is provided.
  • These oligonucleotides have a sequence complementary to a second portion of the sequence of the nucleic acid, and the nucleic acid bound to the substrate is contacted with the second type of nanoparticle-oligonucleotide conjugates under conditions effective to allow hybridization of the oligonucleotides on the second type of nanoparticle-oligonucleotide conjugates with the nucleic acid.
  • the second type of nanoparticle-oligonucleotide conjugates becomes bound to the substrate.
  • any unbound nanoparticle- oligonucleotide conjugates and nucleic acid are washed from the substrate.
  • a change (e.g., color change) may be detectable at this point.
  • the oligonucleotides on the second type of nanoparticles may all have the same sequence or may have different sequences that hybridize with different portions of the nucleic acid to be detected.
  • each nanoparticle may have all of the different oligonucleotides attached to it or, preferably, the different oligonucleotides may be attached to different nanoparticles. See Figure 17.
  • a binding oligonucleotide having a selected sequence having at least two portions, the first portion being complementary to at least a portion of the sequence of the oligonucleotides on the second type of nanoparticles is contacted with the second type of nanoparticle-oligonucleotide conjugates bound to the substrate under conditions effective to allow hybridization of the binding oligonucleotide to the oligonucleotides on the nanoparticles.
  • the binding oligonucleotide becomes bound to the substrate.
  • unbound binding oligonucleotides are washed from the substrate.
  • a third type of nanoparticles having oligonucleotides attached thereto is provided.
  • the oligonucleotides have a sequence complementary to the sequence of a second portion of the binding oligonucleotide.
  • the nanoparticle-oligonucleotide conjugates are contacted with the binding oligonucleotide bound to the substrate under conditions effective to allow hybridization of the binding oligonucleotide to the oligonucleotides on the nanoparticles. After the nanoparticles are bound, unbound nanoparticle-oligonucleotide conjugates are washed from the substrate. The combination of hybridizations produces a detectable change.
  • each of the second type of nanoparticles has multiple oligonucleotides (having the same or different sequences) attached to it, each of the second type of nanoparticle- oligonucleotide conjugates can hybridize to a plurality of the third type of nanoparticle-oligonucleotide conjugates (through the binding oligonucleotide). Also, the second type of nanoparticle-oligonucleotide conjugates may be hybridized to more than one portion of the nucleic acid to be detected.
  • the amplification provided by the multiple hybridizations may make the change detectable for the first time or may increase the magnitude of the detectable change. The amplification increases the sensitivity of the assay, allowing for detection of small amounts of nucleic acid.
  • additional layers of nanoparticles can be built up by successive additions of the binding oligonucleotides and second and third types of nanoparticle- oligonucleotide conjugates.
  • the nanoparticles immobilized per molecule of target nucleic acid can be further increased with a corresponding increase in intensity of the signal.
  • the use of the binding oligonucleotide can be eliminated, and the second and third types of nanoparticle-oligonucleotide conjugates can be designed so that they hybridize directly to each other.
  • Methods of making the nanoparticles and the oligonucleotides and of attaching the oligonucleotides to the nanoparticles are described above.
  • the hybridization conditions are well known in the art and can be readily optimized for the particular system employed (see above).
  • FIG. 13B An example of this method of detecting nucleic acid (analyte DNA) is illustrated in Figure 13B.
  • the combination of hybridizations produces dark areas where nanoparticle aggregates are linked to the substrate by analyte DNA. These dark areas may be readily observed with the naked eye as described above.
  • this embodiment of the method of the invention provides another means of amplifying the detectable change.
  • Another amplification scheme employs liposomes. In this scheme, oligonucleotides are attached to a substrate. Suitable substrates are those described above, and the oligonucleotides can be attached to the substrates as described above.
  • the substrate is glass
  • this can be accomplished by condensing the oligonucleotides through phosphoryl or carboxylic acid groups to aminoalkyl groups on the substrate surface (for related chemistry see Grabar et al., Anal. Chem., 67, 735- 743 (1995)).
  • the oligonucleotides attached to the substrate have a sequence complementary to a first portion of the sequence of the nucleic acid to be detected.
  • the nucleic acid is contacted with the substrate under conditions effective to allow hybridization of the oligonucleotides on the substrate with the nucleic acid. In this manner the nucleic acid becomes bound to the substrate. Any unbound nucleic acid is preferably washed from the substrate before adding additional components of the system.
  • the nucleic acid bound to the substrate is contacted with liposomes having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a second portion of the sequence of the nucleic acid, and the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the liposomes with the nucleic acid. In this manner the liposomes become bound to the substrate. After the liposomes are bound to the substrate, the substrate is washed to remove any unbound liposomes and nucleic acid.
  • the oligonucleotides on the liposomes may all have the same sequence or may have different sequences that hybridize with different portions of the nucleic acid to be detected.
  • each liposome may have all of the different oligonucleotides attached to it or the different oligonucleotides may be attached to different liposomes.
  • oligonucleotide-liposome conjugates To prepare oligonucleotide-liposome conjugates, the oligonucleotides are linked to a hydrophobic group, such as cholesteryl (see Letsinger et al., J. Am. Chem. Soc, 115, 7535-7536 (1993)), and the hydrophobic-oligonucleotide conjugates are mixed with a solution of liposomes to form liposomes with hydrophobic- oligonucleotide conjugates anchored in the membrane (see Zhang et al., Tetrahedron Lett., 37, 6243-6246 (1996)).
  • cholesteryl see Letsinger et al., J. Am. Chem. Soc, 115, 7535-7536 (1993)
  • hydrophobic-oligonucleotide conjugates are mixed with a solution of liposomes to form liposomes with hydrophobic- oligonucleotide conjugates anchored
  • the loading of hydrophobic-oligonucleotide conjugates on the surface of the liposomes can be controlled by controlling the ratio of hydrophobic-oligonucleotide conjugates to liposomes in the mixture. It has been observed that liposomes bearing oligonucleotides attached by hydrophobic interaction of pendent cholesteryl groups are effective in targeting polynucleotides immobilized on a nitrocellulose membrane (Id.). Fluorescein groups anchored in the membrane of the liposome were used as the reporter group. They served effectively, but sensitivity was limited by the fact that the signal from fluorescein in regions of high local concentration (e.g., on the liposome surface) is weakened by self quenching.
  • the liposomes are made by methods well known in the art. See Zhang et al., Tetrahedron Lett, 37, 6243 (1996).
  • the liposomes will generally be about 5-50 times larger in size (diameter) than the nanoparticles used in subsequent steps. For instance, for nanoparticles about 13 nm in diameter, liposomes about 100 nm in diameter are preferably used.
  • the liposomes bound to the substrate are contacted with a first type of nanoparticles having at least a first type of oligonucleotides attached thereto.
  • the first type of oligonucleotides have a hydrophobic group attached to the end not attached to the nanoparticles, and the contacting takes place under conditions effective to allow attachment of the oligonucleotides on the nanoparticles to the liposomes as a result of hydrophobic interactions. A detectable change may be observable at this point.
  • the method may further comprise contacting the first type of nanoparticle- oligonucleotide conjugates bound to the liposomes with a second type of nanoparticles having oligonucleotides attached thereto.
  • the first type of nanoparticles have a second type of oligonucleotides attached thereto which have a sequence complementary to at least a portion of the sequence of the oligonucleotides on the second type of nanoparticles
  • the oligonucleotides on the second type of nanoparticles have a sequence complementary to at least a portion of the sequence of the second type of oligonucleotides on the first type of nanoparticles.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the first and second types of nanoparticles.
  • This hybridization will generally be performed at mild temperatures (e.g., 5°C to 60°C), so conditions (e.g., 0.3-1.0 M NaCl) conducive to hybridization at room temperature are employed.
  • conditions e.g., 0.3-1.0 M NaCl
  • unbound nanoparticle-oligonucleotide conjugates are washed from the substrate.
  • the combination of hybridizations produces a detectable change.
  • the detectable changes are the same as those described above, except that the multiple hybridizations result in an amplification of the detectable change.
  • each of the liposomes since each of the liposomes has multiple oligonucleotides (having the same or different sequences) attached to it, each of the liposomes can hybridize to a plurality of the first type of nanoparticle-oligonucleotide conjugates.
  • each of the first type of nanoparticles has multiple oligonucleotides attached to it, each of the first type of nanoparticle-oligonucleotide conjugates can hybridize to a plurality of the second type of nanoparticle-oligonucleotide conjugates.
  • the liposomes may be hybridized to more than one portion of the nucleic acid to be detected.
  • the amplification provided by the multiple hybridizations may make the change detectable for the first time or may increase the magnitude of the detectable change. This amplification increases the sensitivity of the assay, allowing for detection of small amounts of nucleic acid.
  • additional layers of nanoparticles can be built up by successive additions of the first and second types of nanoparticle-oligonucleotide conjugates. In this way, the number of nanoparticles immobilized per molecule of target nucleic acid can be further increased with a corresponding increase in the intensity, of the signal.
  • nanoparticles bearing oligonucleotides that would serve to bring the nanoparticles together as a consequence of hybridization with binding oligonucleotides could be used.
  • Methods of making the nanoparticles and the oligonucleotides and of attaching the oligonucleotides to the nanoparticles are described above.
  • a mixture of oligonucleotides functionalized at one end for binding to the nanoparticles and with or without a hydrophobic group at the other end can be used on the first type of nanoparticles.
  • the relative ratio of these oligonucleotides bound to the average nanoparticle will be controlled by the ratio of the concentrations of the two oligonucleotides in the mixture.
  • the hybridization conditions are well known in the art and can be readily optimized for the particular system employed (see above).
  • FIG. 18 An example of this method of detecting nucleic acid is, illustrated in Figure 18.
  • the hybridization of the first type of nanoparticle-oligonucleotide conjugates to the liposomes may produce a detectable change. In the case of gold nanoparticles, a pink/red color may be observed or a pu ⁇ le/blue color may be observed if the nanoparticles are close enough together.
  • the hybridization of the second type of nanoparticle-oligonucleotide conjugates to the first type of nanoparticle- oligonucleotide conjugates will produce a detectable change. In the case of gold nanoparticles, a pu ⁇ le/blue color will be observed. All of these color changes may be observed with the naked eye.
  • an "aggregate probe” can be used.
  • the aggregate probe can be prepared by allowing two types of nanoparticles having complementary oligonucleotides (a and a') attached to them to hybridize to form a core (illustrated in Figure 28A). Since each type of nanoparticle has a plurality of oligonucleotides attached to it, each type of nanoparticles will hybridize to a plurality of the other type of nanoparticles. Thus, the core is an aggregate containing numerous nanoparticles of both types. The core is then capped with a third type of nanoparticles having at least two types of oligonucleotides attached to them.
  • the first type of oligonucleotides has a sequence b which is complementary to the sequence b' of a portion of a nucleic acid to be detected.
  • the second type of oligonucleotides has sequence a or a' so that the third type of nanoparticles will hybridize to nanoparticles on the exterior of the core.
  • the aggregate probe can also be prepared by utilizing two types of nanoparticles (see Figure 28B). Each type of nanoparticles has at least two types of oligonucleotides attached to them.
  • the first type of oligonucleotides present on each of the two types of nanoparticles has sequence b which is complementary to the sequence b' of a portion of the nucleic acid to be detected.
  • the second type of oligonucleotides on the first type of nanoparticles has a sequence a which is complementary to the sequence a' of the second type of oligonucleotides on the second type of nanoparticles (see Figure 28B) so that the two types of nanoparticles hybridize to each other to form the aggregate probe. Since each type of nanoparticles has a plurality of oligonucleotides attached to it, each type of nanoparticles will hybridize to a plurality of the other type of nanoparticles to form an aggregate containing numerous nanoparticles of both types.
  • the aggregate probe can be utilized to detect nucleic acid in any of the above assay formats performed on a substrate, eliminating the need to build up layers of individual nanoparticles in order to obtain or enhance a detectable change.
  • layers of aggregate probes can be built up by using two types of aggregate probes, the first type of aggregate probe having oligonucleotides attached to it that are complementary to oligonucleotides on the other type of aggregate probe.
  • the aggregate probes can hybridize to each other to form the multiple layers.
  • a type of oligonucleotides comprising sequence c is attached to a substrate (see Figure 28C).
  • Sequence c is complementary to the sequence c' of a portion of a nucleic acid to be detected.
  • the target nucleic acid is added and allowed to hybridize to the oligonucleotides attached to the substrate, after which the aggregate probe is added and allowed to hybridize to the portion of the target nucleic acid having sequence b', thereby producing a detectable change.
  • the target nucleic acid can first be hybridized to the aggregate probe in solution and subsequently hybridized to the oligonucleotides on the substrate, or the target nucleic acid can simultaneously be hybridized to the aggregate probe and the oligonucleotides on the substrate.
  • the target nucleic acid is allowed to react with the aggregate probe and another type of nanoparticles in solution (see Figure 28D).
  • oligonucleotides attached to this additional type of nanoparticles comprise sequence c so that they hybridize to sequence c' of the target nucleic acid and some of the oligonucleotides attached to this additional type of nanoparticles comprise sequence d so that they can subsequently hybridize to oligonucleotides comprising sequence d' which are attached to the substrate.
  • the core itself can also be used as a probe to detect nucleic acids.
  • Figure 28E One possible assay format is illustrated in Figure 28E. As illustrated there, a type of oligonucleotides comprising sequence b is attached to a substrate. Sequence b is complementary to the sequence b' of a portion of a nucleic acid to be detected.
  • the target nucleic acid is contacted with the substrate and allowed to hybridize to the oligonucleotides attached to the substrate. Then, another type of nanoparticles is added. Some of the oligonucleotides attached to this additional type of nanoparticles comprise sequence c so which is complementary to sequence c' of the target nucleic acid so that the nanoparticles hybridize to the target nucleic acid bound to the substrate. Some of the oligonucleotides attached to the additional type of nanoparticles comprise sequence a or a' complementary to sequences a and a' on the core probe, and the core probe is added and allowed to hybridize to the oligonucleotides on the nanoparticles.
  • each core probe has sequences a and a' attached to the nanoparticles which comprise the core, the core probes can hybridize to each other to form multiple layers attached to the substrate, providing a greatly enhanced detectable change.
  • the target nucleic acid could be contacted with the additional type of nanoparticles in solution prior to being contacted with the substrate, or the target nucleic acid, the nanoparticles and the substrate could all be contacted simultaneously.
  • the additional type of nanoparticles could be replaced by a linking oligonucleotide comprising both sequences c and a or a'.
  • a substrate When a substrate is employed, a plurality of the initial types of nanoparticle- oligonucleotide conjugates or oligonucleotides can be attached to the substrate in an array for detecting multiple portions of a target nucleic acid, for detecting multiple different nucleic acids, or both.
  • a substrate may be provided with rows of spots, each spot containing a different type of oligonucleotide or oligonucleotide- nanoparticle conjugate designed to bind to a portion of a target nucleic acid.
  • a sample containing one or more nucleic acids is applied to each spot, and the rest of the assay is performed in one of the ways described above using appropriate oligonucleotide-nanoparticle conjugates, oligonucleotide-liposome conjugates, aggregate probes, core probes, and binding oligonucleotides.
  • a detectable change can be produced or further enhanced by silver staining.
  • Silver staining can be employed with any type of nanoparticles that catalyze the reduction of silver.
  • noble metals e.g., gold and silver.
  • the nanoparticles being employed for the detection of a nucleic acid do not catalyze the reduction of silver, then silver ions can be complexed to the nucleic acid to catalyze the reduction. See Braun et al., Nature, 391, 775 (1998).
  • silver stains are known which can react with the phosphate groups on nucleic acids.
  • Silver staining can be used to produce or enhance a detectable change in any assay performed on a substrate, including those described above.
  • silver staining has been found to provide a huge increase in sensitivity for assays employing a single type of nanoparticle, such as the one illustrated in Figure 25 A, so that the use of layers of nanoparticles, aggregate probes and core probes can often be eliminated.
  • the detectable change can be observed with an optical scanner.
  • Suitable scanners include those used to scan documents into a computer which are capable of operating in the reflective mode (e.g., a flatbed scanner), other devices capable of performing this function or which utilize the same type of optics, any type of greyscale-sensitive measurement device, and standard scanners which have been modified to scan substrates according to the invention (e.g., a flatbed scanner modified to include a holder for the substrate) (to date, it has not been found possible to use scanners operating in the transmissive mode).
  • the resolution of the scanner must be sufficient so that the reaction area on the substrate is larger than a single pixel of the scanner.
  • the scanner can be used with any substrate, provided that the detectable change produced by the assay can be .
  • the scanner can be a black-and-white scanner or, preferably, a color scanner. Most preferably, the scanner is a standard color scanner of the type used to scan documents into computers. Such scanners are inexpensive and readily available commercially. For instance, an Epson Expression 636 (600 x 600 dpi), a UMAX Astra 1200 (300 x 300 dpi), or a Microtec 1600 (1600 x 1600 dpi) can be used. The scanner is linked to a computer loaded with software for processing the images obtained by scanning the substrate.
  • the software can be standard software which is readily available commercially, such as Adobe Photoshop 5.2 and Corel Photopaint 8.0. Using the software to calculate grayscale measurements provides a means of quantitating the results of the assays.
  • the software can also provide a color number for colored spots and can generate images (e.g., printouts) of the scans which can be reviewed to provide a qualitative determination of the presence of a nucleic acid, the quantity of a nucleic acid, or both.
  • the sensitivity of assays such as that described in Example 5 can be increased by subtracting the color that represents a negative result (red in Example 5) from the color that represents a positive result (blue in Example 5).
  • the computer can be a standard personal computer which is readily available commercially.
  • a standard scanner linked to a standard computer loaded with standard software can provide a convenient, easy, inexpensive means of detecting and quantitating nucleic acids when the assays are performed on substrates.
  • the scans can also be stored in the computer to maintain a record of the results for further reference or use.
  • more sophisticated instruments and software can be used, if desired.
  • a nanoparticle-oligonucleotide conjugate which may be used in an assay for any nucleic acid is illustrated in Figures 17D-E.
  • This "universal probe" has oligonucleotides of a single sequence attached to it. These oligonucleotides can hybridize with a binding oligonucleotide which has a sequence comprising at least two portions. The first portion is complementary to at least a portion of the sequence of the oligonucleotides on the nanoparticles. The second portion is complementary to a portion of the sequence of the nucleic acid to be detected.
  • a plurality of binding oligonucleotides having the same first portion and different second portions can be used, in which case the "universal probe", after hybridization to the binding oligonucleotides, can bind to multiple portions of the nucleic acid to be detected or to different nucleic acid targets.
  • the detectable change is created by labeling the oligonucleotides, the nanoparticles, or both with molecules (e.g., fluorescent molecules and dyes) that produce detectable changes upon hydridization of the oligonucleotides on the nanoparticles with the target nucleic acid.
  • molecules e.g., fluorescent molecules and dyes
  • oligonucleotides attached to metal and semiconductor nanoparticles can have a fluorescent molecule attached to the end not attached to the nanoparticles.
  • Metal and semiconductor nanoparticles are known fluorescence quenchers, with the magnitude of the quenching effect depending on the distance between the nanoparticles and the fluorescent molecule.
  • the oligonucleotides attached to the nanoparticles interact with the nanoparticles, so that significant quenching will be observed. See Figure 20A.
  • the fluorescent molecule Upon hybridization to a target nucleic acid, the fluorescent molecule will become spaced away from the nanoparticles, diminishing quenching of the fluorescence. See Figure 20A. Longer oligonucleotides should give rise to larger changes in fluorescence, at least until the fluorescent groups are moved far enough away from the nanoparticle surfaces so that an increase in the change is no longer observed. Useful lengths of the oligonucleotides can be determined empirically.
  • Metallic and semiconductor nanoparticles having fluorescent-labeled oligonucleotides attached thereto can be used in any of the assay formats described above, including those performed in solution or on substrates.
  • oligonucleotides Methods of labeling oligonucleotides with fluorescent molecules and measuring fluorescence are well known in the art. Suitable fluorescent molecules are also well known in the art and include the fluoresceins, rhodamines and Texas Red. The oligonucleotides will be attached to the nanoparticles as described above.
  • Suitable particles include polymeric particles (such as polystyrene particles, polyvinyl particles, acrylate and methacrylate particles), glass particles, latex particles, Sepharose beads and others like particles well known in the art. Methods of attaching oligonucleotides to such particles are well known in the art.
  • Functional groups include carboxylic acids, aldehydes, amino groups, cyano groups, ethylene groups, hydroxyl groups, mercapto groups, and the like.
  • Nanoparticles including metallic and semiconductor nanoparticles, can also be used.
  • the two fluorophores are designated d and a for donor and acceptor.
  • a variety of fluorescent molecules useful in such combinations are well known in the art and are available from, e.g., Molecular Probes.
  • An attractive combination is fluorescein as the donor and Texas Red as acceptor.
  • the two types of nanoparticle- oligonucleotide conjugates with d and a attached are mixed with the target nucleic acid, and fluorescence measured in a fluorimeter.
  • the mixture will be excited with light of the wavelength that excites d, and the mixture will be monitored for fluorescence from a.
  • d and a will be brought in proximity (see Figure 20B).
  • hybridization will be shown by a shift in fluorescence from that for d to that for a or by the appearance of fluorescence for a in addition to that for d.
  • the flurophores will be too far apart for energy transfer to be significant, and only the fluorescence of d will be observed.
  • lack of hybridization will be shown by a lack of fluorescence due to d or a because of quenching (see above).
  • Hybridization will be shown by an increase in fluorescence due to a.
  • the above described particles and nanoparticles having oligonucleotides labeled with acceptor and donor fluorescent molecules attached can be used in the assay formats described above, including those performed in solution and on substrates.
  • the oligonucleotide sequences are preferably chosen so that they bind to the target nucleic acid as illustrated in Figures 15A-G.
  • the binding oligonucleotides may be used to bring the acceptor and donor fluorescent molecules on the two nanoparticles in proximity.
  • the oligonucleotides attached the substrate may be labeled with d.
  • other labels besides fluorescent molecules can be used, such as chemiluminescent molecules, which will give a detectable signal or a change in detectable signal upon hybridization.
  • Another embodiment of the detection method of the invention is a very sensitive system that utilizes detection of changes in fluorescence and color (illustrated in Figure 21).
  • This system employs latex microspheres to which are attached oligonucleotides labeled with a fluorescent molecule and gold nanoparticles to which are attached oligonucleotides.
  • the oligonucleotide-nanoparticle conjugates can be prepared as described above. Methods of attaching oligonucleotides to latex microspheres are well known (see, e.g., Charreyre et al., Langmuir, 13:3103-3110 (1997); Elaissari et al., J.
  • oligonucleotides on the latex microspheres and the oligonucleotides on the gold nanoparticles have sequences capable of hybridizing with different portions of the sequence of a target nucleic acid, but not with each other.
  • a target nucleic acid comprising sequences complementary to the sequences of the oligonucleotides on the latex microspheres and gold nanoparticles is contacted with the two probes, a network structure is formed (see Figure 21).
