WO2011059453A1 - Methods for producing surface bound oligonucleotide on solid substrate and uses thereof - Google Patents

Methods for producing surface bound oligonucleotide on solid substrate and uses thereof Download PDF

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WO2011059453A1
WO2011059453A1 PCT/US2009/064556 US2009064556W WO2011059453A1 WO 2011059453 A1 WO2011059453 A1 WO 2011059453A1 US 2009064556 W US2009064556 W US 2009064556W WO 2011059453 A1 WO2011059453 A1 WO 2011059453A1
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oligonucleotide
method
ch
solid substrate
complex
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PCT/US2009/064556
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French (fr)
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Joon Won Park
Bong Jin Hong
Duk Hoe Kim
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Postech Academy-Industry Foundation
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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813Hybridisation assays
    • C12Q1/6834Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • CCHEMISTRY; METALLURGY
    • C40COMBINATORIAL CHEMISTRY
    • C40BCOMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES, IN SILICO LIBRARIES
    • C40B80/00Linkers or spacers specially adapted for combinatorial chemistry or libraries, e.g. traceless linkers or safety-catch linkers
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01QSCANNING-PROBE TECHNIQUES OR APPARATUS; APPLICATIONS OF SCANNING-PROBE TECHNIQUES, e.g. SCANNING PROBE MICROSCOPY [SPM]
    • G01Q60/00Particular types of SPM [Scanning Probe Microscopy] or microscopes; Essential components thereof
    • G01Q60/24AFM [Atomic Force Microscopy] or apparatus therefor, e.g. AFM probes
    • G01Q60/38Probes, their manufacture, or their related instrumentation, e.g. holders
    • G01Q60/42Functionalisation
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277Apparatus
    • B01J2219/00351Means for dispensing and evacuation of reagents
    • B01J2219/00387Applications using probes
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277Apparatus
    • B01J2219/00497Features relating to the solid phase supports
    • B01J2219/00504Pins
    • B01J2219/00509Microcolumns
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00277Apparatus
    • B01J2219/00497Features relating to the solid phase supports
    • B01J2219/00527Sheets
    • B01J2219/00529DNA chips
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583Features relative to the processes being carried out
    • B01J2219/00603Making arrays on substantially continuous surfaces
    • B01J2219/00605Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00608DNA chips
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583Features relative to the processes being carried out
    • B01J2219/00603Making arrays on substantially continuous surfaces
    • B01J2219/00605Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00612Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports the surface being inorganic
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583Features relative to the processes being carried out
    • B01J2219/00603Making arrays on substantially continuous surfaces
    • B01J2219/00605Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00614Delimitation of the attachment areas
    • B01J2219/00617Delimitation of the attachment areas by chemical means
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583Features relative to the processes being carried out
    • B01J2219/00603Making arrays on substantially continuous surfaces
    • B01J2219/00605Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00614Delimitation of the attachment areas
    • B01J2219/00621Delimitation of the attachment areas by physical means, e.g. trenches, raised areas
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583Features relative to the processes being carried out
    • B01J2219/00603Making arrays on substantially continuous surfaces
    • B01J2219/00605Making arrays on substantially continuous surfaces the compounds being directly bound or immobilised to solid supports
    • B01J2219/00623Immobilisation or binding
    • B01J2219/00626Covalent
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00583Features relative to the processes being carried out
    • B01J2219/00603Making arrays on substantially continuous surfaces
    • B01J2219/00653Making arrays on substantially continuous surfaces the compounds being bound to electrodes embedded in or on the solid supports
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01JCHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
    • B01J2219/00Chemical, physical or physico-chemical processes in general; Their relevant apparatus
    • B01J2219/00274Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
    • B01J2219/00718Type of compounds synthesised
    • B01J2219/0072Organic compounds
    • B01J2219/00722Nucleotides

Abstract

The present invention relates to methods for producing an oligonucleotide on a solid substrate surface and methods for using the same. Some aspects of the invention provide methods for selecting a single DNA molecule reproducibily with an atomic force microscope (AFM).