  • the fluorescence of the oligonucleotides attached to the latex microspheres is quenched while part of this network. Indeed, one gold nanoparticle can quench many fluorophore molecules since gold nanoparticles have very large abso ⁇ tion coefficients.
  • the fluorescence of a solution containing nucleic acid and the two particles can be monitored to detect the results, with a reduction in, or elimination of, fluorescence indicating a positive result.
  • the results of the assay are detected by placing a droplet of the solution onto a microporous material (see Figure 21).
  • the microporous material should be transparent or a color (e.g., white) which allows for detection of the pink/red color of the gold nanoparticles.
  • the microporous material should also have a pore size sufficiently large to allow the gold nanoparticles to pass through the pores and sufficiently small to retain the latex microspheres on the surface of the microporous material when the microporous material is washed.
  • the size (diameter) of the latex microspheres must be larger than the size (diameter) of the gold nanoparticles.
  • the microporous material must also be inert to biological media.
  • microporous materials include various filters and membranes, such as modified polyvinylidene fluoride (PVDF, such as DuraporeTM membrane filters purchased from Millipore Co ⁇ .) and pure cellulose acetate (such as AcetatePlusTM membrane filters purchased from Micron Separations Inc.).
  • PVDF modified polyvinylidene fluoride
  • AcetatePlusTM membrane filters purchased from Micron Separations Inc.
  • Such a microporous material retains the network composed of target nucleic acid and the two probes, and a positive result (presence of the target nucleic acid) is evidenced by a red/pink color (due to the presence of the gold nanoparticles) and a lack of fluorescence (due to quenching of fluorescence by the gold nanoparticles) (see Figure 21).
  • a negative result is evidenced by a white color and fluorescence, because the gold nanoparticles would pass through the pores of the microporous material when it is washed (so no quenching of the fluorescence would occur), and the white latex microspheres would be trapped on top of it (see Figure 21).
  • changes in fluorescence and color can be observed as a function of temperature. For instance, as the temperature is raised, fluorescence will be observed once the dehybridization temperature has been reached. Therefore, by looking at color or fluorescence as a function of temperature, information can be obtained about the degree of complementarity between the oligonucleotide probes and the target nucleic acid.
  • this detection method exhibits high sensitivity. As little as 3 femtomoles of single-stranded target nucleic acid 24 bases in length and 20 femtomoles of double-stranded target nucleic acid 24 bases in length have been detected with the naked eye.
  • the method is also very simple to use. Fluorescence can be generated by simply illuminating the solution or microporous material with a UV lamp, and the fluorescent and colorimetric signals can be monitored by the naked eye. Alternatively, for a more quantitative result, a fluorimeter can be employed in front-face mode to measure the fluorescence of the solution with a short path length.
  • the above embodiment has been described with particular reference to latex microspheres and gold nanoparticles.
  • microsphere or nanoparticle having the other properties described above and to which oligonucleotides can be attached, can be used in place of these particles.
  • Many suitable particles and nanoparticles are described above, along with techniques for attaching oligonucleotides to them.
  • microspheres and nanoparticles having other measurable properties may be used.
  • polymer-modified particles and nanoparticles, where the polymer can be modified to have any desirable property, such as fluorescence, color, or electrochemical activity can be used. See, Watson et al., J. Am. Chem. Soc, 121, 462-463 (1999) (polymer-modified gold nanoparticles).
  • magnetic, polymer- coated magnetic, and semiconducting particles can be used. See Chan et al., Science, 281, 2016 (1998); Bruchez et al., Science, 281, 2013 (1998); Kolarova et al., Biotechniques, 20, 196-198 (1996).
  • two probes comprising metallic or semiconductor nanoparticles having oligonucleotides labeled with fluorescent molecules attached to them are employed (illustrated in Figure 22).
  • the oligonucleotide-nanoparticle conjugates can be prepared and labeled with fluorescent molecules as described above.
  • the oligonucleotides on the two types of oligonucleotide-nanoparticle conjugates have sequences capable of hybridizing with different portions of the sequence of a target nucleic acid, but not with each other.
  • the fluorescence of the oligonucleotides attached to the nanoparticles is quenched while part of this network.
  • the fluorescence of a solution containing nucleic acid and the two probes can be monitored to detect the results, with a reduction in, or elimination of, fluorescence indicating a positive result.
  • the results of the assay are detected by placing a droplet of the solution onto a microporous material (see Figure 22).
  • the microporous material should have a pore size sufficiently large to allow the nanoparticles to pass through the pores and sufficiently small to retain the network on the surface of the microporous material when the microporous material is washed (see Figure 22).
  • Many suitable microporous materials are known in the art and include those described above. Such a microporous material retains the network composed of target nucleic acid and the two probes, and a positive result (presence of the target nucleic acid) is evidenced by a lack of fluorescence (due to quenching of fluorescence by the metallic or semiconductor nanoparticles) (see Figure 22).
  • a negative result is evidenced by fluorescence because the nanoparticles would pass through the pores of the microporous material when it is washed (so no quenching of the fluorescence would occur) (see Figure 22). There is low background fluorescence because unbound probes are washed away from the detection area.
  • changes in fluorescence can be observed as a function of temperature. For instance, as the temperature is raised, fluorescence will be observed once the dehybridization temperature has been reached. Therefore, by looking at fluorescence as a function of temperature, information can be obtained about the degree of complementarity between the oligonucleotide probes and the target nucleic acid.
  • Fluorescence can be generated by simply illuminating the solution or microporous material with a UV lamp, and the fluorescent signal can be monitored by the naked eye.
  • a fluorimeter can be employed in front-face mode to measure the fluorescence of the solution with a short path length.
  • a "satellite probe” is used (see Figure 24).
  • the satellite probe comprises a central particle with one or several physical properties that can be exploited for detection in an assay for nucleic acids (e.g., intense color, fluorescence quenching ability, magnetism).
  • Suitable particles include the nanoparticles and other particles described above.
  • the particle has oligonucleotides (all having the same sequence) attached to it (see Figure 24). Methods of attaching oligonucleotides to the particles are described above. These oligonucleotides comprise at least a first portion and a second portion, both of which are complementary to portions of the sequence of a target nucleic acid (see Figure 24).
  • the satellite probe also comprises probe oligonucleotides.
  • Each probe oligonucleotide has at least a first portion and a second portion (see Figure 24).
  • the sequence of the first portion of the probe oligonucleotides is complementary to the first portion of the sequence of the oligonucleotides immobilized on the central particle (see Figure 24). Consequently, when the central particle and the probe oligonucleotides are brought into contact, the oligonucleotides on the particle hybridize with the probe oligonucleotides to form the satellite probe (see Figure 24).
  • Both the first and second portions of the probe oligonucleotides are complementary to portions of the sequence of the target nucleic acid (see Figure 24).
  • Each probe oligonucleotide is labeled with a reporter molecule (see Figure 24), as further described below.
  • the amount of hybridization overlap between the probe oligonucleotides and the target is as large as, or greater than, the hybridization overlap between the probe oligonucleotides and the oligonucleotides attached to the particle (see Figure 24). Therefore, temperature cycling resulting in dehybridization and rehybridization would favor moving the probe oligonucleotides from the central particle to the target. Then, the particles are separated from the probe oligonucleotides hybridized to the target, and the reporter molecule is detected.
  • the satellite probe can be used in a variety of detection strategies.
  • the central particle has a magnetic core and is covered with a material capable of quenching the fluorescence of fluorophores attached to the probe oligonucleotides that surround it
  • this system can be used in an in situ fluorometric detection scheme for nucleic acids.
  • Functionalized polymer-coated magnetic particles Fe 3 O 4
  • Dynal Dynal
  • Bangs Laboratories EstaporTM
  • silica-coated magnetic Fe 3 O 4 nanoparticles could be modified (Liu et al., Chem.
  • DABCYL 4-((4-(dimethylamino)phenyl)-azo)benzoic acid
  • Probes forms extremely stable amide bonds upon reaction with primary alkylamino . groups.
  • any magnetic particle or polymer-coated magnetic particle with primary alkyl amino groups could be modified with both oligonucleotides, as well as these quencher molecules.
  • the DABCYL quencher could be attached directly to the surface-bound oligonucleotide, instead of the alkyl amino-modified surface.
  • the satellite probe comprising the probe oligonucleotides is brought into contact with the target. The temperature is cycled so as to cause dehybridization and rehybridization, which causes the probe oligonucleotides to move from the central particle to the target. Detection is accomplished by applying a magnetic field and removing the particles from solution and measuring the fluorescence of the probe oligonucleotides remaining in solution hybridized to the target.
  • This approach can be extended to a colorimetric assay by using magnetic particles with a dye coating in conjunction with probe oligonucleotides labeled with a dye which has optical properties that are distinct from the dye on the magnetic nanoparticles or perturb those of the dye on the magnetic nanoparticles.
  • the particles and the probe oligonucleotides are in solution together, the solution will exhibit one color which derives from a combination of the two dyes.
  • the probe oligonucleotides will move from the satellite probe to the target.
  • This approach also can be further extended to an electrochemical assay by using an oligonucleotide-magnetic particle conjugate in conjunction with a probe oligonucleotide having attached a redox-active molecule.
  • Any modifiable redox- active species can be used, such as the well-studied redox-active ferrocene derivative.
  • a ferrocene derivatized phosphoramidite can be attached to oligonucleotides directly using standard phosphoramidite chemistry. Mucic et al., Chem. Commun., 555 (1996); Eckstein, ed., in Oligonucleotides and Analogues, 1st ed., Oxford University, New York, NY (1991).
  • the ferrocenylphosphoramidite is prepared in a two-step synthesis from 6-bromohexylferrocene.
  • 6- bromohexylferrocene is stirred in an aqueous HMPA solution at 120°C for 6 hours to from 6-hydroxyhexylferrocene.
  • the 6-hydroxyhexylferrocene is added to a THF solution of N,N-diisopropylethylamine and beta-cyanoethyl-N,N- diisopropylchlorophosphoramide to form the ferrocenylphosphoramidite.
  • Oligonucleotide-modified polymer-coated gold nanoparticles could also be utilized. Watson et al., J. Am. Chem. Soc, 121, 462-463 (1999). A copolymer of amino reactive sites (e.g., anhydrides) could be inco ⁇ orated into the polymer for reaction with arnino- modified oligonucleotides. Moller et al., Bioconjugate Chem., 6, 174-178 (1995). In the presence of target and with temperature cycling, the redox-active probe oligonucleotides will move from the satellite probe to the target.
  • a copolymer of amino reactive sites e.g., anhydrides
  • the magnetic field will remove the magnetic particles from solution leaving behind the redox-active probe oligonucleotides hybridized with the target nucleic acid.
  • the amount of target then can be determined by cyclic voltammetry or any electrochemical technique that can interrogate the redox-active molecule.
  • a nucleic acid is detected by contacting the nucleic acid with a substrate having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a first portion of the sequence of the nucleic acid.
  • the oligonucleotides are located between a pair of electrodes located on the substrate.
  • the substrate must be made of a material which is not a conductor of electricity (e.g., glass, quartz, polymers, plastics).
  • the electrodes may be made of any standard material (e.g., metals, such as gold, platinum, tin oxide).
  • the electrodes can be fabricated by conventional microfabrication techniques. See, e.g., Introduction To Microlithography (L.F.
  • the substrate may have a plurality of pairs of electrodes located on it in an array to allow for the detection of multiple portions of a single nucleic acid, the detection of multiple different nucleic acids, or both.
  • Arrays of electrodes can be purchased (e.g., from AbbtechScientific, Inc., Richmond, Virginia) or can be made by conventional microfabrication techniques. See, e.g., Introduction To Microlithography (L.F. Thompson et al., eds., American Chemical Society, Washington, D.C. 1983).
  • Suitable photomasks for making the arrays can be purchased (e.g., from Photronics, Milpitas, CA).
  • Each of the pairs of electrodes in the array will have a type of oligonucleotides attached to the substrate between the two electrodes.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the substrate with the nucleic acid.
  • the nucleic acid bound to the substrate is contacted with a type of nanoparticles.
  • the nanoparticles must be made of a material which can conduct electricity. Such nanoparticles include those made of metal, such as gold nanoparticles, and semiconductor materials.
  • the nanoparticles will have one or more types of oligonucleotides attached to them, at least one of the types of oligonucleotides having a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the contacting takes place under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles with the nucleic acid. If the nucleic acid is present, the circuit between the electrodes should be closed because of the attachment of the nanoparticles to the substrate between the electrodes, and a change in conductivity will be detected.
  • the binding of a single type of nanoparticles does not result in closure of the circuit, this situation can be remedied by using a closer spacing between the electrodes, using larger nanoparticles, or employing another material that will close the circuit (but only if the nanoparticles have been bound to the substrate between the electrodes).
  • the substrate can be contacted with silver stain (as described above) to deposit silver between the electrodes to close the circuit and produce the detectable change in conductivity.
  • Another way to close the circuit in the case where the addition of a single type of nanoparticles is not sufficient is to contact the first type of nanoparticles bound to the substrate with a second type of nanoparticles having oligonucleotides attached to them that have a sequence complementary to the oligonucleotides on the first type of nanoparticles.
  • the contacting will take place under conditions effective so that the oligonucleotides on the second type of nanoparticle hybridize to those on the first type of oligonucleotides.
  • additional layers of nanoparticles can be built up by alternately adding the first and second types of nanoparticles until a sufficient number of nanoparticles are attached to the substrate to close the circuit.
  • kits for detecting nucleic acids comprises at least one container, the container holding at least two types of nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides on the first type of nanoparticles have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the oligonucleotides on the second type of nanoparticles have a sequence complementary to the sequence of a second portion of the nucleic acid.
  • the container may further comprise filler oligonucleotides having a sequence complementary to a third portion of the nucleic acid, the third portion being located between the first and second portions.
  • the filler oligonucleotide may also be provided in a separate container.
  • the kit comprises at least two containers.
  • the first container holds nanoparticles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the second container holds nanoparticles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a second portion of the nucleic acid.
  • the kit may further comprise a third container holding a filler oligonucleotide having a sequence complementary to a third portion of the nucleic acid, the third portion being located between the first and second portions.
  • kits can have the oligonucleotides and nanoparticles in separate containers, and the oligonucleotides would have to be attached to the nanoparticles prior to performing an assay to detect a nucleic acid.
  • the oligonucleotides and/or the nanoparticles may be functionalized so that the oligonucleotides can be attached to the nanoparticles.
  • the oligonucleotides and/or nanoparticles may be provided in the kit without functional groups, in which case they must be functionalized prior to performing the assay.
  • the kit comprises at least one container.
  • the container holds metallic or semiconductor nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a portion of a nucleic acid and have fluorescent molecules attached to the ends of the oligonucleotides not attached to the nanoparticles.
  • the kit comprises a substrate, the substrate having attached thereto nanoparticles.
  • the nanoparticles have oligonucleotides attached thereto which have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the kit also includes a first container holding nanoparticles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a second portion of the nucleic acid.
  • the oligonucleotides may have the same or different sequences, but each of the oligonucleotides has a sequence complementary to a portion of the nucleic acid.
  • the kit further includes a second container holding a binding oligonucleotide having a selected sequence having at least two portions, the first portion being complementary to at least a portion of the sequence of the oligonucleotides on the nanoparticles in the first container.
  • the kit also includes a third container holding nanoparticles having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to the sequence of a second portion of the binding oligonucleotide.
  • the kit comprises a substrate having oligonucleotides attached thereto which have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the kit also includes a first container holding nanoparticles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a second portion of the nucleic acid.
  • the oligonucleotides may have the same or different sequences, but each of the oligonucleotides has a sequence complementary to a portion of the nucleic acid.
  • the kit further includes a second container holding nanoparticles having oligonucleotides attached thereto which have a sequence complementary to at least a portion of the oligonucleotides attached to the nanoparticles in the first container.
  • kits can have the substrate, oligonucleotides and nanoparticles in separate containers.
  • the substrate, oligonucleotides, and nanoparticles would have to be appropriately attached to each other prior to performing an assay to detect a nucleic acid.
  • the substrate, oligonucleotides and/or the nanoparticles may be functionalized to expedite this attachment.
  • the substrate, oligonucleotides and/or nanoparticles may be provided in the kit without functional groups, in which case they must be functionalized prior to performing the assay.
  • the kit comprises a substrate having oligonucleotides attached thereto which have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the kit also includes a first container holding liposomes having oligonucleotides attached thereto which have a sequence complementary to the sequence of a second portion of the nucleic acid and a second container holding nanoparticles having at least a first type of oligonucleotides attached thereto, the first type of oligonucleotides having a cholesteryl group attached to the end not attached to the nanoparticles so that the nanoparticles can attach to the liposomes by hydrophobic interactions.
  • the kit may further comprise a third container holding a second type of nanoparticles having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to at least a portion of the sequence of a second type of oligonucleotides attached to the first type of nanoparticles.
  • the second type of oligonucleotides attached to the first type of nanoparticles having a sequence complementary to the sequence of the oligonucleotides on the second type of nanoparticles.
  • the kit may comprise a substrate having nanoparticles attached to it.
  • the nanoparticles have oligonucleotides attached to them which have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the kit also includes a first container holding an aggregate probe.
  • the aggregated probe comprises at least two types, of nanoparticles having oligonucleotides attached to them.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to each of them.
  • At least one of the types of nanoparticles of the aggregate probe has oligonucleotides attached to it which have a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the kit may comprise a substrate having oligonucleotides attached to it.
  • the oligonucleotides have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the kit further includes a first container holding an aggregate probe.
  • the aggregate probe comprises at least two types of nanoparticles having oligonucleotides attached to them.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to each of them.
  • At least one of the types of nanoparticles of the aggregate probe has oligonucleotides attached thereto which have a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the kit may comprise a substrate having oligonucleotides attached to it and a first container holding an aggregate probe.
  • the aggregate probe comprises at least two types of nanoparticles having oligonucleotides attached to them.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to each of them.
  • At least one of the types of nanoparticles of the aggregate probe has oligonucleotides attached to it which have a sequence complementary to a first portion of the sequence of the nucleic acid.
  • the kit also includes a second container holding nanoparticles.
  • the nanoparticles have at least two types of oligonucleotides attached to them.
  • the first type of oligonucleotides has a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the second type of oligonucleotides has a sequence complementary to at least a portion of the sequence of the oligonucleotides attached to the substrate.
  • the kit may comprise a substrate which has oligonucleotides attached to it.
  • the oligonucleotides have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the kit also comprises a first container holding liposomes having oligonucleotides attached to them.
  • the oligonucleotides have a sequence complementary to the sequence of a second portion of the nucleic acid.
  • the kit further includes a second container holding an aggregate probe comprising at least two types of nanoparticles having oligonucleotides attached to them.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to each of them.
  • At least one of the types of nanoparticles of the aggregate probe has oligonucleotides attached to it which have a hydrophobic groups attached to the ends not attached to the nanoparticles.
  • the kit may comprise a first container holding nanoparticles having oligonucleotides attached thereto.
  • the kit also includes one or more additional containers, each container holding a binding oligonucleotide.
  • Each binding oligonucleotide has a first portion which has a sequence complementary to at least a portion of the sequence of oligonucleotides on the nanoparticles and a second portion which has a sequence complementary to the sequence of a portion of a nucleic acid to be detected.
  • the sequences of the second portions of the binding oligonucleotides may be different as long as each sequence is complementary to a portion of the sequence of the nucleic acid to be detected.
  • the kit comprises a container holding one type of nanoparticles having oligonucleotides attached thereto and one or more types of binding oligonucleotides.
  • Each of the types of binding oligonucleotides has a sequence comprising at least two portions. The first portion is complementary to the sequence of the oligonucleotides on the nanoparticles, whereby the binding oligonucleotides are hybridized to the oligonucleotides on the nanoparticles in the container(s). The second portion is complementary to the sequence of a portion of the nucleic acid.
  • kits may comprise one or two containers holding two types of particles.
  • the first type of particles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a first portion of a nucleic acid.
  • the oligonucleotides are labeled with an energy donor on the ends not attached to the particles.
  • the second type of particles having oligonucleotides attached thereto which have a sequence complementary to the sequence of a second portion of a nucleic acid.
  • the oligonucleotides are labeled with an energy acceptor on the ends not attached to the particles.
  • the energy donors and acceptors may be fluorescent molecules.
  • the kit comprises a first container holding a type of latex microspheres having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a first portion of the sequence of a nucleic acid and are labeled with a fluorescent molecule.
  • the kit also comprises a second container holding a type of gold nanoparticles having oligonucleotides attached thereto. These oligonucleotides have a sequence complementary to a second portion of the sequence of the nucleic acid.
  • the kit comprises a first container holding a first type of metallic or semiconductor nanoparticles having oligonucleotides attached thereto.
  • the oligonucleotides have a sequence complementary to a first portion of the sequence of a nucleic acid and are labeled with a fluorescent molecule.
  • the kit also comprises a second container holding a second type of metallic or semiconductor nanoparticles having oligonucleotides attached thereto. These oligonucleotides have a sequence complementary to a second portion of the sequence of a nucleic acid and are labeled with a fluorescent molecule.
  • the kit comprises a container holding a satellite probe.
  • the satellite probe comprises a particle having attached thereto oligonucleotides.
  • the oligonucleotides have a first portion and a second portion, both portions having sequences complementary to portions of the sequence of a nucleic acid.
  • the satellite probe also comprises probe oligonucleotides hybridized to the oligonucleotides attached to the nanoparticles.
  • the probe oligonucleotides have a first portion and a second portion. The first portion has a sequence complementary to the sequence of the first portion of the oligonucleotides attached to the particles, and both portions have sequences complementary to portions of the sequence of the nucleic acid.
  • the probe oligonucleotides also have a reporter molecule attached to one end.
  • the kit may comprise a container holding an aggregate probe.
  • the aggregate probe comprises at least two types of nanoparticles having oligonucleotides attached to them.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to each of them.
  • At least one of the types of nanoparticles of the aggregate probe has oligonucleotides attached to it which have a sequence complementary to a portion of the sequence of a nucleic acid.
  • the kit may comprise a container holding an aggregate probe.
  • the aggregate probe comprises at least two types of nanoparticles having oligonucleotides attached to them.
  • the nanoparticles of the aggregate probe are bound to each other as a result of the hybridization of some of the oligonucleotides attached to each of them. At least one of the types of nanoparticles of the aggregate probe has oligonucleotides attached to it which have a hydrophobic group attached to the end not attached to the nanoparticles. .
  • the invention provides a kit comprising a substrate having located thereon at least one pair of electrodes with oligonucleotides attached to the substrate between the electrodes.
  • the substrate has a plurality of pairs of electrodes attached to it in an array to allow for the detection of multiple portions of a single nucleic acid, the detection of multiple different nucleic acids, or both.
  • kits may also contain other reagents and items useful for detecting nucleic acid.
  • the reagents may include PCR reagents, reagents for silver staining, hybridization reagents, buffers, etc.
  • Other items which may be provided as part of the kit include a solid surface (for visualizing hybridization) such as a TLC silica plate, microporous materials, syringes, pipettes, cuvettes, containers, and a thermocycler (for controlling hybridization and de-hybridization temperatures).