Description

METHODS FOR PRODUCING SURFACE BOUND OLIGONUCLEOTIDE ON SOLID SUBSTRATE AND USES THEREOF

FIELD OF THE INVENTION

[0001] The present invention relates to methods for producing an oligonucleotide on a solid substrate surface and methods for using the same.

BACKGROUND OF THE INVENTION

[0002] Many conventional biological assay methods use a probe that is attached to a solid substrate surface. Typically, these methods utilize a solid substrate in which a tailor- made probe is attached. In general, such methods require each solid substrate be fabricated with the desired probe. While such methods are suitable for instances where the probes are different, there are instances where different probes share a common feature. Conventional methods require that even in these instances, where many probes share a common feature, each probe must be independently fabricated and attached to a solid substrate. Such methods are analogous to a stepwise synthesis in organic chemistry, in which each piece of the molecule is made in a stepwise manner.

[0003] It is well known in organic chemistry that a convergent synthesis method typically yields a higher efficiency compared to a stepwise synthesis method. Furthermore, unlike a stepwise synthesis method, a convergent synthesis method allows an efficient synthesis of a wide variety of structurally related products from a common intermediate. Unfortunately, conventional methods for attaching a probe to a solid substrate surface often mimic a stepwise synthesis method in organic chemistry.

[0004] Therefore, there is a need for a method for attaching a probe to a solid substrate surface that is analogous to a convergent synthesis method in organic chemistry.

SUMMARY OF THE INVENTION

[0005] Some aspects of the invention provide methods for producing a surface bound oligonucleotide on a solid substrate in a manner analogous to a convergent synthesis method in organic chemistry. Typically, such methods of the invention attach separate portions of the oligonucleotide to the solid substrate using a template oligonucleotide and covalently link the unlinked oligonucleotides to produce a one-piece oligonucleotide probe. Often such methods comprise:

contacting a target oligonucleotide with a first oligonucleotide bound to a surface of a first solid substrate under conditions sufficient to produce a partially hybridized oligonucleotide complex, wherein the target oligonucleotide comprises an oligonucleotide sequence that is complementary to the first oligonucleotide sequence;

contacting a second oligonucleotide with the partially hybridized oligonucleotide complex under conditions sufficient to produce a segmented hybridized oligonucleotide complex, wherein the second oligonucleotide comprises an oligonucleotide sequence that is complementary to an unhybridized portion of the target oligonucleotide of the partially hybridized oligonucleotide complex; and

contacting the segmented hybridized oligonucleotide complex with a ligase under conditions sufficient to covalently link the first oligonucleotide and the second oligonucleotide to produce a surface bound oligonucleotide complex comprising a surface bound oligonucleotide which comprises a nucleotide sequence that is complementary to the nucleotide sequence of the target oligonucleotide.

[0006] In some embodiments, the step of contacting the target oligonucleotide with the first substrate surface comprises contacting the first oligonucleotide with the target oligonucleotide that is bound to a surface of a second solid substrate under conditions sufficient to hybridize the first oligonucleotide to a portion of the target oligonucleotide.

[0007] Yet in other embodiments, the second oligonucleotide further comprises an additional oligonucleotide such that the segmented hybridized oligonucleotide complex comprises at least a portion of the second oligonucleotide that is not hybridized to the target oligonucleotide. Within these embodiments, in some instances methods of the invention further comprise the step of ligating at least a portion of the second oligonucleotide that is not hybridized to the target oligonucleotide prior to said step of forming a covalent link between the first oligonucleotide and the second oligonucleotide.

[0008] Still in other embodiments, the first or the second oligonucleotide can also comprise a label. In this manner, the resulting surface bound oligonucleotide can be labeled for a particular application. Exemplary labels include, but are not limited to, fluorescent labels, radio active labels, labels that can change frequency of emission, metals such as gold, nanowires, nanotubes, nanoparticles as well as other types of labels known to one skilled in the art. Alternatively, or in addition, the first or the second oligonucleotide can comprise a ligand a receptor, or any other moiety that is useful for assaying. In this manner, the resulting oligonucleotide can include a tethered moiety that is useful in a wide variety of applications. [0009] In other embodiments, methods can further comprise a step of subjecting the surface bound oligonucleotide complex under conditions sufficient to remove the target oligonucleotide from the surface bound oligonucleotide complex to produce the first substrate surface bound oligonucleotide that comprises a complementary nucleotide sequence of the target oligonucleotide. As discussed in detail below, the oligonucleotide complex can include other components such as a protein or other peptide, a ligand or a receptor, and other molecules that are useful in various assays or detections.

[0010] In some embodiments, the first oligonucleotide is bound to the first substrate surface by a first linker. Within these embodiments, in some instances the first linker comprises a dendron. In some cases, the dendron is of the formula:

-Z-[Rl]m-Ql-{ [R2-Q2]a-{ (R3-Q3)b-[(R4-Q4)c-(R5-Y)x]y }z}n

I

where

each of m, a, b, and c is independently 0 or 1;

x is 1 when c is 0 or when c is 1, x is an integer from 1 to the oxidation state of Q4-l; y is 1 when b is 0 or when b is 1, y is an integer from 1 to the oxidation state of Q -1; z is 1 when a is 0 or when a is 1, z is an integer from 1 to the oxidation state of Q -1; n is an integer from 1 to the oxidation state of Qx-1;

Q1 is a central atom having the oxidation state of at least 3;

each of Q 2 , Q 3 and Q 4 is independently a branch atom having the oxidation state of at least 3;

each of R1, R2, R3, R4, and R5 is independently a linker;

Z is a functional group linked to the first oligonucleotide; and

each of Y is independently a functional group, wherein a plurality of Y are attached to the first solid substrate surface,

provided the product of n, x, y, and z is at least 3. In some particular embodiments, Z comprises a heteroatom selected from the group consisting of N, O, S, P, and a combination thereof. It should be appreciated that typically Z does not include what one skilled in the art of organic chemistry to be an unstable functional group such as peroxides, -O-S- linkage, etc. In some instances Z comprises a functional group selected from the group consisting of -NR-C(=X) -0-, -0-C(=X) -0-, -NR-C(=X) -, -0-C(=X) -, wherein X is N, O, or S, and R is hydrogen, alkyl, cycloalkyl, aralkyl, aryl, or (cycloalkyl)alkyl.

[0011] In some embodiments, each of R1, R2, R3, R4, and R5 is independently a linker comprising 4 to 20 linker chain atoms, wherein each linker chain atom is independently selected from the group consisting of C, O, N, S, and P. Typically, the linker does not include what one skilled in the art of organic chemistry to be an unstable functional group such as peroxides, -O-S- linkage, etc. In some instances, the linker comprises a carbon atom chain with a functional group that allows a linkage to respective Q moiety. For example, the linker can include a functional group similar to those described for Z. Still in other instances, the linker can include in the chain an oxygen atom (e.g., an ether linkage), a nitrogen atom (e.g., an amino linkage), a sulfur atom (e.g., a thioether linkage), etc.

[0012] Methods of the invention can be used to attach oligonucleotides to any suitable solid substrates known to one skilled in the art including, but not limited to, glass, porous solids, silicon wafers, metals, ceramics, alloys, polymers, etc. Moreover, methods of the invention are applicable to porous solids as well as non-porous solids. In some embodiments, the first solid substrate is an atomic force microscope tip. In some instances, methods of the invention are used to attach 5 or less, typically 3 or less, and often a single surface bound oligonucleotide. Methods of the invention typically produce an oligonucleotide which comprises a nucleotide sequence that is complementary to the nucleotide sequence of the target oligonucleotide.

[0013] Yet in other embodiments, the first oligonucleotide comprises at least 10, typically at least 20, often at least 30, and more often at least 50 oligonucleotide sequence. Still in other embodiments, the second oligonucleotide comprises at least 10, typically at least 20, often at least 30, and more often at least 50 oligonucleotide sequence.