  • Reagents for functionalizing the nucleotides or nanoparticles may also be included in the kit. The precipitation of aggregated nanoparticles provides a means of separating a selected nucleic acid from other nucleic acids.
  • This separation may be used as a step in the purification of the nucleic acid.
  • Hybridization conditions are those described above for detecting a nucleic acid. If the temperature is below the Tm (the temperature at which one-half of an oligonucleotide is bound to its complementary strand) for the binding of the oligonucleotides on the nanoparticles to the nucleic acid, then sufficient time is needed for the aggregate to settle.
  • the temperature of hybridization e.g., as measured by Tm
  • the temperature of hybridization varies with the type of salt (NaCl or MgCl 2 ) and its concentration. Salt compositions and concentrations are selected to promote hybridization of the oligonucleotides on the nanoparticles to the nucleic acid at convenient working temperatures without inducing aggregation of the colloids in the absence of the nucleic acid.
  • the invention also provides a method of nanofabrication.
  • the method comprises providing at least one type of linking oligonucleotide having a selected sequence.
  • a linking oligonucleotide used for nanofabrication may have any desired sequence and may be single-stranded or double-stranded. It may also contain chemical modifications in the base, sugar, or backbone sections.
  • the sequences chosen for the linking oligonucleotides and their lengths and strandedness will contribute to the rigidity or flexibility of the resulting nanomaterial or nanostructure, or a portion of the nanomaterial or nanostructure.
  • the use of a single type of linking oligonucleotide, as well as mixtures of two or more different types of linking oligonucleotides, is contemplated.
  • the number of different linking oligonucleotides used and their lengths will contribute to the shapes, pore sizes and other structural features of the resulting nanomaterials and nanostructures.
  • the sequence of a linking oligonucleotide will have at least a first portion and a second portion for binding to oligonucleotides on nanoparticles.
  • the first, second or more binding portions of the linking oligonucleotide may have the same or different sequences.
  • binding portions of a linking oligonucleotide have the same sequence, only a single type of nanoparticle with oligonucleotides having a complementary sequence attached thereto need be used to form a nanomaterial or nanostructure. If the two or more binding portions of a linking oligonucleotide have different sequences, then two or more nanoparticle-oligonucleotide conjugates must be used. See, e.g., Figure 17.
  • the oligonucleotides on each of the nanoparticles will have a sequence complementary to one of the two or more binding portions of the sequence of the linking oligonucleotide
  • the number, sequence(s) and length(s) of the binding portions and the distance(s), if any, between them will contribute to the structural and physical properties of the resulting nanomaterials and nanostructures.
  • the linking oligonucleotide comprises two or more portions
  • the sequences of the binding portions must be chosen so that they are not complementary to each other to avoid having one portion of the linking nucleotide bind to another portion.
  • the linking oligonucleotides and nanoparticle-oligonucleotide conjugates are contacted under conditions effective for hybridization of the oligonucleotides attached to the nanoparticles with the linking oligonucleotides so that a desired nanomaterial or nanostructure is formed wherein the nanoparticles are held together by oligonucleotide connectors.
  • hybridization conditions are well known in the art and can be optimized for a particular nanofabrication scheme (see above). Stringent hybridization conditions are preferred.
  • the invention also provides another method of nanofabrication.
  • This method comprises providing at least two types of nanoparticle-oligonucleotide conjugates.
  • the oligonucleotides on the first type of nanoparticles have a sequence complementary to that of the oligonucleotides on the second type of nanoparticles.
  • the oligonucleotides on the second type of nanoparticles have a sequence . complementary to that of the oligonucleotides on the first type of nanoparticles.
  • nanoparticle-oligonucleotide conjugates are contacted under conditions effective to allow hybridization of the oligonucleotides on the nanoparticles to each other so that a desired nanomaterial or nanostructure is formed wherein the nanoparticles are held together by oligonucleotide connectors.
  • these hybridization conditions are well-known in the art and can be optimized for a particular nanofabrication scheme.
  • nanoparticles having one or more different types of oligonucleotides attached thereto are contemplated.
  • the number of different oligonucleotides attached to a nanoparticle and the lengths and sequences of the one or more oligonucleotides will contribute to the rigidity and structural features of the resulting nanomaterials and nanostructures.
  • the size, shape and chemical composition of the nanoparticles will, contribute to the properties of the resulting nanomaterials and nanostructures. These properties include optical properties, optoelectronic properties, electrochemical properties, electronic properties, stability in various solutions, pore and channel size variation, ability to separate bioactive molecules while acting as a filter, etc.
  • optical properties include optical properties, optoelectronic properties, electrochemical properties, electronic properties, stability in various solutions, pore and channel size variation, ability to separate bioactive molecules while acting as a filter, etc.
  • the use of mixtures of nanoparticles having different sizes, shapes and/or chemical compositions, as well as the use of nanoparticles having uniform sizes, shapes and chemical composition are contemplated. In either fabrication method, the nanoparticles in the resulting nanomaterial or nanostructure are held together by oligonucleotide connectors.
  • oligonucleotide connectors The sequences, lengths, and strandedness of the oligonucleotide connectors, and the number of different oligonucleotide connectors present will contribute to the rigidity and structural properties of the nanomaterial or nanostructure. If an oligonucleotide connector is partially double-stranded, its rigidity can be increased by the use of a filler oligonucleotide as described above in connection with the method of detecting nucleic acid.
  • the rigidity of a completely double-stranded oligonucleotide connector can be increased by the use of one or more reinforcing oligonucleotides having complementary sequences so that they bind to the double-stranded oligonucleotide connector to form triple-stranded oligonucleotide connectors.
  • the use of quadruple- stranded oligonucleotide connectors based on deoxyquanosine or deoxycytidine quartets is also contemplated.
  • FIG. 1 Several of a variety of systems for organizing nanoparticles based on oligonucleotide hybridization are illustrated in the figures.
  • a simple system ( Figure 1) one set of nanoparticles bears oligonucleotides with a defined sequence and another set of nanoparticles bears oligonucleotides with a complementary sequence.
  • the two types of particles are linked by double stranded oligonucleotide connectors which serve as spacers to position the nanoparticles at selected distances.
  • An attractive system for spacing nanoparticles involves the addition of one free linking oligonucleotide as illustrated in Figure 2.
  • the sequence of the linking oligonucleotide will have at least a first portion and a second portion for binding to oligonucleotides on nanoparticles.
  • This system is basically the same as utilized in the nucleic acid detection method, except that the length of the added linking oligonucleotide can be selected to be equal to the combined lengths of oligonucleotides attached to the nanoparticles.
  • the related system illustrated in Figure 3 provides a convenient means to tailor the distance between nanoparticles without having to change the sets of nanoparticle-oligonucleotide conjugates employed.
  • FIG. 4 A further elaboration of the scheme for creating defined spaces between nanoparticles is illustrated in Figure 4.
  • a double stranded segment of DNA or RNA containing overhanging ends is employed as the linking oligonucleotide.
  • Hybridization of the single-stranded, overhanging segments of the linking oligonucleotide with the oligonucleotides attached to the nanoparticles affords multiple double-stranded oligonucleotide cross-links between the nanoparticles.
  • Stiffer nanomaterials and nanostructures, or portions thereof, can be generated by employing triple-stranded oligonucleotide connectors between nanoparticles.
  • one set of nanoparticles is conjugated with a defined strand containing pyrimidine nucleotides and the other set is conjugated with a complementary oligonucleotide containing purine nucleotides.
  • Attachment of the oligonucleotides is designed such that the nanoparticles are separated by the double- stranded oligonucleotide formed on hybridization.
  • a free pyrimidine oligonucleotide with an orientation opposite that for the pyrimidine strand linked to the nanoparticle is added to the system prior to, simultaneously with, or just subsequent to mixing the nanoparticles.
  • oligonucleotide components For construction of nanomaterials and nanostructures, it may be desirable in some cases to "lock" the assembly in place by covalent cross-links after formation of the nanomaterial or nanostructure by hybridization of the oligonucleotide components. This can be accomplished by inco ⁇ orating functional groups that undergo a triggered irreversible reaction into the oligonucleotides.
  • An example of a functional group for this pu ⁇ ose is a stilbenedicarboxamide group. It has been demonstrated that two stilbenedicarboxamide groups aligned within hybridized oligonucleotides readily undergo cross-linking on irradiation with ultraviolet light (340 nm) (Lewis, F.D. et al. (1995) J Am. Chem. Soc. Ill, 8785-8792).
  • a 5'-O-tosyl group from an oligonucleotide, held at the 3 '-position to a nanoparticle by .a mercaptoalkly group, with a thiophosphoryl group at the 3 '-end of an oligonucleotide held to an nanoparticle by a mercaptoalkyl group.
  • thiophosphoryl oligonucleotides do not react with gold nanoparticles under the conditions employed in attaching mercaptoalkyl- oligonucleotides to gold nanoparticles enables one to prepare gold nanoparticle- oligonucleotide conjugates anchored through the mercapto group to the nanoparticles and containing a terminal thiophosphoryl group free for the coupling reaction.
  • a related coupling reaction to lock the assembled nanoparticle system in place utilizes displacement of bromide from a terminal bromoacetylaminonucleoside by a terminal thiophosphoryl-oligonucleotide as described in Gryaznov and Letsinger, J. Am. Chem. Soc, 115, 3808. This reaction proceeds much like the displacement of tosylate described above, except that the reaction is faster. Nanoparticles bearing oligonucleotides terminated with thiophosphoryl groups are prepared as described above.
  • oligonucleotide terminated at one end by an aminonucleoside e.g., either 5'-amino-5'-deoxythymidine or 3'-amino-3'- deoxythymidine
  • aminonucleoside e.g., either 5'-amino-5'-deoxythymidine or 3'-amino-3'- deoxythymidine
  • Molecules of this oligonucleotide are then anchored to the nanoparticles through the mercapto groups, and the nanoparticle-oligonucleotide conjugate is then converted the N- bromoacetylamino derivative by reaction with a bromoacetyl acylating agent.
  • a fourth coupling scheme to lock the assemblies in place utilizes oxidation of nanoparticles bearing oligonucleotides terminated by thiophosphoryl groups.
  • Mild oxidizing agents such as potassium triiodide, potassium ferricyanide (see Gryaznov and Letsinger, Nucleic Acids Research, 21, 1403) or oxygen, are preferred.
  • the properties of the nanomaterials and nanostructures can be altered by inco ⁇ orating into the interconnecting oligonucleotide chains organic and inorganic functions that are held in place by covalent attachment to the oligonucleotide chains.
  • backbone, base and sugar modifications are well known (see for example Uhlmann, E., and Peyman, A. Chemical Reviews, 90, 544-584 (1990).
  • the oligonucleotide chains could be replaced by "Peptide Nucleic Acid” chains (PNA), in which the nucleotide bases are held by a polypeptide backbone (see Wittung, P. et al., Nature, 368, 561-563 (1994).
  • the nanofabrication method of the invention is extremely versatile.
  • the nanomaterials and nanostructures that can be made by the nanofabrication method of the invention include nanoscale mechanical devices, separation membranes, bio-filters, and biochips. It is contemplated that the nanomaterials and nanostructures of the invention can be used as chemical sensors, in computers, for drug delivery, for protein engineering, and as templates for biosynthesis/nanostrucrure fabrication/directed assembly of other structures. See generally Seeman et al., New J. Chem., 17, 739 (1993) for other possible applications.
  • the nanomaterials and nanostructures that can be made by the nanofabrication method of the invention also can include electronic devices. Whether nucleic acids, could transport electrons has been the subject of substantial controversy. As shown in Example 21 below, nanoparticles assembled by DNA conduct electricity (the DNA connectors function as semiconductors).
  • the invention provides methods of making unique nanoparticle- oligonucleotide conjugates.
  • oligonudeotides are bound to charged nanoparticles to produce stable nanoparticle-oligonucleotide conjugates.
  • Charged nanoparticles include nanoparticles made of metal, such as gold nanoparticles.
  • the method comprises providing oligonucleotides having covalently bound thereto a moiety comprising a functional group which can bind to the nanoparticles.
  • the moieties and functional groups are those described above for binding (i.e., by chemiso ⁇ tion or covalent bonding) oligonucleotides to nanoparticles.
  • oligonucleotides having an alkanethiol, an alkanedisulfide or a cyclic disulfide covalently bound to their 5' or 3' ends can be used to bind the oligonucleotides to a variety of nanoparticles, including gold nanoparticles.
  • the oligonucleotides are contacted with the nanoparticles in water for a time sufficient to allow at least some of the oligonucleotides to bind to the nanoparticles by means of the functional groups.
  • a time can be determined empirically. For instance, it has been found that a time of about 12-24 hours gives good results.
  • Other suitable conditions for binding of the oligonucleotides can also be determined empirically. For instance, a concentration of about 10-20 nM nanoparticles and incubation at room temperature gives good results.
  • the salt can be any water-soluble salt.
  • the salt may be sodium chloride, magnesium chloride, potassium chloride, ammonium chloride, sodium acetate, ammonium acetate, a combination of two or more of these salts, or one of these salts in phosphate buffer.
  • the salt is added as a concentrated solution, but it could be added as a solid.
  • the salt can be added to the water all at one time or the salt is added gradually over time. By “gradually over time” is meant that the salt is added in at least two portions at intervals spaced apart by a period of time. Suitable time intervals can be determined empirically.
  • the ionic strength of the salt solution must be sufficient to overcome at least partially the electrostatic repulsion of the oligonucleotides from each other and, either the electrostatic attraction of the negatively-charged oligonucleotides for positively- charged nanoparticles, or the electrostatic repulsion of the negatively-charged oligonucleotides from negatively-charged nanoparticles. Gradually reducing the electrostatic attraction and repulsion by adding the salt gradually over time has been found to give the highest surface density of oligonucleotides on the nanoparticles. Suitable ionic strengths can be determined empirically for each salt or combination of salts. A final concentration of sodium chloride of from about 0.1 M to about 1.0 M in phosphate buffer, preferably with the concentration of sodium chloride being increased gradually over time, has been found to give good results.
  • the oligonucleotides and nanoparticles are incubated in the salt solution for an additional period of time sufficient to allow sufficient additional oligonucleotides to bind to the nanoparticles to produce the stable nanoparticle-oligonucleotide conjugates.
  • an increased surface density of the oligonucleotides on the nanoparticles has been found to stabilize the conjugates.
  • the time of this incubation can be determined empirically. A total incubation time of about 24-48, preferably 40 hours, has been found to give good results (this is the total time of incubation; as noted above, the salt concentration can be increased gradually over this total time).
  • This second period of incubation in the salt solution is referred to herein as the "aging" step.
  • Other suitable conditions for this "aging” step can also be determined empirically. For instance, incubation at room temperature and pH 7.0 gives good results.
  • the conjugates produced by use of the "aging” step have been found to be considerably more stable than those produced without the “aging” step. As noted above, this increased stability is due to the increased density of the oligonucleotides on the surfaces of the nanoparticles which is achieved by the "aging” step.
  • the surface density achieved by the “aging” step will depend on the size and type of nanoparticles and on the length, sequence and concentration of the oligonucleotides. A surface density adequate to make the nanoparticles stable and the conditions necessary to obtain it for a desired combination of nanoparticles and oligonucleotides can be determined empirically.
  • a surface density of at least 10 picomoles/cm 2 will be adequate to provide stable nanoparticle-oligonucleotide conjugates.
  • the surface density is at least 15 picomoles/cm 2 . Since the ability of the oligonucleotides of the conjugates to hybridize with nucleic acid and oligonucleotide targets can be diminished if the surface density is too great, the surface density is preferably no greater than about 35-40 picomoles/cm 2 .
  • stable means that, for a period of at least six months after the conjugates are made, a majority of the oligonucleotides remain attached to the nanoparticles and the oligonucleotides are able to hybridize with nucleic acid and oligonucleotide targets under standard conditions encountered in methods of detecting nucleic acid and methods of nanofabrication.
  • the nanoparticle-oligonucleotide conjugates made by this method exhibit other remarkable properties. See, e.g., Examples 5, 7, and 19 of the present application.
  • they will assemble into large aggregates in the presence of a target nucleic acid or oligonucleotide.
  • the temperature over which the aggregates form and dissociate has unexpectedly been found to be quite narrow, and this unique feature has important practical consequences.
  • it increases the selectivity and sensitivity of the methods of detection of the present invention.
  • a single base mismatch and as little as 20 femtomoles of target can be detected using the conjugates.
  • recognition oligonucleotides are oligonucleotides which comprise a sequence complementary to at least a portion of the sequence of a nucleic acid or oligonucleotide target.
  • the recognition oligonucleotides comprise a recognition portion and a spacer portion, and it is the recognition portion which hybridizes to the nucleic acid or oligonucleotide target.
  • the spacer portion of the recognition oligonucleotide is designed so that it can bind to the nanoparticles.
  • the spacer portion could have a moiety covalently bound to it, the moiety comprising a functional group which can bind to the nanoparticles. These are the same moieties and functional groups as described above.
  • the recognition portion is spaced away from the surface of the nanoparticles and is more accessible for hybridization with its target.
  • the length and sequence of the spacer portion providing good spacing of the recognition portion away from the nanoparticles can be determined empirically.
  • a spacer portion comprising at least about 10 nucleotides, preferably 10-30 nucleotides, gives good results.
  • the spacer portion may have any sequence which does not interfere with the ability of the recognition oligonucleotides to become bound to the nanoparticles or to a nucleic acid or oligonucleotide target.
  • the spacer portions should not sequences complementary to each other, to that of the recognition olignucleotides, or to that of the nucleic acid or oligonucleotide target of the recognition oligonucleotides.
  • the bases of the nucleotides of the spacer portion are all adenines, all thymines, all cytidines, or all guanines, unless this would cause one of the problems just mentioned. More preferably, the bases are all adenines or all thymines. Most preferably the bases are all thymines. It has further been found that the use of diluent oligonucleotides in addition to recognition oligonucleotides provides a means of tailoring the conjugates to give a desired level of hybridization.
  • the diluent and recognition oligonucleotides have been found to attach to the nanoparticles in about the same proportion as their ratio in the solution contacted with the nanoparticles to prepare the conjugates.
  • the ratio of the diluent to recognition oligonucleotides bound to the nanoparticles can be controlled so that the conjugates will participate in a desired number of hybridization events.
  • the diluent oligonucleotides may have any sequence which does not interfere with the ability of the recognition oligonucleotides to be bound to the nanoparticles or to bind to a nucleic acid or oligonucleotide target.
  • the diluent oligonulceotides should not have a sequence complementary to that of the recognition olignucleotides or to that of the nucleic acid or oligonucleotide target of the recognition oligonucleotides.
  • the diluent oligonucleotides are also preferably of a length shorter than that of the recognition oligonucleotides so that the recognition oligonucleotides can bind to their nucleic acid or oligonucleotide targets. If the recognition oligonucleotides comprise spacer portions, the diluent oligonulceotides are, most preferably, about the same length as the spacer portions.
  • the diluent oligonucleotides do not interefere with the ability of the recognition portions of the recognition oligonucleotides to hybridize with nucleic acid or oligonucleotide targets. Even more preferably, the diluent oligonucleotides have the same sequence as the sequence of the spacer portions of the recognition oligonucleotides.
  • Protein receptors and other specific binding pair members can be functionalized with oligonucleotides and immobilized onto.oligonucleotide-modified nanoparticles to generate a new class of hybrid particles (nanoparticle-receptor conjugates) that exhibit the high stability of the oligonucleotide modified particles but with molecular recognition properties that are dictated by the protein receptor rather than DNA.
  • the use of these novel nanoparticle-receptor conjugates in analyte detection strategies have been evaluated in a number of ways including identification of targets and screening for protein-protein interactions.
  • novel hybrid particles or nanoparticle- receptor conjugates that are stable in a wide range of aqueous salt concentrations, have a long shelf life, and enable use of proteins that are poorly soluble in water as well as those of high water solubility are provided.
  • the probe system (see representative Construct II, Figure 47) can be used to screen an array of proteins immobilized at discrete positions on a surface ( Figure 48).
  • Figure 49 where A and B can be a protein, peptide, carbohydrate, sugar, oligo- or polynucleotide, synthetic polymer or oligomer, or a small molecule and any combination thereof).
  • the basic concept is to attach a "receptor unit" (A in Figure 49) to an oligonucleotide which is complementary to oligonucleotides bound to the nanoparticle.
  • Hybridization then generates a nanoparticle probe containing a sheath of oligonucleotides around the nanoparticle matrix which serves to enhance water solubility of the system and to stabilize the colloids with respect to aggregation.
  • Probe IF is then used to interrogate a target (B) immobilized on a solid surface. Binding of A to B is monitored by detection of the nanoparticles bound to the solid- surface (e.g. colorimetrically, by fluorescence, silver staining, etc.).
  • This scheme can be used for any molecules wherein A can be conjugated to an oligonucleotide and B can be immobilized on a surface.
  • I is a gold nanoparticle bearing a large number of oligonucleotides linked firmly to the gold surface (e.g. via a sulfur-gold bond) and 1 is a protein containing a pendant oligonucleotide with a sequence complementary to the sequence for the oligonucleotides attached to the nanoparticle.
  • Procedures for constructing nanoparticle-oligonucleotide conjugates having a high surface density of oligonucleotides are described herein. See for instance Example 3 and C. A. Mirkin et al. Nature, 382, 607-609 (1996); R. Elghanian et al., Science, 277, 1078-1081 (1997); J. J.
  • FIG. 50(b) An alternative embodiment of the nanoparticle receptor conjugate is shown in Figure 50(b) which entails the use of a linking oligonucleotide that brings the nanoparticle-oligonucleotide constructs and oligonucleotide-protein conjugate together under conditions for hybridization.
  • the linker oligonucleotide has one segment (a') complementary to oligonucleotide (a) bound to the nanoparticle and another segment (b') complementary to oligonucleotide (b) bound to the receptor.
  • FIG 51 illustrates a number of representative detection schemes that can employ the nanoparticle-protein conjugates as a probe.
  • the nanoparticle-protein conjugates have a wide variety of applications including identifying target analytes, screening a library of molecules such as drugs immobilized in array onto a support ( Figure 51(a)) or in histochemical applications to identify for the presence of analytes in cells or tissues.
  • the probe can also be used in a spot test where the analyte, e.g., protein or drug, has multiple binding sites.
  • the gold probe-receptor-ligand target combinations resulting from these assays can be observed by visually (e.g., spot test or formation of aggregates or silver staining) or by any known procedure.
  • the nanoparticle-protein conjugate system can be used to develop a colorimetric test for nucleic acids, which relies on the aggregate properties of the nanoparticle/DNA/protein composite, Figure 52 (A).
  • solutions of a complex comprised of streptavidin bound to four biotin -oligonucleotide conjugates (1-STV) and a gold nanoparticle DNA conjugate (2-Au) with and without target nucleic acid (3) were prepared.
  • the sequence of the target nucleic acid has two portions.
  • the oligonucleotides bound to the complex is complementary to the first portion of the nucleic acid while the oligonucleotides bound to the nanoparticles are complementary to the . second part of the nucleic acid.
  • the solutions were heated to 53 °C for 30 min, and then 3 ⁇ L , aliquots of the solutions were spotted on a C18 reverse-phase thin-layer chromatography plate.
  • the solution with target nucleic acid showed a blue spot and the solution without target showed a red spot.
  • This result and the sha ⁇ melting curve demonstrate that one of the gold nanoparticle probes in the above-described spot test ( Figure 52 (B)) can be replaced by streptavidin/DNA conjugates, which are simpler to prepare than gold probes.
  • the system shown in 52(a) can also be used to prepare novel 3-dimensional nanomaterials or assemblies as discussed above.
  • Figure 52(c) no linking oligonucleotides are used and the oligonucleotide attached to the complex are complementary to the oligonucleotides bound to the nanoparticles.
  • nanoparticle-protein probes (II) have unique features which provide significant advantages over the previously describe nanoparticle protein conjugates.
  • the high density oligonucleotides on the surface of the nanoparticles function as a polyanionic sheath to enhance solubility and stability of the nanoparticles-protein conjugates in water over a very wide range of solubility and stability of the nanoparticles-protein conjugates in water over a very wide range of salt concentrations.
  • the reversibility of the oligonucleotide-ohgonucleotide binding provides an extra means for characterizing the complex that is formed with the target.
  • the nanoparticle-proteins are more resistant to non-specific binding (see Figure 53).
  • nanoparticle-protein complexes are based on gold nanoparticles
  • other particles based on a wide variety of other materials (e.g., silver, platinum, mixtures of gold and silver, magnetic particles, semiconductors, quantum dots) can be used, and the particle sizes may range from 2-100 nm as described above.
  • U.S. Patent application Serial No. 09/344,667 and PCT application WO 98/04740 both of which are inco ⁇ orated herein by reference in their entirety, describe suitable nanoparticles and methods of attaching oligonucleotides to them.
  • the nanoparticle-oligonucleotide-protein complexes (II) are employed as probes in detecting specific target molecules such as proteins immobilized on a smooth surface. See, for instance, Figures 48, 49 51 and 54. For this pu ⁇ ose, a number of different proteins may be immobilized at different discrete spots as array on a glass slide. A number of linkage methods may be used.
  • One method, well known in the art, is to treat the glass with 3-aminopropyltriethoxysilane followed by 1,4-phenylene disothiocyanate. This sequence generates a surface holding pendant isothicyanate groups that can be used to bind substances containing one or more amino groups.
  • Targets containing amino groups can be immobilized directly onto tins modified surface.
  • an aminoalkyl group can be tethered to the target to provide the necessary reactive group.
  • the surface is exposed to a colloidal solution of II.
  • the amino groups on the proteins react to form covalent bonds without significant disruption of the three dimensional structure of the protein so the proteins can still react with receptors and other targeting molecules.
  • the specific target molecules or analytes can be bound to oligonucleotides to form oligonucleotide-analyte conjugates where the olignonucleotides bound to the analytes have a sequence that is complementary to the sequence of oligonucleotides bound to a support.
  • SMPB sulfosuccinimidyl 4-[p-maleimidophenyl]butyrate
  • the probe is then contacted with the support. After sufficient time for the protein-protein specific binding interaction to occur, the excess nanoparticle conjugates are washed away and the nanoparticles are detected.
  • the metallic nanoparticles may be detected directly by their color or as gray spots following silver staining. Hence, specific protein/receptor binding interactions may be exploited as a way of indicating the presence of one or the other on a glass slide ( Figure 54).
  • biotinylated DNA hybridized to one portion of a glass slide with complementary DNA could be probed by exposing the glass slide to a solution containing streptavidin bound to biotinylated DNA hybridized to our high DNA density gold nanoparticle probes described herein.
  • the probes bind to the portion of the slide with biotin.
  • the signal associated with the complexed probes could be further developed by treating with silver enhancing solution (see Figure 54).
  • useful probes of type II can be made using a great variety of substances as the functional recognition elements.
  • the scheme for synthesis and application of the probes, shown in Figures 49 and 50, is completely analogous to that presented in Figure 48 for studying protein-protein interactions.
  • the conjugate probe is designated IF, the receptor unit as A, and the target immobilized on the solid surface as B.
  • the system in Figure 48 and variations described herein is a special case of the general system shown in Figure 49.
  • oligonucleotide-nanoparticle probes of type II that are constructed from non-metal nanoparticles.
  • Type II probes based on inherently fluorescent nanoparticles may be observed by their fluorescence.
  • Other nanoparticles can be made fluorescent by appending fluorescent tags to the particles either before or after the oligonucleotide sheath has been added.
  • a novel protein detection method is provided. Protein binding molecules are joined to gold nanoparticle-oligonucleotide conjugates through a linking oligonucleotide where the linking DNA can be used as a marker for the specific protein.
  • Figure 55 describes a protein detection method utilizing the linking oligonucleotide as reporter DNA. In this method, oligonucleotides are modified with protein binding molecules in a way such that each protein molecule has a different oligonucleotide sequence, and then the protein- oligonucleotide conjugates are immobilized on Au particles as a result of hybridization.
  • biotinylated DNA can be immobilized on gold nanoparticle-olignonucleotide conjugates to generate biotin nanoparticle conjugatess.
  • streptavidin the biotin modified nanoparticles will form aggregates and the aggregates can be easily separated from other particles.
  • the aggregates are then disassembled by DNA dehybridization, and the reporter DNA is isolated from Au particles and proteins. Since each protein binding molecule has a unique DNA sequence, the protein can be identified by well established DNA detection methods such as the use of a DNA chip. Once the reporter DNA is isolated, the detection limit can be very low because the reporter DNA can be amplified by PCR.
  • a common feature of all these nanoparticle-oligonucleotide-receptor conjugate systems is that the signal for interaction of the components being tested, e.g. receptor A and B in Figure 49, depends both on A binding to B and on the interaction of oligonucleotide a with oligonucleotide a'. Since the dissociation temperature for the oligonucleotide duplex segment can be tuned by controlling the length and sequence of the complementary strands and the salt concentration, one can in many cases design systems such that the oligonucleotide duplexes will dissociate at a lower temperature, or a higher temperature, than the components being tested, according to the wishes of the investigator.
  • any of the above conjugates can be, and are preferably, used in any of the methods of detecting analytes such as nucleic acids described above, and the invention also provides a kit comprising a container holding any of the above conjugates.
  • the conjugates can be, and are preferably, used in any of the methods of nanofabrication of the invention and the method of separating nucleic acids.
  • the invention also relates to the use of an electric field to facilitate hybridization of inventive nanoparticle-oligonucleotide conjugates to complementary oligonucleotides on an electrode surface.
  • the electric field strength in particular the current level and density
  • these electric fields can be extended to facilitate other interactions involving nanoparticle-charged molecule . conjugates that include, but are not limited to, most molecular biological procedures, such as specific binding pair interactions, antibody/antigen reaction, cell separations, and related clinical diagnostics.
  • Biosensors are discussed in some detail in Protein immobilization, Fundamentals & Applications, R.F. Taylor, ed. (1991) (chapter 8); and Immobilized Affinity Ligand Techniques, Hermanson et al. (1992) (chapter 5). See also U.S. Patent No. 5,965,452 and references cited therein.
  • Nanogen and others have developed microelectronic nucleic acid array methods and devices in that utilize electric fields as an independent parameter to control transport, hybridization and stringency of nucleic acid interactions. These are "active" array devices in that they exploit microelectronic as well as microfabrication technology. See, for instance, Edman et al., Nucleic Acids Res., 1997, Vol. 25 (24), 4907-14; U.S. Patent Nos. 6,051,380; 6,068,818; 5,929,208; 5,632,957; 5,565,322; 5,605,662; 5,849,486; 6,048,690; 6,013,166; and 5,965,452, which are inco ⁇ orated by reference in their entirety.
  • Combinatorial oligonucleotide array (or "gene chip”) technology depends on the quantitative detection of target DNA hybridized to complementary array elements. We recently reported a "scanometric" method for detecting DNA targets hybridized to gene arrays in which oligonucleotide-functionalized, 13 nm diameter gold nanoparticles serve as the indicators of target hybridization to the chip. [Taton, T.A.; Mirkin, C.A.; Letsinger, R.L. Science 200, 289, 1757].
  • the selectivity of the scanometric DNA detection system was intrinsically higher (by a factor of 4) than that of a conventional array system based upon fluorophore probes.
  • enlarging the array-bound nanoparticles by gold-promoted reduction of silver (I) permitted the arrays to be imaged, in black-and- white by a flatbed optical scanner, with 100 times the sensitivity than that typically observed by confocal fluorescence imaging of fluorophore-labeled gene chips.
  • Metal nanoparticles that differ in size and composition can be designed to scatter light of different wavelengths according to their distinct surface plasmon resonances [Mie, G. Ann. Phys. 1908, 25, 377]. Scattered light from different sized nanoparticles has been used in histochemical imaging [Schultz, S,; Smith, D.R.;
  • nanoparticle labels have not been used for multicolor labeling in array-based detection schemes.
  • Particles of varying size and composition which have been modified with a dense layer of oligonucleotides, can be used to yield DNA detection systems with multicolor capabilities and, in principle, the same selectivity advantages observed in the scanometric detection system.
  • oligonucleotide-nanoparticle conjugates and oligonucleotide targets were cohybridized to the DNA a ⁇ ays in 0.3 M PBS hybridization buffer [0.3 M NaCl, 10 nM NaH 2 PO_ ⁇ /Na 2 HPO ' pH 7] at room temperature for 2 h. [ See Examples 30 and 31 below]. The a ⁇ ays were then washed with clean buffer to remove unhybridized target and nanoparticle probes.
  • the a ⁇ ay slides were mounted on a microscope stage and illuminated in the plane of the slide by a fiber optic illuminator [Darklite Illuminator (Micro Video Instruments, Avon, MA)]; in this configuration, the slide served as a planar waveguide, preventing any light from reaching the microscope objective by total internal reflectance.
  • a fiber optic illuminator Darklite Illuminator (Micro Video Instruments, Avon, MA)]
  • the slide served as a planar waveguide, preventing any light from reaching the microscope objective by total internal reflectance.
  • evanescently coupled light [M ⁇ ller, G.J. In Multichannel Image Detectors; Talmi, Y., Ed.; ACS Symposium Series 102; American Chemical Society: Washington, DC, 1979; pp 239-262] was scattered out of the guide plane and was imaged as bright, colored spots on a dark background.
  • the DNA array imaging method described herein based on scattered light from larger oligonucleotide-functionalized nanoparticles, provides the opportunity for sensitive, ultraselective, multicolor labeling of DNA a ⁇ ays.
  • the method described will be extendable to additional colors using nanoparticles of different compositions and sizes [Link, S.; Wang, Z.L.; El-Sayed, M.A. J. Phys. Chem. B 1999, 103, 3529].
  • the inventive method involves detecting the scattering of light directed into the waveguide, the scattering being the result of light scattering nanoparticle conjugates of the invention specifically bound to the waveguide within the penetration depth of an evanescent wave.
  • the waveguide may be transparent plastic or glass or any suitable material and the binding is typically by oligonucleotide hybridization or if desired, by immunological capture as described above.
  • Light scattering detectable nanoparticle probes may be prepared from any of the novel metal or semiconductor nanoparticles, including gold, prepared by the inventive ageing process described above. Real-time binding and dissociation can be monitored visually or by video imaging, such as with a CCD camera and frame grabber software. Hybridization mismatches of as few as one base can be distinguished by real-time melting curves.
  • the waveguide should be made of an optically transparent material such as glass, quartz, plastics such as polycarbonate, acrylic, or polystyrene.
  • the refractive index of the waveguide must be greater than the refractive index of the sample fluid, as is known in the art for effecting total internal reflectance.
  • the refractive index, n is about 1.33, so the waveguide typically has a refractive index of greater than 1.35, usually about 1.5 or more.
  • the waveguide includes a light receiving end such as the one shown in Figures 64 and 65B.
  • the waveguide may be a piece of plastic or glass, for example, a standard glass microscope slide or cover slip may be used.
  • the surface of the waveguide may be treated by any suitable method described above to attach oligonucleotides thereto to supports, preferably in a covalent manner.
  • Light source for generating the incident light beam may be nearly any source of electromagnetic energy, including energy in the visible, ultraviolet, and near-IR spectra.
  • the term "light” is thus construed quite broadly and is not confined to the visible range, except in the embodiments that are visually detected. Non- visible wavelengths are detected by detectors optimized for the particular wavelength as is well known in the art.
  • the light may be monochromatic or polychromatic, collimated or uncollimated, polarized or unpolarized.
  • Prefe ⁇ ed light sources include lasers, light emitting diodes, flash lamps, arc lamps, incandescent lamps and fluorescent discharge lamps.
  • the light source used to illuminate the waveguide element can be a low wattage helium-neon laser.
  • the light source can be a small incandescent light bulb powered by a battery, such as is used in pocket flashlight.
  • the light source includes potentiometer means for varying the intensity of the light source.
  • filters and/or lenses may be employed to adjust the intensity to a suitable level.
  • Detection means for determining the degree of light scattering are described in detail below but briefly comprise both instrument and visual means. It is an important feature of the invention that light scattering events across the entire waveguide can be monitored essentially simultaneously, whether by the eye and brain of an observer or by photodetection devices including CCD cameras forming images that are digitized and processed using computers. In each case only a single, multifunctional surface is used and is illuminated simultaneously by the evanescent wave.
  • the invention also relates to a salt-based stringency wash for enhancing target selectivity in a detection method.
  • Increasing target nucleic acid analyte selectivity generally involves a adjustment of the hybridization conditions or the use of a thermal based stringency wash at melting temperatures in a post-hybridization step that results in dehybridization of nucleic acid duplexes from base mismatched or non-complementary strands.
  • the greater the stringency of the subsequent wash step the fewer, if any, mismatches remain in the duplex structure.
  • the nanoparticle-oligonucleotide conjugates of the invention have been found to exhibit a remarkable salt concentration dependent hybridization behavior that can be exploited to achieve superior target selectivity in a detection system without the need for a post- hybridization thermal stringency wash.
  • Example 32 demonstrates that the oligonucleotide-modified nanoparticles of the invention exhibit unusually sha ⁇ denaturation properties over salt concentration gradients.
  • Such a salt-based stringency wash detection system would be useful in a hand-held DNA detection system, would be amenable to massive multiplexing, and would exhibit higher selectivity relative to fluorophore based systems.
  • salt concentration as a stringency tool rather than temperature is provides a number of su ⁇ rising and unexpected advantages, including eliminating the need for thermocyclers in nanoparticle-based detection systems and providing higher selectivity than temperature-based stringency for nanoparticle probes.
  • use of salt concentration as a stringency tool is useful where the detection probe are not stable at elevated temperature.
  • a method for detecting a nucleic acid comprises providing a substrate having oligonucleotides bound thereto, the oligonucleotides bound to the substrate have a sequence that is complementary to a first portion of a sequence of a nucleic acid; providing labels, such as nanoparticles, having oligonucleotides bound thereto, at least some of the oligonucleotides having a sequence that is complementary to the sequence of a second portion of the nucleic acid; contacting the substrate, nucleic acid, and labels, the contacting taking place under conditions effective to allow hybridization between the oligonucleotides bound to the substrate with the nucleic acids and between the nucleic acid and the oligonucleotide bound to the label so as to form a test substrate having labels complexed thereto; contacting the test substrate with an aqueous salt solution having a salt concentration effective to substantially remove non-specifically bound labels; and observing
  • stringency may be adjusted in a post-hybridization wash step that employs an aqueous salt solution of a proper cationic strength.
  • Any suitable stringency wash solution may be employed in practicing this invention including wash solutions described in Maniatis's Molecular Cloning: A Laboratory Manual, Second edition (Cold Spring Harbor Laboratory Press), 1989 and Ausubel et al., Short Protocols in Molecular Biology, fourth Edition (John Wiley & Sons), 1999.
  • Representative aqueous salt solution comprise a salt selected from the group consisting of sodium chloride, magnesium chloride, potassium chloride, ammonium chloride, sodium acetate, ammonium acetate, a combination of two or more of these salts, one of these salts in a phosphate buffer, and a combination of two or more of these salts in a phosphate buffer. While phosphate buffer is prefe ⁇ ed, any other buffer or combination of two or more suitable buffers may be used. Representative examples of suitable buffers include, without limitation, tris (hydroxymethyl)aminomethane (TRIS) and TRIS-HC1 buffer.
  • TRIS-HC1 buffer Tris (hydroxymethyl)aminomethane
  • any suitable concentration of the salt and buffer components in the stringency wash solution may be used.
  • the skilled artisan will know how to adjust the salt, solution to achieve a proper cationic concentration. For instance, the skilled artisan may evaluate a range of solutions of different cationic concentration and further prepare a dissociation curve, similar to the one shown in Figure 69(C) (Example 32).
  • a representative stringency solution is described in Example 32 and includes sodium chloride in a phosphate buffer.
  • the sodium chloride salt component generally ranges from about 0 M to about 0.5 M, preferably from about 0.005 M to about 0.1 M.
  • the phosphate buffer component generally ranges from about 0.01 mM to about 15 mM, preferably about 10 mM.
  • the stringency buffer may have any suitable pH, generally about pH 7. In using the salt based wash as a post-hybridization wash, stringency levels of at least 90% or greater, preferably at least 95% or 97%, may be achieved.
  • the salt-based stringency wash system can be expanded to any other suitably charged labels having oligonucleotides.
  • Representative labels include, without limitation, radioisotopes, fluorescent dyes such as fluorescein or tetramethylrhodamine, enzymes such as alkaline or horseradish peroxidase, reporter groups such as biotin of digoxigenin, polyanionic polymers, and spectroscopic labels such as raman dyes.
  • the salt concentration dependent post-hybridization stringency conditions rely, in part, on the adjustment of the cationic strength of the solution.
  • the salt-based stringency wash may be used to detect target nucleic acid(s) have at least two portions in a method comprising the steps of (a) contacting a nucleic acid with a substrate having oligonucleotides attached thereto, the oligonucleotides being located between a pair of electrodes, the oligonucleotides having a sequence complementary to a first portion of the sequence of said nucleic acid, the contacting taking place under conditions effective to allow hybridization of the oligonucleotides on the substrate with said nucleic acid; (b) contacting said nucleic acid bound to the substrate with a first type of labels such as nanoparticles, the labels being made of a material which can conduct electricity, the labels having one or more types of oligonucleotides attached thereto, at least one of
  • the substrate may include a plurality of pairs of electrodes located on it in an a ⁇ ay to allow for the detection of multiple portions of a single nucleic acid, the detection of multiple different nucleic acids, or both, each of , the pairs of electrodes having a type of oligonucleotides attached to the substrate between them.
  • the circuit between the electrodes should be closed or can be made to close by any suitable material as discussed herein including the use of silver, gold, or any other conductive materials such as metals or material that can catalyze the local aggrandization of material that can conduct electricity including elemental carbon.
  • the presence of the closed circuit can be detected by any suitable means such as a change in the electrical property of the electrodes. Such a change can be detected by any suitable means including, without limitation, a change in conductivity, resistivity, capacitance, or impedance.
  • a or “an” entity refers to one or more of that entity.
  • a characteristic refers to one or more characteristics or at least one characteristic.
  • the terms “a” (or “an”), “one or more” and “at least one” are used interchangeably herein. It is also to be noted that the terms “comprising”, “including”, and “having” have been used interchangeably.
  • Gold colloids (13 nm diameter) were prepared by reduction of HAuCl with citrate as described in Frens, Nature Phys. Sci., 241, 20 (1973) and Grabar, Anal. Chem., 67, 735 (1995). Briefly, all glassware was cleaned in aqua regia (3 parts HC1, 1 part HNO 3 ), rinsed with Nanopure H 2 O, then oven dried prior to use. HAuCl and sodium citrate were purchased from Aldrich Chemical Company. Aqueous HAuCl 4 (1 mM, 500 mL) was brought to reflux while stirring. Then, 38.8 mM sodium citrate (50 mL) was added quickly.
  • Au colloids were characterized by UV-vis spectroscopy using a Hewlett Packard 8452A diode array spectrophotometer and by Transmission Electron Microscopy (TEM) using a Hitachi 8100 transmission electron microscope. Gold particles with diameters of 13 nm will produce a visible color change when aggregated with target and probe oligonucleotide sequences in the 10-35 nucleotide range.
  • DTT dithiothreitol
  • 5'-Thiol-Modif ⁇ er C 6 -phosphorar ⁇ idite reagent was purchased from Glen Research, 44901 Falcon Place, Sterling, Va 20166. The oligonucleotides were synthesized, and the final DMT protecting group removed. Then, 1 ml of dry acetonitrile was added to 100 ⁇ mole of the 5' Thiol Modifier C 6 - phosphoramidite.
  • the support was then washed with a 1 : 1 mixture of CH 3 CN/pyridine (2 1 mL) for 1 minute, followed by a final wash with dry acetonitrile (2 1 mL) with subsequent drying of the column with a stream of nitrogen.
  • the trityl protecting group was not removed, which aids in purification.
  • Reverse phase HPLC was performed with a Dionex DX500 system equipped with a Hewlett Packard ODS hypersil column (4.6 x 200 mm, 5 mm particle size) using 0.03 M Et 3 NH + OAc- buffer (TEAA), pH 7, with a 1%/min. gradient of 95% CH 3 CN/5%
  • TEAA Trimethyl methacrylate
  • the flow rate was 1 mL/ min. with UV detection at 260 nm.
  • Preparative HPLC was used to purify the DMT-protected unmodified oligonucleotides (elution at 27 min). After collection and evaporation of the buffer, the DMT was cleaved from the oligonucleotides by treatment with 80% acetic acid for 30 min at room temperature. The solution was then evaporated to near dryness, water was added, and the cleaved DMT was extracted from the aqueous oligonucleotide solution using ethyl acetate.
  • the amount of oligonucleotide was determined by absorbance at 260 nm, and final purity assessed by reverse phase HPLC (elution time 14.5 minutes).
  • the same protocol was used for purification of the 3'-thiol-oligonucleotides, except that DTT was added after extraction of DMT to reduce the amount of disulfide formed. After six hours at 40°C, the DTT was extracted using ethyl acetate, and the oligonucleotides repurified by HPLC (elution time 15 minutes).
  • preparatory HPLC was performed under the same conditions as for unmodified oligonucleotides.
  • the trityl protecting group was removed by adding 150 ⁇ L of a 50 mM AgNO 3 solution to the dry oligonucleotide sample.
  • the sample turned a milky white color as the cleavage occu ⁇ ed.
  • 200 ⁇ L of a 10 mg/ml solution of DTT was added to complex the Ag (five minute reaction time), and the sample was centrifuged to precipitate the yellow complex.
  • the oligonucleotide solution ( ⁇ 50 OD) was then transferred onto a desalting NAP-5 column (Pharmacia Biotech, Uppsala, Sweden) for purification (contains DNA Grade Sephadex G-25 Medium for desalting and buffer exchange of oligonucleotides greater than 10 bases).