[0014] Other aspects of the invention provide methods for attaching a single- stranded oligonucleotide on a first solid substrate surface. Typically, such methods comprise:

contacting a single- stranded target oligonucleotide with a first single-stranded

oligonucleotide bound to a surface of a first solid substrate under conditions sufficient to produce a first hybridized partially double- stranded oligonucleotide complex, wherein the target oligonucleotide comprises a nucleotide sequence that is complementary to the nucleotide sequence of the first single stranded oligonucleotide;

contacting a second oligonucleotide with the first hybridized partially double-stranded oligonucleotide complex under conditions sufficient to produce a segmented hybridized double-stranded oligonucleotide complex, wherein the second oligonucleotide comprises a nucleotide sequence that is complementary to an unhybridized portion of the target oligonucleotide of the first hybridized partially double-stranded oligonucleotide complex; contacting the segmented hybridized double- stranded oligonucleotide complex with a ligase under conditions sufficient to covalently link the first oligonucleotide and the second oligonucleotide to produce a first solid substrate surface bound double-stranded oligonucleotide complex comprising a nucleotide sequence that is complementary to the nucleotide sequence of the target oligonucleotide; and

subjecting the first solid substrate surface bound double-stranded oligonucleotide complex to conditions sufficient to denature the first solid substrate surface bound double- stranded oligonucleotide complex to produce a first solid substrate surface bound single- stranded oligonucleotide, wherein the first solid substrate surface bound single- stranded oligonucleotide comprises nucleotide sequence that is complementary to the nucleotide sequence of the target oligonucleotide.

[0015] Still other aspects of the invention provide methods for determining the presence of a particular oligonucleotide in a sample. Such methods typically utilize a probe oligonucleotide that comprises a single-stranded oligonucleotide bound to the solid substrate surface produced by a method described herein. Typically, methods for determining the presence of a particular oligonucleotide in a sample comprise:

contacting the sample with a probe oligonucleotide bound to a solid substrate surface under conditions sufficient to produce a probe-ligand hybridized complex when the sample comprises a particular oligonucleotide having a nucleotide sequence that is complementary to the nucleotide sequence of the probe oligonucleotide, wherein the probe oligonucleotide comprises a single- stranded oligonucleotide bound to the solid substrate surface produced by a method described herein; and

determining the presence of the probe-ligand hybridized complex on the solid

substrate surface,

wherein the presence of the probe-ligand hybridized complex on the solid substrate surface is indication that the particular oligonucleotide is present in the sample.

[0016] In some embodiments, the first solid substrate is an atomic force microscope tip. In some instances, the atomic force microscope tip comprises a single surface bound oligonucleotide probe. BRIEF DESCRIPTION OF THE DRAWINGS

[0017] Figure 1A is a schematic illustration of picking a single target DNA molecule with AuNP AFM. For clarity, DNA molecules at the center are enlarged.

[0018] Figure IB is a DNA sequence used for the picking a single DNA molecule illustrated in Figure 1A

[0019] Figure 1C shows structures of the 9-acid and 27-acid.

[0020] Figure 2 shows transmission electron microscopy (TEM) images of the AFM tips after picking. Images taken after picking a DNA- AuNP conjugate from the substrate (inset scale bars, 10 nm). In some cases, the AuNP was very close to the top of the tip (left image), but more frequently the AuNP was away from the top (right image). The right schematic diagram illustrates the position of the AuNP.

[0021] Figure 3A shows a schematic diagram showing hybridization with the picked single DNA. For visualization, a DNA- AuNP conjugate was also employed.

[0022] Figure 3B shows a TEM image of the resulting AFM tip of Figure 3A (inset scale bar, 10 nm).

[0023] Figure 3C is a DNA sequence used for post-modification of AFM tip of Figure

3A.

[0024] Figure 4 is a schematic illustration of processes for preparing an AFM tip having a single DNA conjugated with the DNA at the apex. After picking the target DNA, hybridization with a new DNA, ligation, and washing were followed. A single copy of new DNA was introduced only at the apex of the AFM tip.