  • the amount of 5' thiol modified oligonucleotide was determined by UV-vis spectroscopy by measuring the magnitude of the absorbance at 260 nm.
  • the oligonucleotide-modified nanoparticles are stable at elevated temperatures (80°C) and high salt concentrations (1M NaCl) for days and have not been observed to undergo particle growth. Stability in high salt concentrations is important, since such conditions are required for the hybridization reactions that form the basis of the methods of detection and nanofabrication of the invention.
  • Example 1 They had the following sequences:
  • DNA solutions were approximately 1 absorbance unit(s) (OD), buffered at pH 7 using 10 mM phosphate buffer and at 1M NaCl concentration.
  • non-thiolated oligonucleotides having sequences complementary to the sticky ends of the linking oligonucleotide and reacted with nanoparticles did not produce reversible aggregation when the nanoparticles were combined with the linking oligonucleotide.
  • Example 3 Preparation of Oligonucleotide-Modified Gold Nanoparticles
  • Gold colloids (13 nm diameter) were prepared as described in Example 1.
  • the method of attaching thiol-oligonucleotides to gold nanoparticles described in Example 1 was found not to produce satisfactory results in some cases.
  • the oligonucleotide-colloid conjugates were not stable in the presence of a large excess of high molecular weight salmon sperm DNA used as model for the background DNA that would normally be present in a diagnostic system.
  • Longer exposure of the colloids to the thiol-oligonucleotides produced oligonucleotide-colloid conjugates that were stable to salmon sperm DNA, but the resulting conjugates failed to hybridize satisfactorily.
  • the solution was next centrifuged at 14,000 ⁇ m in an Eppendorf Centrifuge 5414 for about 15 minutes to give a very pale pink supernatant containing most of the oligonucleotide (as indicated by the absorbance at 260 nm) along with 7-10% of the colloidal gold (as indicated by the absorbance at 520 nm), and a compact, dark, gelatinous residue at the bottom of the tube.
  • the supernatant was removed, and the residue was resuspended in about 200 ⁇ L of buffer (10 mM phosphate, 0.1 M NaCl) and recentrifuged.
  • Example 4 Acceleration Of Hybridization of Nanoparticle-Oligonucleotide Conjugates
  • the oligonucleotide-gold colloid conjugates I and II illustrated in Figure 11 were prepared as described in Example 3. The hybridization of these two conjugates was extremely slow. In particular, mixing samples of conjugates I and II in aqueous 0.1 M NaCl or in 10 mM MgCl 2 plus 0.1 M NaCl and allowing the mixture to stand at room temperature for a day produced little or no color change.
  • a second way to obtain faster results is to warm the conjugates and target.
  • oligonucleotide-gold colloid conjugates and an oligonucleotide target sequence in a 0.1 M NaCl solution were warmed rapidly to 65°C and allowed to cool to room temperature over a period of 20 minutes. On spotting on a C-18 silica plate and drying, a blue spot indicative of hybridization was obtained. In contrast, incubation of the conjugates and target at room temperature for an hour in 0.1 M NaCl solution did not produce a blue color indicative of hybridization. Hybridization is more rapid in 0.3 M NaCl.
  • Example 5 Assays Using Nanoparticle-Oligonucleotide Conjugates
  • the oligonucleotide-gold colloid conjugates 1 and 2 illustrated in Figures 12A-F were prepared as described in Example 3, and the oligonucleotide target 3 illustrated in Figure 12A was prepared as described in Example 2.
  • Mismatched and deletion targets 4, 5, 6, and 7 were purchased from the Northwestern University Biotechnology Facility, Chicago, IL.
  • These oligonucleotides were synthesized on a 40 nmol scale and purified on an reverse phase C18 cartridge (OPC). Their purity was determined by performing ion exchange HPLC.
  • OPC reverse phase C18 cartridge
  • hybridization was achieved by heating rapidly and then cooling rapidly to the stringent temperature. For example, hybridization was carried out in 100 ⁇ L of 0.1 M NaCl plus 5 mM MgCl 2 containing 15 nM of each oligonucleotide-colloid conjugate 1 and 2, and 3 nanomoles of target oligonucleotide 3, 4, 5, 6, or 7, heating to 74°C, cooling to the temperatures indicated in Table 1 below, and incubating the mixture at this temperature for 10 minutes. A 3 ⁇ L sample of each reaction mixture was then spotted on a C-18 TLC silica plate. On drying (5 minutes), a strong blue color appeared if hybridization had taken place. The results are presented in Table 1 below.
  • Pink spots signify a negative test (i.e., that the nanoparticles were not brought together by hybridization), and blue spots signify a positive test (i.e., that the nanoparticles were brought into proximity due to hybridization involving both of the oligonucleotide-colloid conjugates).
  • hybridization at 60°C gave a blue spot only for the fully-matched target 3.
  • Hybridization at 50°C yielded blue spots with both targets 3 and 6.
  • Hybridization at 45°C gave blue spots with targets 3, 5 and 6.
  • a target containing a single mismatch T nucleotide was found to give a positive test at 58°C (blue color) and a negative test (red color) at 64°C with conjugates 1 and 2.
  • the fully-matched target (3) gave a positive test at both temperatures, showing that the test can discriminate between a target that is fully matched and one containing a single mismatched base.
  • hybridization was carried out in 100 ⁇ L of 0.1 M NaCl containing 15 nM of each oligonucleotide-colloid conjugate 1 and 2, and 10 picomoles of target oligonucleotide 3, 4, 5, 6, or 7, freezing in a dry ice-isopropyl alcohol bath for 5 minutes, thawing at room temperature, then warming rapidly to the temperatures indicated in Table 2 below, and incubating the mixture at this temperature for 10 minutes. A 3 ⁇ L sample of each reaction mixture was then spotted on a C-18 TLC silica plate. The results are presented in Table 2. TABLE 2
  • a mismatch in either segment is more destabilizing than a mismatch in a longer probe (e.g., an oligonucleotide 30 bases long) in a comparable two-component detection system.
  • the signal at 260 nm obtained on hybridization of the target oligonucleotides with the nanoparticle conjugates in solution, is nanoparticle-based, not DNA-based. It depends on dissociation of an assembly of nanoparticles organized in a polymeric network by multiple oligonucleotide duplexes. This results in a narrowing of the temperature range that is observed for aggregate dissociation, as compared with standard DNA thermal denaturation.
  • the temperature range for aggregate melting is very narrow (4°C) as compared with the temperature range associated with melting the comparable system without nanoparticles (12°C). Even more striking and advantageous for this detection approach is the temperature range for the colorimetric response ( ⁇ 1°C) observe on the CI 8 silica plates.
  • this three-component nanoparticle based strategy will be more selective than any two-component detection system based on a single-strand probe hybridizing with target nucleic acid.
  • a master solution containing 1 nmol of target 3 was prepared in 100 ⁇ l of hybridization buffer (0.3 M NaCl, 10 mM phosphate, pH 7). One ⁇ l of this solution corresponds to 10 picomole of target oligonucleotide. Serial dilutions were performed by taking an aliquot of the master solution and diluting it to the desired concentration with hybridization buffer. Table 3 shows the sensitivity obtained using 3 ⁇ l of a mixture of probes 1 and 2 with different amounts of target 3. After performing the hybridization using freeze-thaw conditions, 3 ⁇ l aliquots of these solutions were spotted onto C-18 TLC plates to determine color. In Table 3 below, pink signifies a negative test, and blue signifies a positive test.
  • DNA modified nanoparticles were adsorbed onto modified transparent substrates as shown in Figure 13B.
  • This method involved the linking of DNA modified • nanoparticles to nanoparticles that were attached to a glass substrate, using DNA hybridization interactions.
  • Glass microscope slides were purchased from Fisher scientific. Slides were cut into approximately 5 15 mm pieces, using a diamond tipped scribing pen. Slides were cleaned by soaking for 20 minutes in a solution of 4:1 H 2 SO 4 :H 2 0 at 50°C. Slides were then rinsed with copious amounts of water, then ethanol, and dried under a stream of dry nitrogen.
  • the slides were soaked in a degassed ethanolic 1% (by volume) mercaptopropyl-trimethoxysilane solution for 12 hours.
  • the slides were removed from the ethanol solutions and rinsed with ethanol, then water.
  • Nanoparticles were adsorbed onto the thiol terminated surface of the slides by soaking in solutions containing the 13 nm diameter gold nanoparticles (preparation described in Example 1). After 12 hours in the colloidal solutions, the slides were removed and rinsed with water.
  • the resulting slides have a pink appearance due to the adsorbed nanoparticles and exhibit similar UV-vis absorbance profiles (surface plasmon absorbance peak at 520 nm) as the aqueous gold nanoparticle colloidal solutions. See Figure 14A.
  • DNA was attached to the nanoparticle modified surface by soaking the glass slides in 0.2 OD (1.7 ⁇ M) solution containing freshly purified 3' thiol oligonucleotide (3' thiol ATGCTCAACTCT [SEQ ID NO:33]) (synthesized as described in Examples 1 and 3). After 12 hours of soaking time, the slides were removed and rinsed with water.
  • linking oligonucleotide prepared as described in Example 2 was 24 bp long (5'
  • the substrate was then soaked in a hybridization buffer (0.5 M NaCl, 10 mM phosphate buffer pH 7) solution containing the linking oligonucleotide (0.4 OD, 1.7 ⁇ M) for 12 hours.
  • the substrate was soaked in a solution containing 13 nm diameter gold nanoparticles which had been modified with an oligonucleotide (TAGGACTTACGC 5' thiol [SEQ ID NO;35]) (prepared as described in Example 3) that is complementary to the unhybridized portion of the linking oligonucleotide attached to the substrate.
  • an oligonucleotide (TAGGACTTACGC 5' thiol [SEQ ID NO;35]) (prepared as described in Example 3) that is complementary to the unhybridized portion of the linking oligonucleotide attached to the substrate.
  • the, substrate was removed and rinsed with the hybridization buffer.
  • the substrate color had darkened to a pu ⁇ le color and the UV-vis absorbance at 520 nm approximately doubled ( Figure 14A).
  • a melting curve was performed.
  • the substrate was placed in a cuvette containing 1 mL of hybridization buffer and the same apparatus used in Example 2, part B, was used.
  • the absorbance signal due to the nanoparticles (520 nm) was monitored as the temperature of the substrate was increased at a rate of 0.5°C per minute.
  • the nanoparticle signal dramatically dropped when the temperature passed 60°C. See Figure 14B.
  • a first derivative of the signal showed a melting temperature of 62°C, which corresponds with the temperature seen for the three DNA sequences hybridized in solution without nanoparticles. See Figure 14B.
  • 15A-G were prepared as described in Example 3, except that the nanoparticles were redispersed in hybridization buffer (0.3 M NaCl, 10 mM phosphate, pH 7).
  • the final nanoparticle-oligonucleotide conjugate concentration was estimated to be 13 nM by measuring the reduction in intensity of the surface plasmon band at 522 nm which gives rise to the red color of the nanoparticles.
  • the oligonucleotide targets illustrated in Figures 15A-G were purchased from the Northwestern University Biotechnology Facility, Evanston, IL.
  • the solution was diluted to 1 ml with hybridization buffer, and the optical signature of the aggregates at 260 nm was recorded at one minute intervals as the temperature was increased from 25 C to 75 ° C, with a holding time of 1 minute/degree.
  • T m melting temperature
  • FW ⁇ 2 -13.5 C).
  • the 'melting analysis' of the oligonucleotide solution without nanoparticles was performed under similar conditions as the analysis with nanoparticles, except that the temperature was increased from 10-80 ° C. Also, the solution was 1.04 ⁇ M in each oligonucleotide component.
  • the T m for the aggregate formed from the perfect complement 4 of probes 1 and 2 was compared with the T m 's for aggregates formed from targets that contained one base mismatches, deletions, or insertions ( Figures 15A-G).
  • All of the gold nanoparticle-oligonucleotide aggregates that contained imperfect targets exhibited significant, measurable destabilization when compared to the aggregates formed from the perfect complement, as evidenced by T m values for the various aggregates (see Figures 15A-G).
  • the solutions containing the imperfect targets could easily be distinguished from the solution containing the perfect complement by their color when placed in a water bath held at 52.5 C.
  • This temperature is above the T m of the mismatched polynucleotides, so only the solution with the perfect target exhibited a pu ⁇ le color at this temperature.
  • a 'melting analysis' was also performed on the probe solution which contained the half-complementary target. Only a minute increase in absorbance at 260 nm was observed.
  • the colorimetric transition that can be detected by the naked eye occurs over less than 1 C, thereby allowing one to easily distinguish the perfect target 4 from the targets with mismatches (5 and 6), an end deletion (7), and a one base insertion at the point in the target where the two oligonucleotide probes meet (8) (see Table 4).
  • T c is close in temperature, but not identical, to T m . In both controls, there were no signs of particle aggregation or instability in the solutions, as evidenced by the pinkish red color which was observed at all temperatures, and they showed negative spots (pink) in the plate test at all temperatures (Table 4).
  • the results indicate that any one base mismatch along the target strand can be detected, along with any insertions into the target strand.
  • the temperature range over which a color change can be detected is extremely sha ⁇ , and the change occurs over a very narrow temperature range.
  • This sha ⁇ transition indicates that there is a large degree of cooperativity in the melting process involving the large network of colloids which are linked by the target oligonucleotide strands. This leads to the remarkable selectivity as shown by the data.
  • Example 8 Assays Using Nanoparticle-Oligonucleotide Conjugates A set of experiments were performed involving hybridization with 'filler' duplex oligonucleotides. Nanoparticle-oligonucleotide conjugates 1 and 2 illustrated in Figure 16A were incubated with targets of different lengths (24, 48 and 72 bases in length) and complementary filler oligonucleotides, as illustrated in Figures 16A-C. Otherwise, the conditions were as described in Example 7. Also, the oligonucleotides and nanoparticle- oligonucleotide conjugates were prepared as described in Example 7.
  • the color changes observed in this and other examples occur when the distance between the gold nanoparticles (the inte ⁇ article distance) is approximately the same or less than the diameter of the nanoparticle.
  • the size of the nanoparticles, the size of the oligonucleotides attached to them, and the spacing of the nanoparticles when they are hybridized to the target nucleic acid affect whether a color change will be observable when the oligonucleotide-nanoparticle conjugates hybridize with the nucleic acid targets to form aggregates.
  • gold nanoparticles with diameters of 13 nm will produce a color change when aggregated using oligonucleotides attached to the nanoparticles designed to hybridize with target sequences 10-35 nucleotides in length.
  • the spacing of the nanoparticles when they are hybridized to the target nucleic acid adequate to give a color change will vary with the extent of aggregation, as the results demonstrate.
  • the results also indicate that the solid surface enhances further aggregation of already-aggregated samples, bringing the gold nanoparticles closer together.
  • the color change observed with gold nanoparticles is attributable to a shift and broadening of the surface plasmon resonance of the gold. This color change is unlikely for gold nanoparticles less than about 4 nm in diameter because the lengths of the oligonucleotides necessary for specific detection of nucleic acid would exceed the nanoparticle diameter.
  • a solution containing 12.5 microliters of each probe 1 and 2 and 0.25 microliters of target 3 was heated to 70°C. After cooling to room temperature, 2.5 microliters of a saliva solution (human saliva diluted 1:10 with water) was added. After the resultant solution was frozen, thawed and then spotted onto a C-18 TLC plate, a blue spot was obtained, indicating hybridization of the probes with the target. In control experiments with no target added, blue spots were not observed.
  • a saliva solution human saliva diluted 1:10 with water
  • the slides were soaked in a 1% solution of trimethoxysilylpropyldiethyltriamine (DET A, purchased from United Chemical Technologies, Bristol, PA) in 1 mM acetic acid in Nanopure water for 20 minutes at room temperature.
  • the slides were rinsed with water, then ethanol. After drying with a dry nitrogen stream, the slides were baked at 120°C for 5 minutes using a temperature-controlled heating block.
  • the slides were allowed to cool, then were soaked in a 1 mM succinimidyl 4-(malemidophenyl)-butyrate (SMPB, purchased from Sigma Chemicals) solution in 80:20 methanol;dimethoxysulfoxide for 2 hours at room temperature.
  • SMPB succinimidyl 4-(malemidophenyl)-butyrate
  • amine sites that were not coupled to the SMPB crosslinker were capped as follows. First, the slides were soaked for 5 minutes in a 8:1 THF:pyridine solution containing 10% 1 -methyl imidazole. Then the slides were soaked in 9:1 THF: acetic anhydride solution for five minutes. These capping solutions were purchased from Glen Research, Sterling, VA. The slides were rinsed with THF, then ethanol, and finally water.
  • DNA was attached to the surfaces by soaking the modified glass slides in a 0.2 OD (1.7 ⁇ M) solution containing freshly purified oligonucleotide (3' thiol ATGCTCAACTCT [SEQ ID NO:33]). After 12 hours of soaking time, the slides were removed and rinsed with water.
  • a linking oligonucleotide was prepared.
  • the linking oligonucleotide was 24 bp long (5' TACGAGTTGAGAATCCTGAATGCG [SEQ ID NO:34]) with a sequence containing a 12 bp end that was complementary to the DNA already adsorbed onto the substrate surface.
  • the substrate was then soaked in a hybridization buffer (0.5 M NaCl, 10 mM phosphate buffer pH 7) solution containing the linking oligonucleotide (0.4 OD, 1.7 ⁇ M) for 12 hours.
  • the substrate was soaked in a solution containing 13 nm diameter gold nanoparticles which had been modified with an oligonucleotide (TAGGACTTACGC 5' thiol [SEQ ID NO:35]) that is complementary to the unhybridized portion of the linking oligonucleotide attached to the substrate.
  • an oligonucleotide TAGGACTTACGC 5' thiol [SEQ ID NO:35]
  • the substrate was removed and rinsed with the hybridization buffer.
  • the glass substrate's color had changed from clear and colorless to a transparent pink color. See Figure 19 A.
  • Additional layers of nanoparticles were added to the slides by soaking the slides in a solution of the linking oligonucleotide as described above and then soaking in a solution containing 13 nm gold nanoparticles having oligonucleotides (3' thiol ATGCTCAACTCT [SEQ ID NO:33]) attached thereto. After soaking for 12 hours, the slides were removed from the nanoparticle solution and rinsed and soaked in hybridization buffer as described above. The color of the slide had become noticeably more red. See Figure 19A.
  • a final nanoparticle layer was added by repeating the linking oligonucleotide and nanoparticle soaking procedures using 13 nm gold nanoparticles which had been modified with an oligonucleotide (TAGGACTTACGC 5' thiol [SEQ ID NO:35]) as the final nanoparticle layer. Again, the color darkened, and the UV-vis absorbance at 520 nm increased. See Figure 19 A.
  • a melting curve was performed.
  • a slide was placed in a cuvette containing 1.5 mL of hybridization buffer, and an apparatus similar to that used in Example 2, part B, was used.
  • the absorbance signal due to the nanoparticles (520 nm) was monitored at each degree as the temperature of the substrate was increased from 20°C to 80°C, with a hold time of 1 minute at each integral degree.
  • the nanoparticle signal dramatically dropped when the temperature passed 52°C. See Figure 19B.
  • a first derivative of the signal showed a melting temperature of 55°C, which corresponds with the temperature seen for the oligonucleotide-nanoparticle conjugates and linking oligonucleotides hybridized in solution. See Figure 19B.
  • Example 11 Assay of a Polyribonucleotide Using
  • the previous Examples utilized oligo-deoxyribonucleotides as targets in the assays.
  • the present example demonstrates that the nanoparticle-oligonucleotide conjugates can also be used as probes in assaying a polyribonucleotide.
  • the experiment was carried out by adding 1 ⁇ L of a solution of poly(rA) (0.004 A 260 Units) to 100 ⁇ L of gold nanoparticles ( ⁇ 10 nM in particles) conjugated to dT 20 (a 20-mer oligonucleotide containing thymidylate residues) through a mercaptoalkyl linker at the 5'-terminus.
  • the conjugation procedure was that described in Example 3.
  • Example 12 Assay for Protective Antigen DNA Segment of Anthrax Using Nanoparticle-Oligonucleotide Conjugates
  • nanoparticle-oligonucleotide conjugates can be used to assay for a DNA strand in the presence of its complement (i.e., assaying for a single strand after thermal dehybridization of a double-stranded target) and can recognize and specifically bind to an amplicon obtained from a PCR reaction.
  • a PCR solution containing a 141 base pair duplex amplicon of the Protective Antigen segment of Anthrax was provided by the Navy (sequence given in Figure 23).
  • the assay for this amplicon was carried out by isolating the DNA from 100 ⁇ L of the PCR solution using a Qiaquick Nucleotide Removal Kit (Qiagen, Inc., Santa Clarita, CA) and the standard protocol for this kit, with the exception that elution of the DNA was effected with 10 mM phosphate buffer at pH 8.5, rather than with the buffer provided with the kit.
  • the eluant was then evaporated to dryness on a Speed Vac (Savant).
  • a master mix prepared by mixing equal volumes of each of two solutions of two different oligonucleotide-nanoparticle probes (see Figure 23). Each oligonucleotide-nanoparticle probe was prepared as described in Example 3.
  • the solutions of the probes which were combined to form the master mix were prepared by adding 10 ⁇ L of 2 M NaCl and 5 ⁇ L of oligonucleotide blocker solution (50 pmoles of each Blocker oligonucleotide (see Figure 23 and below) in a 0.3 M NaCl, 10 mM phosphate, pH 7.O., solution) to 5 ⁇ L of full-strength (about 10 nM) nanoparticle- oligonucleotide solution.
  • the amplicon-probe mixture was heated to 100°C for 3 minutes, then frozen in a DRY ICE/ethanol bath and allowed to come to room temperature. A small aliquot (2 ⁇ L) was spotted on a C18 TLC plate and allowed to dry. A strong blue spot indicative of hybridization was obtained.
  • the oligonucleotide Blockers were added to inhibit binding of the second strand of the initial duplex target (i.e., the strand complementary to the target strand) to regions of the target nucleic acid strand outside the segment that binds to the probes (see Figure 23 for sequences), since such binding interferes with binding of the nanoparticle oligonucleotide probes to the target strand.
  • the Blocker oligonucleotides were complementary to the single-stranded target in regions not covered by the probes.
  • An alternative scheme is to use blocker oligonucleotides that are complementary to the PCR complementary strand (the strand complementary to the target strand) outside the region that competes with the probe oligonucleotides.
  • Example 13 Direct assay of PCR Amplicons without isolation of the amplicons from the PCR solution
  • Example 12 The procedure described in Example 12 involved separation of the PCR amplicon from the PCR solution before addition of the nanoparticle-oligonucleotide probes. For many purposes it would be desirable to be able to carry out the assay directly in the PCR solution without preliminary isolation of the polynucleotide products.
  • a protocol for such an assay has been developed and is described below. This protocol has been performed successfully with several PCR products derived under standard conditions using a GeneAmp PCR Reagent Kit with Amplitaq DNA polymerase.
  • double-stranded targets were dehybridized by heating to generate single strands which interacted with single-stranded oligonucleotide probes bound to nanoparticles.
  • the present example demonstrates that in cases where triple- stranded complexes can form, double-stranded oligonucleotide sequences can be recognized by the nanoparticle probes without prior dehybridization of the target.
  • Tests were carried out with two different systems— polyA:polyU and dAr ⁇ . ⁇ K) — by adding 1 ⁇ L of a solution containing 0.8 A 260 Units of the target duplex in 100 ⁇ L of buffer (0.1 M NaCl, 10 mM phosphate, pH 7.0) to 100 ⁇ L of a colloidal solution of Au- sdT 20 nanoparticle-oligonucleotide conjugate ( ⁇ 10 nM in particles; see Example 11) in 0.3 M NaCl, 10 mM phosphate buffer at pH 7.0.
  • a DMF solution of a one thousand fold excess of 1,4-phenylene diisothiocyanate was added to an aqueous borate buffer solution (0.1 M, pH 9.3) of the amino-modified oligonucleotide. After several hours, the excess 1,4-phenylene diisothiocyanate was extracted with butanol and the aqueous solution lyophilized. The activated oligonucleotides were redissolved in borate buffer and reacted with the amino-functionalized latex microspheres in a carbonate buffer (0.1 M, pH 9.3, 1 M NaCl).
  • the target oligonucleotide (1-5 ⁇ l, 3 nM) was added to 3 ⁇ l of fluorophore- labeled oligonucleotide-modified latex microsphere probe solution (3.1 ⁇ m; 100 fM). After 5 minutes, 3 ⁇ l of the 5' oligonucleotide-modified gold nanoparticle probe solution (13 nm; 8 nM) were added to the solution containing the target and latex microsphere probes. Upon standing for an additional 10 minutes, the solution containing both probes and target was vacuum-filtered through the AcetatePlus membrane. The membrane retained the relatively large latex particles and allowed any non-hybridized gold nanoparticle probes to pass through.
  • a double-stranded target oligonucleotide (1-5 ⁇ l, 20 nM), 3 ⁇ l of a solution of fluorophore-labeled- oligonucleotide-latex microspheres (3.1 ⁇ m; 100 fM) and 3 ⁇ l of a solution of 5'-oligonucleotide-gold nanoparticles (13 nm; 8 nM) were combined and heated to 100 °C for 3 minutes. Then, the solution was immediately frozen by immersing the reaction vessel containing it in a liquid N 2 bath for 3 minutes. This solution was then thawed at room temperature and filtered as described above. For a 24-base pair model system, using the unaided eye, 20 femtomoles of duplex target oligonucleotide could be detected colorimetrically.
  • 25 femtomoles could be detected colorimetrically by the naked eye. Fluorescent spots could be visualized by the naked eye with a hand-held UV-lamp until the target amount in the 3 ⁇ l aliquot used to form the spot was as low as 50 femtomoles. It is believed that optimization of this system will allow for detection of even lower amounts of target nucleic acid.
  • Example 16 Assays Employing Silver Staining DNA hybridization tests on oligonucleotide-modified substrates are commonly used to detect the presence of specific DNA sequences in solution. The developing promise of combinatorial DNA arrays for probing genetic information illustrates the importance of these heterogeneous sequence assays to future science. In most assays, the hybridization of fluorophore-labeled targets to surface-bound probes is monitored by fluorescence microscopy or densitometry. Although fluorescence detection is very sensitive, its use is limited by the expense of the experimental equipment and by background emissions from most common substrates.
  • oligonucleotide-modified gold nanoparticles and unmodified DNA target could be hybridized to oligonucleotide probes attached to a glass substrate in a three-component sandwich assay (see Figures 25A-B).
  • the nanoparticles can either be individual ones (see Figure 25 A) or "trees" of nanoparticles (see Figure 25B).
  • the “trees” increase signal sensitivity as compared to the individual nanoparticles, and the hybridized gold nanoparticles "trees" often can be observed with the naked eye as dark areas on the glass substrate.
  • the hybridized gold nanoparticles can be treated with a silver staining solution.
  • the “trees” accelerate the staining process, making detection of target nucleic acid faster as compared to individual nanoparticles.
  • Capture oligonucleotides (3* - HS(CH 2 ) 3 - A 10 ATGCTCAACTCT; SEQ ID NO: 43) were immobilized on a glass substrate as described in Example 10.
  • a target oligonucleotide (5' - TACGAGTTGAGAATCCTGAATGCG - 3*, SEQ ID NO: 44, concentrations given below in Table 6 for each experiment) was hybridized with the capture oligonucleotides in 0.3 M NaCl, 10 mM phosphate buffer as described in Example 10.
  • the substrate was rinsed twice with the same buffer solution and immersed in a solution containing gold nanoparticle probes functionalized with target-complementary DNA (5' - HS(CH 2 ) 6 A 10 CGCATTCAGGAT, SEQ ID NO: 45)(preparation described in Example 3) for 12 hours.
  • the substrate was rinsed copiously with 0.3 M NaNO to remove Cir.
  • the substrate was then developed with silver staining solution (1:1 mixture of Silver Enhancer Solutions A and B, Sigma Chemical Co., # S-5020 and # S-5145) for 3 minutes.
  • Greyscale measurements were made by scanning the substrate on a flatbed scanner (normally used for scanning documents into a computer) linked to a computer loaded with software capable of calculating greyscale measurements (e.g., Adobe Photoshop). The results are presented in Table 6 below.
  • Example 17 Assemblies Containing Quantum Dots This example describes the immobilization of synthetic single-stranded DNA on semiconductor nanoparticle quantum dots (QDs). Native CdSe/ZnS core/shell QDs (-4 nm) are soluble only in organic media, making direct reaction with alkylthiol-terminated single-stranded DNA difficult. This problem was circumvented by first capping the QDs with 3-mercaptopropionic acid.
  • QDs semiconductor nanoparticle quantum dots
  • the carboxylic acid group was then deprotonated with 4- (dimethylamino)pyridine, rendering the particles water soluble, and facilitating reaction of the QDs with either 3'-propylthiol- or 5'-hexylthiol-modified oligonucleotide sequences.
  • the particles were separated from unreacted DNA by dialysis.
  • a "linker" DNA strand was then hybridized to surface-bound sequences, generating extended assemblies of nanoparticles.
  • the QD assemblies which were characterized by TEM, UV/Visible spectroscopy, and fluorescence spectroscopy, could be reversibly assembled by controlling the temperature of the solution.
  • the temperature dependent TJV-Vis spectra were obtained for the novel QD assemblies and composite aggregates formed between QDs and gold nanoparticles ( ⁇ 13 nm).
  • Nanopure water (18.1 M ⁇ ) prepared using a NANOpure ultrapure water purification system was employed throughout. Fluorescence spectra were obtained using a Perkin Elmer LS 50 B Luminescence Spectrometer. Melting analyses were performed using a HP 8453 diode array spectrophotometer equipped with a HP 9090a Peltier
  • DNA is the ideal synthon for programming the assembly of nanoscale building blocks into periodic two- and three-dimensional extended structures.
  • the many attributes of DNA which include ease of synthesis, extraordinary binding specificity, and virtually unlimited programmability by virtue of nucleotide sequence, can be exploited for the use of QD assembly.
  • FTIR polyethylene card, 3M: 1710 cm -1 (s), 1472 cm -1 (m), 1278 cm “1 (w), 1189 cm “1 (m), 1045 cm “1 (w), 993 cm 1 (m), 946 cm “1 (w), 776 cm “1 (m), 671 cm “1 (m).
  • the 3-mercaptopropionic acid modified QDs exhibited a characteristic vco band at 1710 cm "1 for the surface bound propionic acid.
  • Precipitate (dissolved in water) was characterized by IR spectroscopy (polyethylene card, 3M). IR (cm "1 ): 1647 (m), 1559 (s), 1462 (m), 1214 (w), 719 (w), 478 (s). After standing for 12 hours, the oligonucleotide-containing solution was brought to 0.15 M NaCl, and the particles were aged for an additional 12 hours. The NaCl concentration was then raised to 0.3 M, and the mixture was allowed to stand for a further 24-40 hours before dialyzing against PBS (0.3 M NaCl, 10 mM phosphate buffer, pH 1, 0.01% sodium azide) using a 100 kDa membrane (Spectra/Por Cellulose Ester Membrane). The dialysis was carried out over a period of 48 hours, during which time the dialysis bath was refreshed tliree times.
  • PBS 0.3 M NaCl, 10 mM phosphate buffer, pH 1, 0.01% sodium azide
  • the clusters generated were not large enough to settle out of solution. However, they could be separated by centrifugation at relatively low speeds (10,000 RPM for 10 min), as compared with the unlinked particles (30,000 RPM for 2-3 hours).
  • the "melting" behavior of the DNA was monitored by observing the UV-Vis spectra of the aggregates as a function of temperature.
  • the precipitate containing the QD/QD assemblies was centrifuged at 10,000 ⁇ m for 10 minutes, washed with 7 ⁇ L of PBS, recentrifuged, and suspended in 0.7 mL of PBS.
  • the UV/Visible spectroscopic signature of the assemblies was recorded at two degree intervals as the temperature was increased from 25°C to 75°C, with a holding time of 1 minute prior to each measurement.
  • Linker DNA (5 ⁇ L, 50 pmol) was added, and the mixture cooled to -78°C, and then allowed to warm slowly to room temperature, generating a reddish-pu ⁇ le precipitate. No aggregation behavior was observed unless both types of particles and a complementary target were present. After centrifugation (1 min at 3,000 ⁇ m) and removal of the supernatant, the precipitate was washed with 100 ⁇ L of PBS and recentrifuged.
  • HAuCl 4 A «3H 2 0 and trisodium citrate were purchased from Aldrich chemical company, Milwaukee, WI. Gold wire, 99.999% pure, and titanium wire were purchased from Goldsmith Inc., Evanston, IL.
  • Silicon wafers (100) with a 1 micron thick oxide layer were purchased from Silicon Quest International, Santa Clara, CA. 5'-thiol- modifier C6-phosphoramidite reagent, 3'-propylthiol modifier CPG, fluorescein phosphoramidite, and other reagents required for oligonucleotide synthesis were purchased from Glen Research, Sterling, VA.
  • oligonucleotides were prepared using an automated DNA synthesizer (Expedite) using standard phosphoramidite chemistry (Eckstein, F. Oligonucleotides and Analogues; 1st ed.; Oxford University Press, New York, 1991). Oligonucleotides containing only 5' hexylthiol modifications were prepared as described in Example 1. 5 -(and 6)-carboxyfTuorescein, succinimidyl ester was purchased from Molecular Probes, Eugene, OR. NAP-5 columns (Sephadex G-25
  • Nanopure H 2 0 (>18.0 M ⁇ ), purified using a Barnstead NANOpure ultrapure water system, was used for all experiments.
  • High Performance Liquid Chromatography (HPLC) was performed using a HP series 1100 HPLC.
  • SA 20 12F contained the same 12mer sequence with the addition of a 20 dA spacer sequence to the 5' end [SEQ ID NO: 51].
  • the thiol-modified oligonucleotides were prepared as described in Storhoff et al., J. Am. Chem.Soc. 120:1959-1964 (1998).
  • An amino-modifier C7 CPG solid support was used in automated synthesis, and the 5' terminus was manually modified with hexylthiol phosphoramidite, as described previously.
  • the 3' amino, 5' trityl-protected thiol modified oligonucleotides were purified by reverse-phase HPLC using an HP ODS Hypersil column (5 mm, 250 x 4 mm) with 0.03 M triethyl ammonium acetate (TEAA), pH 7 and a 1% / minute gradient of 95% CH 3 CN / 5% 0.03 M TEAA at a flow rate of 1 mL/min., while monitoring the UV signal of DNA at 254 nm.
  • the retention times of the 5'-S-trityl, 3' amino modified 12-base and 32-base oligonucleotides were 36 and 32 minutes respectively.
  • the lyophilized product was redispersed in 1 ml of 0.1 M Na 2 C0 3 and, while stirring in the dark, 100 ⁇ L of 10 mg/ml succinimidyl ester of fluorescein (5,6 FAM-SE, Molecular Probes) in dry DMF was added over 1.5 hours according to the directions of the manufacturer (Molecular Probes literature). The solution was stirred at room temperature for an additional 15 hours, then precipitated from 100% ethanol at -20 C. The precipitate was collected by centrifugation, dissolved in H 2 0 and the coupled product separated from unreacted amino-terminated oligonucleotide by ion-exchange HPLC.
  • a Dionex Nucleopac PA- 100 column (250 x 4 mm) was operated with 10 mM NaOH aqueous eluent and a 1% / minute gradient of 1 M NaCl/lOmM NaOH at a flow rate of 0.8 mL/minute. Retention times of 5'-S-trityl, 3' fluorescein modified 12mer and 32mer were 50 and 49 minutes respectively.
  • the oligonucleotide product was desalted by reverse-phase HPLC.
  • trityloligonucleotide was performed using silver nitrate and dithiothreitol (DTT) as previously described (Storhoff et al., J. Am. Chem.Soc. 120:1959-1964 (1998)). The yield and purity of the oligonucleotides were assessed using the techniques previously described for alkylthiol oligonucleotides (Storhoff et al., J. Am. Chem.Soc. 120:1959-1964 (1998)). Oligonucleotides were used immediately after detritylation of the thiol group.
  • DTT dithiothreitol
  • the fluorophore labeled complement (12'F) consisted of 12 bases 3 -GCG-TAA- GTC-CTA-5'-(CH 2 ) 6 -F [SEQ ID NO:53] complementary to the 12mer sequence in S12F and SA 0 12F.
  • the oligonucleotide was synthesized using standard methods, and a syringe-based procedure, similar to the procedure reported above for the 5' alkylthiol modification, was used to couple fluorescein phosphoramidite (6-FAM, Glen Research) to the 5' end of the CPG-bound oligonucleotide.
  • the fluorescein-labeled oligonucleotide had a retention time of 18 min.
  • the fluorophore labeled complement, 3'12F (5'-ATC-CTG-AAT-GCG- F; [SEQ ID NO:54]) was prepared using an amino-modifier C7 CPG solid support for automated synthesis, followed by coupling of 5 -(6)-carboxy fluorescein succinimidyl ester to the 3' amine using the procedure described above.
  • Gold nanoparticles were prepared by citrate reduction of HAuCl 4 as described in Example 1.
  • Transmission Electron Microscopy (TEM) performed with a Hitachi 8100 TEM was used to determine the size distribution of the resulting nanoparticles. At least 250 particles were sized from TEM negatives using graphics software (ImageTool). The average diameter of a typical particle preparation was 15.7 + 1.2 nm. Assuming spherical nanoparticles and density equivalent to that of bulk gold (19.30 g/cm 2 ), an average molecular weight per particle was calculated (2.4 x 10 7 g/mol). The atomic gold concentration in a solution of gold nanoparticles was determined by ICP-AES
  • Gold nanoparticles were modified with fluorescein-alkylthiol oligonucleotides by adding freshly deprotected oligonucleotides to aqueous nanoparticle solution (particle concentration ⁇ 10 nM) to a final oligonucleotide concentration of 3 ⁇ M. After 24 hours, the solution was buffered at pH 7 (0.01 M phosphate), and NaCl solution was added (to final concentration of 0.1 M). The solution was allowed to 'age' under these conditions for an additional 40 hours. Excess reagents were then removed by centrifugation for 30 minutes at 14,000 ⁇ m.
  • Silicon supported gold thin films were immersed in deposition solutions of deprotected alkylthiol modified oligonucleotides for equal times and buffer conditions as for the gold nanoparticles. Following oligonucleotide deposition, the films were rinsed extensively with 0.3 M PBS and stored in buffer solution. Gold was evaporated on one side only, leaving an unpassivated silicon/silicon oxide face. However, alkylthiol modified DNA did not adsorb appreciably to bare silicon oxide surfaces that were rinsed with PBS.
  • the average number of oligonucleotides per particle was obtained by dividing the measured oligonucleotide molar concentration by the original Au nanoparticle concentration. Normalized surface coverage values were then calculated by dividing by the estimated particle surface area (assuming spherical particles) in the nanoparticle solution. The assumption of roundness is based on a calculated average roundness factor of 0.93. Roundness factor is computed as: (4 x pi x Area)/(perimeter x 2) taken from Baxes, Gregory, Digital Image Processing, p. 157 (1994).
  • the fluorophore-labeled oligonucleotides were dehybridized by addition of NaOH (final concentration ⁇ 50 mM, pH 11-12, 4 hr). Following separation of the solution containing the 12'F from the nanoparticle solutions by centrifugation, and neutralization of the solutions by addition of 1 M HC1, the concentrations of hybridized oligonucleotide and corresponding hybridized target surface density were determined by fluorescence spectroscopy. K.
  • the gold nanoparticles absorb a significant amount of light between 200 nm and 530 nm, so their presence in solution during fluorescence measurements acts as a filter and diminishes the available excitation energy, as well as the intensity of emitted radiation.
  • the gold surface plasmon band at 520 nm falls at the emission maximum of fluorescein.
  • Mercaptoethanol (ME) was used to rapidly displace the surface bound oligonucleotides by an exchange reaction. To examine the displacement kinetics, oligonucleotide-modified nanoparticles were exposed to ME (12 mM) for increasing periods of time prior to centrifugation and fluorescence measurements.
  • the intensity of fluorescence associated with the solution free of nanoparticles can be used to determine how much oligonucleotide was released from the nanoparticles.
  • the amount of oligonucleotide freed in exchange with ME increased until about 10 hours of exposure ( Figure 29), which is indicative of complete oligonucleotide displacement.
  • the displacement reaction was rapid, which is presumably due to the inability of the oligonucleotide film to block access of the ME to the gold surface (Biebuyck et al., Langmuir 9:1766 (1993)).
  • the average oligonucleotide surface coverage of alkylthiol-modified 12mer oligonucleotide (S12F) on gold nanoparticles was 34 + 1 pmol/cm 2 (average often independent measurements of the sample.) For 15.7 + 1.2 nm diameter particles, this corresponds to roughly 159 thiol-bound 12mer strands per gold particle. Despite slight particle diameter variation from batch to batch, the area-normalized surface coverages were similar for different nanoparticle preparations.
  • this method was used to displace flourophore-labeled oligonucleotides from gold thin films, and the surface coverage data was compared with experiments aimed at getting similar information but with different techniques.
  • gold thin films were subjected to a similar oligonucleotide modification and ME displacement procedure as the citrate stabilized gold nanoparticles (see above).
  • the oligonucleotide displacement versus time curves for the gold thin films are very similar to those measured for gold nanoparticles.
  • oligonucleotide surface coverages on gold thin films measured by our technique fall within the range of previously reported coverages on oligonucleotide thin films (10 pmol/cm 2 for a 25 base oligonucleotide on gold electrodes determined using electrochemistry or surface plasmon resonance spectroscopy (SPRS) (Steel et al, Anal. Chem. 70:4670-4677 (1998)).
  • SPRS surface plasmon resonance spectroscopy
  • Hybridized 12'F amounted to 1.3 + 0.2 pmol/cm (approximately 6 duplexes per 15.7 nm particle; the average number of duplexes per particle was computed by multiplying the normalized hybridized surface coverage in pmol/cm 2 by the average particle surface area as found from size distributions measured by TEM.).
  • S12F modified gold nanoparticles were exposed to fluorophore-labeled non-complementary 12 base oligonucleotides (12F') in 0.3 M PBS.
  • gold nanoparticles as synthesized irreversibly agglomerate even in very low ionic strength media are naturally incompatible with salts and especially polyanions such as oligonucleotides.
  • This aging treatment is essential for preparing stable oligonucleotide particles. Therefore, the particles must be initially modified with alkylthiol oligonucleotides in water prior to gradually increasing the ionic strength. It is likely that oligonucleotides initially lie flat, bound through weak interactions of the nitrogenous bases with gold. A similar mode of interaction has been proposed for oligonucleotides on thin films (Herne et al., J. Am. Chem. Soc. 119:8916-8920 (1997)).
  • the interaction between oligonucleotides and the positively charged nanoparticle surface is expected to be even stronger.
  • the high ionic strength medium effectively screens charge repulsion between neighboring oligonucleotides, as well as, attraction between the polyanionic oligonucleotide and the positively charged gold surface. This allows more oligonucleotides to bind to the nanoparticle surface, thereby increasing oligonucleotide surface coverage.
  • 20dT spacer segments may extend pe ⁇ endicular from the gold surface, promoting higher surface coverages, while 20dA spacer segments block gold sites by lying flat on the particle surface.
  • another important property of oligonucleotide modified nanoparticles is the possibility of adjusting the total number of hybridization events. This is most readily accomplished by adjusting the surface density of recognition strands.
  • Other researchers have used coadsorbed diluent alkylthiols such as mercaptohexanol with modified oligonucleotides on gold electrodes to control hybridization (Steel et al., Anal. Chem.
  • a thiol modified 20 dA sequence (SA 20 ) [SEQ ID NO:55] proved to be suitable in terms of maintaining particle stability in the high ionic strength buffers which are needed for hybridization and protecting the surface from non-specific adso ⁇ tion.
  • Nanoparticles were modified using solutions containing different recognition strand (SA 20 12F) to diluent (SA 20 ) strand molar ratios. The resulting particles were analyzed by the fluorescence method described above to determine the SA 20 12F surface density, and then tested for hybridization efficiency with 12'F.
  • the SA 20 12F surface density increased linearly with respect to the proportion of SA 20 12F to SA 20 in the deposition solution, Figure 30. This is an interesting result because it suggests that the ratio of SA 20 12F to SA 20 attached to the nanoparticles reflects that of the solution. This result is in contrast to what is normally seen for mixtures of short chain alkyl or T-functionalized thiols, where solubility and chain length play a crucial role in adso ⁇ tion kinetics (Bain et al., J. Am. Chem. Soc. 111:7155-7164 (1989); Bain et al., J. Am. Chem. Soc. 111:7164-7175 (1989)).
  • Sequence-selective DNA detection has become increasingly important as scientists unravel the genetic basis of disease and use this new information to improve medical diagnosis and treatment.
  • Commonly used heterogeneous DNA sequence detection systems such as Southern blots and combinatorial DNA chips, rely on the specific hybridization of surface-bound, single-strand capture oligonucleotides complementary to target DNAs. Both the specificity and sensitivity of these assays are dependent upon the dissociation properties of capture strands hybridized to perfectly- matched and mismatched targets.
  • a single type of nanoparticles hybridized to a substrate exhibits a melting profile that is substantially sha ⁇ er than both the analogous fluorophore-based system and unlabeled DNA.
  • the melting temperature for the nanoparticle duplex is 11 degrees higher than for the analogous fluorophore system with identical sequences.
  • a substrate was fabricated by functionalizing a float glass microscope slide (Fisher Scientific) with amine-modified probe oligonucleotides as described in Example 10. This method was used to generate slides functionalized with a single type of oligonucleotides over their entire surface or in arrays of multiple types of oligonucleotides spotted with a commercial microarrayer. Nanoparticles having indicator oligonucleotides attached to them and synthetic 30-mer oligonucleotide targets (based on the anthrax protective antigen sequence) were then cohybridized to these substrates (see Figure 32). Therefore, the presence of nanoparticles at the surface indicated the detection of a particular 30-base sequence.
  • oligonucleotide- functionalized nanoparticles of the present invention can be further used to improve the selectivity of combinatorial oligonucleotide arrays (or "gene chips") (Fodor, Science 277, 393 (1997)).
  • the relative ratio of target hybridized to different elements of an oligonucleotide array will determine the accuracy of the array in determining the target sequence; this ratio is dependent upon the hybridization properties of the duplex formed between different capture strands and the DNA target.
  • these hybridization properties are dramatically improved by the use of nanoparticle labels instead of fluorophore labels.
  • the ratio of target hybridized to complementary surface probes to that hybridized to mismatched probes after a stringency wash at a specific temperature is much higher with nanoparticle labels than fluorophore labels. This should translate to higher selectivity in chip detection formats.
  • nanoparticle labels should increase array sensitivity by raising the melting temperature (T m ) of surface duplexes, which lowers the critical concentration below which duplexes spontaneously melt at room temperature.
  • test chips were probed with a synthetic target and labeled with both fluorophore and nanoparticle indicators.
  • the test arrays and oligonucleotide target were fabricated according to published protocols (Guo et al., Nucl. Acids Res., 22:5456 (1994); arrays of 175 ⁇ m diameter spots separated by 375 ⁇ m were patterned using a Genetic Microsystems 417 Microarrayer). Arrays contained four elements corresponding to the each of the four possible nucleotides (N) at position 8 of the target (see Figure 32).
  • the synthetic target and either fluorescent-labeled or nanoparticle-labeled probes were hybridized stepwise to a ⁇ ays in hybridization buffer, and each step was followed with a stringency buffer wash at 35 °C.
  • 20 ⁇ L of a 1 nM solution of synthetic target in 2 X PBS (0.3 M NaCl, 10 mM NaH 2 P0 /Na 2 HP0 4 buffer, pH 7) was hybridized to the array for 4 hours at room temperature in a hybridization chamber (Grace Bio-Labs Cover Well PC20), and then washed at 35°C with clean 2 X PBS buffer.
  • the assays utilizing nanoparticle-labeled probes were significantly more sensitive than those utilizing fluorophore-labeled probes.
  • the higher melting temperatures observed for nanoparticle-target complexes immobilized on surfaces undoubtedly contribute to array sensitivity.
  • the greater stability of the probe/target/surface-oligonucleotide complex in the case of the nanoparticle system as compared with the fluorophore system presumably results in less target and probe lost during washing steps.
  • Colorimetric, nanoparticle labeling of combinatorial oligonucleotide arrays will be useful in applications such as single nucleotide polymo ⁇ hism analysis, where single mismatch resolution, sensitivity, cost and ease of use are important factors.
  • the sensitivity of this system which has yet to be totally optimized, points toward a potential method for detecting oligonucleotide targets without the need for target amplification schemes such as polymerase chain reaction.
  • this strategy In addition to providing a new and powerful method for controlling the growth of nan ⁇ particle-based architectures from solid substrates, this strategy also allows one to evaluate the relationship between nanoparticle aggregate size and both melting and optical properties of aggregate DNA-interlinked structures. An understanding of these two physical parameters and their relationship to materials architecture is essential for utilizing nanoparticle network materials, especially in the area ofbiodetection.
  • the oligonucleotide-functionalized, 13-nm-diameter gold nanoparticles used to construct the multilayer assemblies were prepared as described in Examples 1 and 3.
  • the nanoparticles had 5'-hexanethiol-capped oligonucleotide 1 (5'-HS(CH 2 ) 6 0(P0 2 ⁇ )0- CGCATTCAGGAT-3' [SEQ ID NO:50]) and 3"-propanethiol-capped oligonucleotide 2 (3'-HS(CH 2 ) 3 0(P0 2 " )0-ATGCTCAACTCT-5' [SEQ ID NO:59]) attached to them to yield nanoparticles a and b, respectively (see Figure 37).
  • Glass slides were functionalized with 12-mer oligonucleotide 2 as described in Example 10.
  • the substrates were first immersed in a 10 nM solution of 24-mer linker 3 (5'-TACGAGTTGAGAATCCTGAATGCG-3' [SEQ ID NO:60]) and allowed to hybridize with it for 4 hours at room temperature (see Figure 37).
  • the substrates were washed with clean buffer solution, and then hybridized with a 2 nM solution of particle a for 4 hours at room temperature to attach the first nanoparticle layer.
  • a second nanoparticle layer could be attached to the first one by similarly exposing the surface to solutions of linker 3 and nanoparticle b.
  • the dissociation properties of the assembled nanoparticle multilayers were highly dependent upon the number of layers.
  • the multilayer-coated substrates were suspended in buffer solution and the temperature raised above the T m of the linking oligonucleotides (53°C)
  • the nanoparticles dissociated into solution, leaving behind a colorless glass surface.
  • Increasing or decreasing the pH (>11 or ⁇ 3) or decreasing the salt concentration of the buffer suspension (below -0.01 M NaCl) also dissociated the nanoparticles by dehybridizing the linking DNA.
  • the multilayer assembly was fully reversible, and nanoparticles could be hybridized to, and dehybridized from, the glass substrates (e.g. three cycles were demonstrated with no detectable irreversible nanoparticle binding).
  • Electron transport through DNA has been one of the most intensely debated subjects in chemistry over the past five years. (Kelley et al, Science 283:375-381 (1999); Turro et al., JBIC 3:201-209 (1998); Lewis et al., JBIC 3:215-221 (1998); Ratner, M. Nature 397:480-481 (1999); Okahata et al., J. Am. Chem. Soc. 120:6165-6166 (1998)) Some claim that DNA is able to efficiently transport electrons, while others believe it to be an insulator.
  • citrate-stabilized 13 nm gold nanoparticles were modified with 3' and 5' alkanethiol-capped 12-mer oligonucleotides 1 (3' SH (CH 2 ) 3 0(P0 2" )0-ATGCTCAACTCT 5' [SEQ ID NO:59]) and 2 (5' SH (CH 2 ) 6 0(P0 2" )0-CGCATTCAGGAT 3' [SEQ ID NO:50]) as described in Examples 1 and 3.
  • DNA strands with lengths of 24, 48, or 72 bases (3 (5'TACGAGTTGAGAATCCTGAATGCG3 ' [SEQ ID NO:60]), 4
  • 1-modified gold nanoparticles (652 ⁇ l, 9.7 nM) and 2-modified gold nanoparticles (652 ⁇ l, 9.7 nM) were added to linker DNA 3, 4 radical or 5 (30 ⁇ l, 10 nM). After full precipitation, the aggregates were washed with 0.3 M CH 3 COONH solution to remove excess linker DNA and NaCl.
  • the dried DNA-linked aggregates could be redispersed in 0.3 M PBS buffer (1ml), and exhibited excellent melting properties; heating such a dispersion to 60 °C resulted in dehybridization of the DNA interconnects, yielding a red solution of dispersed nanoparticles.
  • This combined with the FE-SEM data conclusively demonstrated that DNA-modified gold nanoparticles are not irreversibly aggregated upon drying.
  • the electrical conductivities of the three samples were measured using a computer-controlled, four-probe technique. Electrical contacts consisted of fine gold wires (25 and 60 ⁇ m diameter) attached to pellets with gold paste. Samples were cooled in a moderate vacuum (10 "3 to 10 “2 torr), and conductivity was measured as the temperature was increased under a dry, low pressure of helium gas. The sample chamber was insulated from light in order to eliminate possible optoelectronic effects. Excitation currents were kept at or below 100 nA, and the voltage across the entire sample was limited to a maximum of 20 V.
  • the conductivities of the aggregates formed from all three linkers ranged from 10 "s to 10 "4 S/cm at room temperature, and they showed similar temperature dependent behavior.
  • the conductivities of the DNA-linked aggregates showed Arrhenius behavior up to about 190°K, which is characteristic of a semiconducting material. This is similar to the behavior of activated electron hopping observed in discontinuous metal island films (Barwinski, Thin Solid Films 128:1-9 (1985)).
  • Gold nanoparticle networks linked by alkanedithiols have shown similar temperature dependence (Brust et al., Adv. Mater. 7:795-797 (1995); Bethell et al., J. Electroanal. Chem. 409:137-143 (1996)).
  • Activation energies of charge transport can be obtained from a plot of In ⁇ versus 1/T using equation (1).
  • the average activation energies calculated from three measurements were 7.4 ⁇ 0.2 meV, 7.5 + 0.3 meV, and 7.6 + 0.4 meV for the 24-, 48-, and 72-mer linkers, respectively. Conductivity data from 50°K to 150°K were used for these calculations.
  • the measured conductivities of the DNA-linked samples showed an anomalous dipping behavior.
  • the conductivity started to decrease abruptly at approximately 190°K and continued to decrease until approximately 250°K, at which point it increased again.
  • the electrical conductivity was measured as the sample was cooled and warmed repeatedly.
  • the dip in conductivity only occurred in the direction of increasing temperature. Since DNA is hydrophilic and water could potentially affect the electrical properties of the hybrid structures, the effect of relative humidity on the conductivity of the gold aggregates was examined. The resistance increased by a factor of 10 with increasing humidity from 1% to 100%>. It should be noted that the characteristic dip was very weak when the sample was kept in vacuum (10 "6 Torr) for 48 hours prior to the conductivity measurement.
  • a method of detecting nucleic acid using gold electrodes is illustrated diagramatically in Figure 41.
  • a glass surface between two gold electrodes was modified with 12-mer oligonucleotides 1 (3' NH 2 (CH 2 ) 7 O(PO 2" )O-ATG-CTC-AAC-TCT [SEQ ID NO:59]) complementary to target DNA 3 (5' TAC GAG TTG AGA ATC CTG.AAT GCG [SEQ ID NO:60]) by the method of Guo at al, Nucleic Acids Res., 22, 5456-5465 (1994).
  • Oligonucleotides 2 (5' SH(CH 2 ) 6 O(P0 2 -)O-CGC-ATT-CAG-GAT [SEQ ID NO:50]) were prepared and attached to 13 nm gold nanoparticles as described in Examples 1 andl8 to yield nanoparticles a.
  • Target DNA 3 and nanoparticles a were added to the device. The color of the glass surface turned pink, indicating that target DNA-gold nanoparticle assemblies were formed on the glass substrate.
  • the device was immersed in 0.3 M NaCl, 10 mM phosphate buffer and heated at 40 °C for 1 hour to remove nonspecifically bound DNA, and then treated with a silver staining solution as described in Example 19 for 5 minutes. The resistance of the electrode was 67 k ⁇ .
  • a control device modified by attaching oligonucleotides 4, instead of oligonucleotides 1, between the electrodes.
  • Oligonucleotides 4 have the same sequence (5' NH 2 (CH 2 ) 6 0(P0 2 -)O-CGC-ATT-CAG-GAT [SEQ ID NO:50]) as oligonucleotides 2 on the nanoparticles and will bind to target DNA 3 so as to prevent binding of the nanoparticles.
  • the test was otherwise performed as described above. The resistance was higher than 40 M ⁇ , the detection limit of the multimeter that was used.
  • Example 23 Preparation of Oligonucleotide-Modified Gold Nanoparticles using cyclic disulfide linkers
  • a new cyclic disulfide linker for binding oligonucleotides to gold surfaces based on steroid disulfide la ( Figure 42) that is simple to prepare, is broadly useful, and affords gold-oligonucleotide conjugates exhibiting greater stability toward DTT than those prepared using mercaptohexyl linkers.
  • a cyclic disulfide was selected as the reactive site of the anchor unit since ester derivatives of 1,2- dithiane-4,5-diol were known to form monolayers on gold surfaces (Nuzzo, et al., J. Am. Chem. Soc.
  • oligonucleotide-gold probes used in previous studies were prepared by the reaction of oligonucleotides being terminal mercaptohexyl groups with gold nanoparticles in an aqueous buffer. They proved to be surprisingly robust, functioning well even after heating to 100°C or after storing for 3 years at 5 °C. We have found, however, that these conjugates lose activity as hybridization probes when soaked in solutions containing thiols, which act by displacing the derivatized oligonucleotides from the gold surface.
  • the oligonucleotides were purified by reversed phase HPLC on a Dionex DX500 system equipped with a Hewlett Packard ODS Hypersil column (4.6 x 200 nm, 5 ⁇ m particle size) using TEAA buffer (pH 7.0) and a 1%/min gradient of 95% CH 3 CN/5% 0.03 TEAA at a flow rate of 1 mL/min.
  • TEAA buffer pH 7.0
  • a 1%/min gradient of 95% CH 3 CN/5% 0.03 TEAA at a flow rate of 1 mL/min A nice feature of the hydrophobic steroid group is that the capped derivatives separate cleanly from uncapped oligomers.
  • Each of the modified oligonucleotides was immobilized on ⁇ 13 nm gold nanoparticles by the procedure used for anchoring oligonucleotides through a mercaptohexyl head group (Storhoff et al. (1998) J. Am. Chem. Soc. 120, 1959-1964). This involved soaking citrate stabilized nanoparticles ( ⁇ 13 nm in diameter) for 56 hours in a buffer-salt solution containing an oligonucleotide bearing a terminal sulfur substituent (HS- or acyclic or cyclic disulfide) followed by addition of NaCL to 0.1 M and 24h of standing.
  • HS- or acyclic or cyclic disulfide a terminal sulfur substituent
  • probes Icl, Ic2, IIcl, IIc2, and IIIcl by immobilizing the modified oligonucleotides on gold nanoparticles ( Figure 2).
  • the oligomers in a given series have the same nucleotide sequence but differ in structure of the 5'-head group Y.
  • Conjugates Icl and Ic2 have steroid-disulfide head groups; IIcl, IIc2, mercaptohexyl head groups; and IIIcl, acylic disulfide head groups.
  • the (dA) 20 chains serve as spacers between the gold and the oligonucleotide recognition regions to facilitate hybridization. Many of the sulfur derivatized oligomers bind to each nanoparticle. Hybridization of pairs of nanoparticle probes with target oligonucleotides leads to formation of three dimensional networks and a change in color from red to blue- gray (Mucic, R. C, et al, J. Am. Chem. Soc. 120, 12674-12675).
  • Hybridization of the probes was examined using a 79-mer oligonucleotide targets, containing sequences complementary to the probes (Figure 43).
  • the reactions were carried out at room temperature by adding 1 ⁇ L of the target solution (10 pmol of IV) to colloidal solutions of the probe pairs Icl, Ic2, and IIcl and IIc2, and IIIcl and IIc2 (50 ⁇ L and 1.0 A 520 Unit of each nanoparticle probe) in 0.5 M NaCl, 10 mM phosphate (pH 7.0). At times 10 seconds, 5 minutes, and 10 minutes, aliquots (3 ⁇ L) were removed and spotted on a C-18 reversed phase TLC plate.
  • colloidal probes derived from oligonucleotides with the mercaptohexyl (IIcl and IIc2) and acyclic oligonucleotide headgroups (IIIcl) reacted rapidly. A red-blue spot was obtained in 20 seconds and a strong blue spot within 5 minutes. By 100 minutes, most of the gold had precipitated. In contrast, no color change was observed for the reaction of the probes prepared with the steroid-cyclic disulfide head group (Icl, Ic2) within 40 minutes. It took 100 minutes to reach the same color obtained with probes prepared with IIcl, IIc2, or with IIIcl in 20 seconds.
  • the rate of reaction of the steroid disulfide probes with DTT is of the order of l/300 th that of the other probes.
  • the probe prepared from the acyclic disulifide anchor 3 c reacts at about the same rate as the probes prepared with the mercaptohexyl anchor.
  • the latter result is not su ⁇ rising in view of evidence that the reaction of an acyclic disulfide with gold probably involves cleavage of the S-S bond (Zhong, C. J., Langmuir, 15, 518-525). Accordingly, an oligonucleotide with an acyclic head group would likely be linked to gold through a single sulfur atom, as in the case of mercaptohexyl-oligonucleotide derivatives.
  • probes prepared from Icl and lc2 in fact still serve as hybridization probes after standing in the presence of DTT, we treated two samples of mixtures of the probes with DTT under the conditions used for the reactions in Table I. After 30 minutes, 1 ⁇ L of a solution of the 79-mer target oligonucleotide (10 pmol) was added to one. Both samples were frozen quickly, allowed to thaw, and assayed by the spot test.
  • Gold nanoparticle-oligonucleotide conjugates made using this cyclic disulfide linker serve as effective probes for detecting specific oligonucleotide sequences, and they exhibit much greater stability toward dithiothreitol than corresponding conjugates prepared with the conventional mercaptohexyl group or an acyclic disulfide unit.
  • the high stability toward thiol deactivation likely results, in part at least, from anchoring each oligonucleotide to gold through two sulfur atoms.
  • Example 24 Preparation of Oligonucleotide-Modified Gold Nanoparticles using a simple cyclic disulfide linker.
  • this Example we prepared a non-steroid cyclic disulfide linker and oligonucleotide-nanoparticle probes from this linker and evaluated the probes stability in the presence of thiol-containing solutions relative to probes prepared with steroidal cyclic disulfide and alkyl thiol linkers. Procedures have been described for preparing probes for detecting DNA or RNA sequences by binding oligonucleotides to gold nanoparticles using alkylthiol anchor groups, I, Figure 44 [C. A.
  • the conjugates prepared using the steroid cyclic disulfide linker have proved advantageous in that they are much more stable in the presence of thiol compounds, such as mercaptoethanol or dithiothreitol (DTT), than are conjugates prepared using an alkylthiol anchor.
  • thiol compounds such as mercaptoethanol or dithiothreitol (DTT)
  • DTT dithiothreitol
  • steroid cyclic anchor (compound 1, Figure 42): (1) the cyclic disulfide, which can in principle provide two binding sites that could act cooperatively in holding a given oligonucleotide at the gold surface, and (2) the steroid unit which could stabilize neighboring chains on the gold by hydrophobic interactions (see for example, R. L. Letsinger et al, J. Am. Chem. Soc. 115, 7535 (1993). To assess the importance of these contributions we have prepared and examined gold conjugates anchored by a cyclic disulfide lacking a steroid group, compound IIIc ( Figure 44).
  • Compound 2a prepared by heating trans- l,2-dithiane-4,5-dithiol with acetol in toluene, was converted to a cyanoethyl N,N-di-i-propyl phosphoramidite reagent, 2b , which was employed in the final coupling step in the synthesis of modified oligonucleotides 2cl and 2c2.
  • One gold conjugate probe was prepared by treating a gold colloid solution with 2c 1 and an equimolar amount of 2d, which serves a diluent on the gold surface.
  • a companion probe was made from 2c2 and 2d in the same way.
  • oligonucleotides 2c 1 and 2d or 2c2 and 2d were added to 13 nm gold colloids (- 10 nM) to provide solutions containing 1.7 ⁇ mole/mL of each oligonucleotide.
  • the solutions were stored in the dark for 24 h; then salts were added to make the solutions 0.3 M in NaCl, 10 mM in phosphate (pH 7.0), and 0.01% in sodium azide. After 24 h the NaCl concentration was increased to 0.8 M and the solution were allowed to stand for another 24 h. The colloid was then filtered to remove any aggregates and the solution was centrifuged to collect the nanoparticles.
  • Displacement studies were carried out at room temperature (22°C) by adding 2 ⁇ L of 0.1 M DTT to 20 ⁇ L of a mixture of equal volumes of the colloidal conjugates obtained from 2c 1 and 2c2. Aliquots (3 ⁇ L) were periodically removed and spotted onto a white Nylon membrane. Initially the spots were red. Displacement of the oligonucleotide sulfur derivatives from the gold by DTT led to mixtures that afforded a blue-gray spot in the spot test. The time for displacement by DTT was taken as the time for the mixture to give a strong blue-gray color in a spot test. For the mixture of conjugates derived from 2c 1 and 2c2 this time was 10 hours.
  • oligonucleotide conjugates were similarly prepared from oligonucleotide sequences cl and c2 ( Figure 44) using the mercaptohexyl anchor (compound 2, Figure 42) and the steroid cyclic disulfide anchor (compound 1, Figure 42).
  • 5'-DMT groups were subsequently removed by dissolving the oligonucleotide in 80% acetic acid for 30 min, followed by evaporation.
  • the oligonucleotide was redissolved in 500 ⁇ L nanopure water and the solution was exfracted with ethyl acetate (3 x 300 ⁇ L). After evaporation of the solvent, the oligonucleotide was obtained as a white solid.
  • the retentipn time of this 5'- tri- disulfide oligonucleotide with no DMT group was around 35 minutes on reverse phase, columns while 24 minutes on the ion-exchange column.
  • oligonucleotide 8 ( Figure 45) was obtained by electrospray MS (calculated: 12242.85, found 12244.1). The three disulfide groups on the DNA stand were reduced tri thiol groups as described above for 5' monothiol DNA; then the oligonucleotide was purified though a NAP-5 column.
  • single thiol oligonucleotide (l)-modified 30 nm gold particles quickly form an aggregate in 0.017M DTT; after 1.5 hours, the colloid totally turns blue.
  • the solution containing disulfide oligonucleotide (4)-modified nanoparticles turns blue after 20 hours under identical conditions.
  • the trithiol-oligonucleotide (cleaved 6) modified nanoparticles it took 40 h to turn the solution blue.
  • Example 26 Detection of an analyte using a nanoparticle-nucleic acid-sfp member conjugate
  • This example demonstrates the detection of an analyte (biotin) using a nanoparticle-streptavidin probe ( Figures 54 and 56).
  • Nanoparticle-nucleic acid conjugates are prepared as described in Example 3.
  • the oligonucleotide modifier used to prepare these conjugates have the following sequence: 5'SH(CH 2 ) 6 -A 10 -CGCATTCAGGAT 3' (2)(SEQ ID NO: 74).
  • biotin labeled oligonucleotide (1) [3' biotin-TEG-A 10 -ATGCTCAACTCT 5'] (SEQ ID NO: 73) is prepared by literature procedure using a Biotin TEG CPG support (Glen Research, Sterling, Virginia; Catalog no. 20-2955-01).
  • streptavidin was.reacted with 1 equivalent of biotin-modified oligonucleotides in 20 mM Tris (pH 7.2), 0.2 mM EDTA buffer solution at room temperature for 2 h on a shaker. Streptavidin complexed to different numbers of oligonucleotides were separated by ion exchange HPLC with 20 mM Tris (pH 7.2) and a 0.5 %/min gradient of 20 mM Tris, 1 M NaCl at a flow rate of 1 mL/min, while monitoring the UV signal of DNA at 260 nm and 280 nm.
  • the streptavidin/biotin-modified oligonucleotide mixture showed four peaks at 45 min, 56 min, 67 min and 71 min, which correspond to the 1:1, 2:1, 3:1, and 4:1 oligonucleotide-streptavidin complexes, respectively.
  • the 1:1 complex of streptavidin/oligonucleotide (10 uM, 5uL) was isolated and premixed with linker DNA [5'TACGAGTTGAGAATCCTGATTGCG3'] (3) (SEQ ID NO: 76) (lOuM, 5uL) in 0.3 M PBS (0.3 M NaCl, 10 mM phosphate buffer, pH 7) and then the mixture was added to the nanoparticle-oligonucleotide conjugates (10 nM, 130 uL) in 0.3 M PBS to prepare a nanoparticle-oligonucleotide-strepavidin conjugate.
  • linker DNA [5'TACGAGTTGAGAATCCTGATTGCG3'] (3) (SEQ ID NO: 76) (lOuM, 5uL) in 0.3 M PBS (0.3 M NaCl, 10 mM phosphate buffer, pH 7) and then the mixture was added to the nanoparticle-oligonucleotide conjugates (10 nM,
  • nanoparticle-oligonucleotide conjugates streptavidin oligonucleotide, and linker DNA was frozen in dry ice for 10 min and thawed to facilitate DNA hybridization. After 12 hr, the solution was centrifuged at 10000 ⁇ m for 20 min and supernatent was removed. Red oily precipitate of nanoparticle-oligonucleotide-strepavidin conjugate was redispersed in 0.3 M PBS buffer.
  • nanoparticle-oligonucleotide-strepavidin conjugate was then used to detect for the presence of a target analyte, biotin immobilized onto a glass surface, (b) Detection of biotin Biotin was immobilized to a glass slide according to the following procedure: Oligonucleotide modified glass slide was prepared by previously reported method (Science, 2000, 289, 1757-1760) and then the biotin modified oligonucleotide was hybridized to the surface DNA. (Biotin modified glass slide can be prepared by various method.
  • One example is to prepare amine modified glass slide and then react the surface amine with various commercially available biotinylation reagents which react with amine.)
  • the immobilized biotin glass slide was then treated with a medium containing the nanoparticle-oligonucleotide-streptavidin (2 nM in 0.3 M PBS).
  • the presence of the captured probe was demonstrated, after washing and treating with silver enhancing solution [silver enhancer solution A (catalog no. S5020, Sigma Company, St. Louis, MO, USA) and silver enhancer solution B (catalog no. S 5145, Sigma Company), see also Science, 2000, 289, 1757], by the appearance of a gray or shiny silver spot.
  • Example 27 Specific binding comparison of gold colloid strepavidin conjugates
  • nonspecific binding of the nanoparticle streptavidin probe prepared in accordance with Example 26 and a commercial Au colloid (20 nm)/ streptavidin conjugate full name: streptavidin-gold labeled
  • specific binding pair members e.g., receptors or ligands
  • Biotin modified DNA (2) was synthesized with Biotin TEG CPG support (Glen Research) and purified by literature methods. See J. J. Storhoff, R. Elghanian, R. C. Mucic, C. A. Mirkin, R. L. Letsinger, J. Am. Chem. Soc. 1998, 120, 1959; T. Brown, D. J. S. Brown, in Oligonuclieotides and Analogues (Ed.: F.
  • Streptavidin was purchased from Sigma and dissolved in 20 mM Tris buffer (30 ⁇ M, pH 7.2). To make the streptavidin/DNA conjugate (1-STV), streptavidin was reacted with 8 equivalents of biotin-oligonucleotide conjugate 1 in 20 mM Tris (pH 7.2), 0.2 mM EDTA buffer solution at room temperature for 2 h on a shaker.
  • the biotin-oligonucleotide conjugate has the sequence: [3' biotin- TEG-A ⁇ o-ATGCTCAACTCT5'](SEQ ID NO:73).
  • streptavidin DNA conjugates were separated from excess DNA by ion exchange HPLC with 20 mM Tris (pH 7.2) and a 0.5 %/min gradient of 20 mM Tris, 1 M NaCl at a flow rate of 1 mL/min, while monitoring the UV signal of DNA at 260 nm and 280 nm.
  • the 1:0.4 streptavidin/DNA mixture showed two peaks at 45 min and 56 min, and the 1:1 mixture showed four peaks at 45 min, 56 min, 67 min and 71 min, which correspond to the 1:1, 2:1, 3:1, and 4:1 oligonucleotide-streptavidin complexes, respectively.
  • the 1:4 mixture showed four peaks at the same positions but with increased intensity of third (67 min) and fourth (71 min) peaks.
  • the HPLC spectrum of 1:8 streptavidin/DNA mixture showed two main peaks, one at 59 min for unreacted DNA and the other at 71 min for the 4: 1 oligonucleotide-streptavidin complex. In addition, a shoulder at 67 min assigned to 3:1 complex was also present.
  • Purified streptavidin-biotinylated DNA conjugates were concentrated and dispersed in 0.3 M PBS by ultrafiltration (centricon 30). Aggregates for TEM, thermal denaturation experiments, and SAXS measurements were prepared by freezing the solution containing 1-STV, 2-Au, and 3 in dry ice for 10 min, and thawed prior to the measurement to facilitate hybridization.
  • linker DNA 3 (10 ⁇ M, 21 ⁇ L) was introduced to the mixture of 2-Au (9.7 nM, 260 ⁇ L) and 1-STV (1.8 ⁇ M, 27 ⁇ L), or linker DNA 3 (10 ⁇ M, 21 ⁇ L) was premixed with 1-STV (1.8 ⁇ M, 27 ⁇ L) and then the mixture was added to 2-Au (9.7 nM, 260 ⁇ L) in 0.3 M PBS. Aggregates with similar properties could be formed by both methods, but premixing 3 and 1-STV facilitates aggregate formation. Since a 13 nm gold nanoparticle is substantially larger than streptavidin (4 nm x 4 nm x 5 nm) [P. C.
  • the transmission electron microscopy (TEM) image ( Figure 57B) shows that the particles within the aggregates retain their physical shape prior to and after annealing, showing no particle fusion and further demonstrating the stabilizing influence of the surface oligonucleotide layer.
  • This requirement of thermal activation for initiating particle assembly is in contrast to the previously studied system involving two gold nanoparticle conjugates ( Figure 52 b) where, under very similar conditions, the oligonucleotide-modified gold particle ' s assemble into aggregates within a few minutes upon adding linker DNA at room temperature.
  • An Au nanoparticle/protein assembly also could be formed through streptavidin/biotin interactions as opposed to hybridizatiori-induced assembly.
  • 3 (10 ⁇ M, 32 ⁇ L) and 2-modified nanoparticles (Au nanoparticle concentration: 9.7 nM, 260 ⁇ L) were mixed in 0.3 M PBS buffer to generate biotin-modified Au particles.
  • the mixture was heated to 60 °C for 10 min and then cooled to room temperature to facilitate hybridization.
  • the solution containing 1, 3, and 2-modified Au nanoparticles was added to streptavidin (10 ⁇ M, 4.2 ⁇ L) in 0.3 M PBS and heated to 50 °C to form the nanoparticle aggregates.
  • streptavidin (10 ⁇ M, 4.2 ⁇ L) in 0.3 M PBS and heated to 50 °C to form the nanoparticle aggregates.
  • the color of the solution turned pu ⁇ le indicating aggregate formation, and the aggregates could be disassembled to 2-modified Au particles, 1-modified streptavidin, and 3 by raising the temperature of the solution above the Tm (65 °C).
  • SAXS Small Angle X-ray Scattering
  • the aggregates linked by DNA showed relatively well defined diffraction peaks, and the Au-STV aggregates exhibited diffraction peaks at smaller 5 values than the Au- Au aggregates formed from the same linker. This suggests a larger Au inte ⁇ article distance in the Au-STV system. Furthermore, the diffraction peaks shift to smaller s values when 48-mer DNA was used as a linker instead of 24-mer for both the Au-Au and Au-STV assemblies, Figure 59.
  • q (47r/ ⁇ )sin(0/2)
  • p particle number density.
  • the nearest neighbor Au inte ⁇ article distances (center to center distance) obtained from the PDDFs are 19.3 nm, 25.4 nm, 28.7 nm, and 40.0 nm for the 24-mer linked Au-Au, 48-mer linked Au-Au, 24-mer linked Au-STV, and 48-mer linked Au-STV assemblies, respectively.
  • a comparison of the inte ⁇ article distances for the Au- STV system and the Au-Au system clearly shows that the Au-STV assembly has the anticipated Au nanoparticle/streptavidin periodicity and that the two components (Au nanoparticle and streptavidin) are well separated by rigid DNA duplex linkers.
  • EXAMPLE 29 Acceleration of nanoparticles across an electric field
  • the invention describes a method of moving nanoparticles such as citrate- stabilized nanoparticles and nanoparticles coated with charged biomolecules through an electric field.
  • Nanoparticles and their use for detecting nucleic acids have been described extensively in WO 98/04740 (Northwestern University) and WO 00/33079 (Nanosphere LLC) which are inco ⁇ orated herein in their entirety.
  • Detection technologies that utilize nanoparticle probes functionalized with biomolecules rely on the ability for probe molecules to find immobilized target or capture strand oligonucleotides (in the case of a chip).
  • This process can accelerate the movement of probes to an electrode surface with "captured target” or a set of probes that have captured target in solution to a surface of interest.
  • the inventive method has important biodiagnostic applications that utilize nanoparticle-based probes. For example, it can be used to accelerate hybridization of a nanoparticle probe or set of probes to a surface functionalized with complementary DNA or a complementary antigen/antibody.
  • CD-50IN-CUV were cut by 0.8 x 1 cm.
  • Two indium-tin-oxide coated glass substrates were employed as a cathode and anode.
  • the electrodes were dipped in a solution of DNA-modified nanoparticles, and a 3 V DC electric field was applied (4 ⁇ A) for 15 min. After application of the field, the electrodes were washed with water. A pink color was observed on the positively-biased electrode (anode) while there was no visible change on the cathode.
  • the capturing of the nanoparticles on the anode was confirmed by enhancing the signal with solver via a solution of Ag(I) and hydroquinone. Both electrodes were immersed in the silver staining solution for 3 min.
  • Test oligonucleotide targets were synthesized by automated solid phase synthesis, and oligonucleotide arrays were fabricated on glass microscope slides using literature procedures.
  • 50 nm and 100 nm diameter gold nanoparticles were functionalized with dithiane-terminated oligonucleotides and isolated by literature methods.
  • oligonucleotide-nanoparticle conjugates and oligonucleotide targets were cohybridized to the DNA arrays in 0.3 M PBS hybridization buffer [0.3 M NaCl, 10 nM NaH 2 PO_t/Na 2 HP0 ' pH 7] at room temperature for 2 h. [ See Examples 30 and 31 below]. The arrays were then washed with clean buffer to remove unhybridized target and nanoparticle probes.
  • the array slides were mounted on a microscope stage and illuminated in the plane of the slide by a fiber optic illuminator [Darklite Illuminator (Micro Video Instruments, Avon, MA)]; in this configuration, the slide served as a planar waveguide, preventing any light from reaching the microscope objective by total internal reflectance.
  • a fiber optic illuminator Darklite Illuminator (Micro Video Instruments, Avon, MA)]
  • the slide served as a planar waveguide, preventing any light from reaching the microscope objective by total internal reflectance.
  • evanescently coupled light [M ⁇ ller, G. J. In Multichannel Image Detectors; Talmi, Y., Ed.; ACS Symposium Series 102; American Chemical Society: Washington, DC, 1979; pp 239-262] was scattered out of the guide plane and was imaged as bright, ⁇ colored spots on a dark background.
  • oligonucleotide synthesis was performed on an Expedite 8909 Nucleic Acid Synthesizer (Applied Biosystems, Foster City, CA) using standard phosphoramidite chemistry. All the reagents required for oliognucleotide synthesis were purchased from
  • Aqueous solutions of 50 nm and 100 nm diameter gold nanoparticles were used as received.
  • To 10 mL of gold colloid solution was added 1.5 nmol of 5 '-steroid disulfide-modified oligonucleotide, prepared using literature procedures [Letsinger, R.L.; Elghanian, R.; Viswanadham, G.; Mirkin, CA. Bioconjugate Chem. 2000, 11, 289], in water.
  • the solution was brought to 0.3 M NaCl, 10 mM NaH 2 P0 4 /Na 2 HP0 4 ⁇ H 7 buffer (0.3 M PBS) gradually by adding aliquots of 2 M NaCl and 0.1 M NaH 2 P0 4 /Na 2 HP0 4' pH 7 buffer solutions every 4 hours. After 48 hours, the particle solutions were centrifuged (for 50 nm gold nanoparticles: 5000 m for 10 min, for 100 nm gold nanoparticles: 2500 ⁇ m for 10 min) in an ultracentrifuge (Avanti 30, Beckman Instruments, Fullerton, CA) to yield a colorless supernatant above a dark red oily precipitate.
  • the dark red oily precipitate was redispersed in fresh 0.3 M PBS buffer (7 mL and 4 mL for 50 nm and 100 nm gold colloids). Centrifugation and redispersion was repeated twice. The final concentrations of the product nanoparticle solutions were estimated from their measured visible abso ⁇ tion of 520 nm and published values for extinction coefficients of the unmodified particles [Yguerabide, J. and Yguerabide, E.E. Anal. Biochem.
  • APS-modified slides were rinsed thoroughly with nanopure water and ethanol, dried under N 2 and baked at 120-130 °C for 20 min. Upon cooling, silanized slides were immediately treated with 2mM solution of succinimidyl 4-[malemidophenyl]-butyrate (SMPB) in 4:1 ethanolDMSO. The slides were allowed to soak in the SMPB solution overnight, rinsed with ethanol and dried under N 2 .
  • SMPB succinimidyl 4-[malemidophenyl]-butyrate
  • the slides were subsequently immersed in 1 : 1 :4 acetic anhydride:pyridine:DMF for 2h, washed with water and dried under N 2 .
  • the SMPB- modified slides were then loaded into a robotic microarrayer (GMS 417, Genetic
  • the well was filled with a 0.3 M PBS buffer solution (0.3 M NaCl, 10 mM NaH 2 P0 4 /Na 2 HP0 4 > pH 7) made 10 nM in 50 nm diameter gold nanoparticles functionalized with oligonucleotide sequence a, 3.5 nM in 100 nm diameter gold nanoparticles functionalized with oligonucleotide sequence b, and 200 nM in oligonucleotide target(s) a'c' anal ⁇ b'd'.
  • the slide assembly was shaken for 2 h at room temperature, the hybridization well removed, and the a ⁇ ay washed three times with clean 0.15 M PBS buffer (0.15 M
  • Dolan-Jenner, Lawrence, MA set to 40% intensity and allowed to equilibrate for at least
  • Glass slides were first functionalized with either DNA sequence c or d over their entire surface by the method described above for DNA microarray fabrication, except that spotting of an array was replaced by immersion of the entire slide in lmM 3 '-thiol- modified capture oligonucleotide c or d.
  • model DNA arrays were prepared to evaluate the selectivity of the inventive scattering detection method described in Example 30.
  • An oligonucleotide array was first fabricated by spotting with the four thiol- modified oligonucleotide sequences shown in Figure 61B.
  • a 100 ⁇ L hybridization well as attached to the array and filled with a 0.3 M PBS buffer solution made 10 nM in oligonucleotide-functionalized 50 nm diameter gold nanoparticle probes and 200 nM in a 30-mer oligonucleotide target bearing an thymidine at position 8 (complementary to the chip sequence with X A, Figure 61B).
  • the slide assembly was shaken for 2 h at room temperature, the hybridization well removed, and the array washed three times with clean 0.15 M PBS buffer.
  • Arrays were prepared and incubated with 50 nm nanoparticle probes (10 nM in 0.3 M PBS) and oligonucleotide target as described above for the selectivity experiments, but with target concentrations varying from 1 ⁇ M down to 10 fM.
  • the slide assembly was shaken for 2 h at room temperature, the hybridization well removed, and the array washed three times with clean 0.15 M PBS buffer.
  • the data obtained is shown in Figure 67.
  • the lowest concentration that can be statistically distinguished from background (> 2 ⁇ ) is 1 pM.
  • the DNA a ⁇ ay imaging technique described in this Example and in Example 30 aboye based on scattered light from larger oligonucleotide-functionalized nanoparticles, provides the opportunity for sensitive, ultraselective, multicolor labeling of DNA arrays.
  • the method described will be extendable to additional colors using nanoparticles of different compositions and sizes [Link, S.; Wang, Z.L.; El-Sayed, M.A. J. Phys. Chem. B 1999, 103, 3529].
  • the use of particles with higher scattering coefficients may permit this system to rival the high sensitivity of the scanometric nanoparticle system 5 and waveguide-based fluorescence a ⁇ ays [Budach, W.;
  • Example 32 Assay-based electrical detection of DNA using nanoparticle probes and a salt-based stringency wash
  • a model DNA array was prepared to evaluate the unusual salt- dependence on the melting properties of the hybridized particles and the use of a salt- based stringency wash, in place of a thermal stringency wash, to differentiate binding events involving mismatached strands from ones based upon perfectly complementary recognition elements.
  • microelectrode preparation In a typical experiment, microelectrodes (60 nm Au on 5nm Ti) with 20 ⁇ m gaps were prepared by standard photolithography on a Si wafer with 1000 angstrom coating of Si0 2 ( Figure 68C). The exposed Si0 2 of the entire chip was modified with succinimidyl 4-[malemidophenyl]-butyrate (SMPB, Sigma Chemical, St. Louis, MO) using literature methodology (T. A. Taton, C. A. Mirkin, R. L. Letsinger, Science 289, 1757 (2000); L. A. Chrisey, G. U. Lee, C. E. O'Ferrall, Nucl. Acids Res. 24, 3031-3039 (1996)).
  • SMPB succinimidyl 4-[malemidophenyl]-butyrate
  • Capture oligonucleotide strands were immobilized onto the activated surface by spotting 0.3 M NaCl, 10 mM phosphate buffer (pH7) solutions (0.3 M PBS) of the appropriate alkylthiol-modified oligonucleotide (1 mM) in the electrode gaps by manual pipetting. All the oligonucleotides used in this study were prepared by automated solid phase syntheses (J. J. Storhoff, R. Elghanian, R. C Mucic, C. A. Mirkin, R. L. Letsinger, J. Am. Chem. Soc. 120, 1959-1964 (1998), F.
  • the chip was stored in a humidity chamber for 24 h allowing the coupling reaction between the SMPB and alkylthiol capped DNA to take place. The chip was then washed with water and immersed in 2% mercaptohexanol in ethanol for 2 h to passivate the chip, including the Au electrodes. Finally, the DNA- functionalized chip was washed with ethanol and water and then dried under a stream of N 2 .
  • the chip was treated with 0.3 M PBS solution of target DNA (10 nM) for 4 h, then rinsed with 0.3 M PBS solution. Thereafter, the chip was treated with a 0.3 M PBS solution of nanoparticle probes (2 nM) for 2 h.
  • the DNA chip was rinsed with 0.3 M NaN0 3 in 10 mM phosphate buffer (pH 7) to remove chloride ions and then treated with a silver enhancer solution (Sigma
  • the silver enhancer solution was replaced every 2 or 3 minutes to avoid the formation of silver particulate in solution.
  • the chip was rinsed with water, dried with N 2) and the resistance values across the electrode gaps were measured using a Fluke 189 multimeter (Fluke, Everett, WA).
  • the gaps with the four different oligonucleotide capture strands exhibit gap resistances larger than 500 M ⁇ , the limit of the multimeter used in the experiment, Figure 69A. In the absence of a stringency wash, the gap resistances decrease with increasing exposure to the silver enhancer solution.
  • the particles are complex materials and when considered on an individual basis, must have slightly different levels of oligonucleotide functionalization and, therefore, different activities with respect to their ability to promote the reduction of Ag + to Ag by hydroquinone.
  • target DNA In the absence of target DNA, there was no detectable signal even after 40 minutes of silver enchancing.
  • target at 500 fM concentration was detected without effort to optimize the system.
  • the detection limit of a conventional system based on fluorescence that utilizes a confocal microscope, these oligonucleotide strands, and a Cy3 -modified probe is -5 pM (T. A. Taton, C A. Mirkin, R. L. Letsinger, Science 289, 1757 (2000)).
  • a conventional way of increasing target selectivity is to wash a DNA chip array with a buffer solution at a temperature that results in the dehybridization of DNA. duplexes formed from noncomplementary strands (G. H. Keller, M. M. Manak, DNA Probes (Stocktonton Press, New York, 1989)). It was previously shown that other nanoparticle-based DNA detection methods exhibit unusually high specificity due to the sha ⁇ melting transitions associated with duplex structures formed from oligonucleotide- modified probes and complementary oligonucleotides. (T. A. Taton, C A. Mirkin, R. L. Letsinger, Science 289, 1757 (2000).
  • oligonucleotide-modified nanoparticles exhibit unusually sha ⁇ denaturation properties over salt concentration gradients, Figure 69C. Indeed, by examining the absorbance at 520 nm of two glass cuvettes functionalized with the complementary capture strand/target strand/probe complex and the capture strand with G-T mismatch/target/probe complex, respectively, as function of solution Na + concentration, the mismatched oligonucleotides can be easily differentiated from the complementary target. Significantly, one obtains better differentiation of the two strands using changes in salt concentration as opposed to changes in temperature, Figure 69C (inset).
  • this system is based upon conventional microelectrodes, it is useful for massive multiplexing through the use of larger arrays of electrode pairs than the four used in this Example.
  • the invention is useful for portable, point- of-site DNA detection method for single-nucleotide polymo ⁇ hism screening, and although the sensitivity of this system has not been fully optimized, it already is superior to the analogous fluorescence-based approach based on a confocal fluorescence microscope. By decreasing gap size, which will decrease the number of particles required to close the circuit, the sensitivity of this system should be dramatically improved.

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Abstract

L'invention concerne des procédés servant à détecter un acide nucléique. Ces procédés consistent à mettre en contact cet acide nucléique avec un ou plusieurs types de particules auxquelles sont fixés des oligonucléotides. Dans un mode de réalisation de ce procédé, les oligonucléotides sont liés à des nanoparticules et possèdent des séquences complémentaires de parties de la séquence de l'acide nucléique. L'hybridation des oligonucléotides sur les nanoparticules à l'acide nucléique provoque une modification pouvant être détectée (de préférence, une modification de couleur). Elle concerne également des compositions et des trousses contenant des particules. Elle concerne, de plus, des procédés de synthèse de conjugués uniques constitués par des nanoparticules et des oligonucléotides, les conjugués obtenus au moyen de ces procédés et des procédés de mise en application de ces conjugués. Elle concerne également des nanomatériaux et des nanostructures comprenant des nanoparticules, ainsi que des procédés de nanofabrication au moyen de ces nanoparticules. Elle concerne enfin un procédé de séparation d'un acide nucléique sélectionné d'autres acides nucléiques.
PCT/US2002/032088 2001-10-09 2002-10-08 Detection electrique d'adn basee sur un ensemble et mettant en application des sondes sous forme de nanoparticules WO2003035829A2 (fr)

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AU2002363062A AU2002363062B2 (en) 2001-10-09 2002-10-08 Nanoparticles having oligonucleotides attached thereto and uses therefor
JP2003538330A JP4347049B2 (ja) 2001-10-09 2002-10-08 オリゴヌクレオチドを付着させたナノ粒子とその使用方法

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