[0025] Figure 5 A (SI A) is a schematic diagram illustrating how to generate the dendron-modified substrate and AFM tip, and how to conjugate a DNA probe molecule to the dendron apex.

[0026] Figure 5B is a schematic diagram showing treatment with APDES and the subsequent steps for the control experiments.

[0027] Figure 6A is a gel image of the AuNP-DNA conjugate mixture. The phosphine-capped AuNPs were injected into column 1, and the various products were separated in column 2.

[0028] Figure 6B is a gel image after conjugating the DNAs for the second hybridization with AuNPs. Reference materials were injected at column 1, and various isomers were separated in column 2.

[0029] Figure 6C is a diagram showing the matching part of DNA used for the second hybridization. [0030] Figure 7 is TEM images of additional AFM tips capturing a single target DNA molecule (inset scale bars, 10 nm). Picking was performed with five cycles at five different spots.

[0031] Figure 8 is TEM images of AFM tips from the control experiments (inset scale bars, 10 nm).

[0032] Figure 9 is TEM images of an AFM tip before and after flipping around the x- axis (inset scale bars, 10 nm). After getting a TEM image of a tip, the tip was rotated 180° around the x-axis. A single AuNP was observed in both cases, and the position of the AuNP after flipping matched expectations.

[0033] Figure 10 is TEM images of an AFM tip in an experiment to determine influence of a relatively fast tip velocity on capturing a single target DNA molecule. The tip velocity was fixed at 10 μιη/s, and the z-range was set to 5 μιη. Five cycles were allowed at five different spots (a total of 25 cycles), and out of nine cases four tips had a single AuNP (inset scale bars, 10 nm).

[0034] Figure 11 is TEM images of an AFM tip in an experiment to determine influence of a relatively slow tip velocity on capturing a single target DNA molecule. The tip velocity was fixed at 0.01 μιη/s, and the z-range was set to 100 nm. Five cycles were allowed at five different spots (a total of 25 cycles), and out of nine cases two tips had a single AuNP (inset scale bars, 10 nm).

[0035] Figure 12 is TEM images of an AFM tip in an experiment to determine the influence of a larger tip radius on capturing a single target DNA molecule. The tip velocity was fixed at 0.2 μητ/s, and the z-range was set to 500 nm. Five cycles were allowed at five different spots (a total of 25 cycles). While the yield was comparable, the tip picked either a single DNA (as in the left two images) or two DNAs (as in the right side image) (inset scale bars, 10 nm).

[0036] Figure 13A is a histogram of unbinding force values recorded at a loading rate of 0.54 μιη sec-1 for interactions between the 20-mer DNA on the AFM tip and the complementary DNA immobilized on the commercially available aldehyde-terminated slide.

[0037] Figure 13 B shows representative force-extension curves for interactions between the 20-mer DNA on the AFM tip and the complementary DNA immobilized on the commercially available aldehyde-terminated slide. DETAILED DESCRIPTION OF THE INVENTION

[0038] Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art to which this invention belongs. The following references provide one of skill with a general definition of many of the terms used in this invention: Singleton et al, DICTIONARY OF MICROBIOLOGY AND MOLECULAR BIOLOGY (2d ed. 1994); THE CAMBRIDGE DICTIONARY OF SCIENCE AND TECHNOLOGY (Walker ed., 1988); THE GLOSSARY OF GENETICS, 5TH ED., R. Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, THE

HARPER COLLINS DICTIONARY OF BIOLOGY (1991).

[0039] The term "dendrimer" refers to a repeatedly branched molecules. Typically a dendrimer is characterized by a core, at least one interior branched layer, and a surface branched layer (see, e.g., Petar et al. in Chem. in Britain, pp. 641-645, August 1994). A "dendron" is a species of dendrimer having branches emanating from a focal point or a central atom, which is or can be joined to a core, either directly or through a linking moiety to form a dendrimer. Dendrimer can comprise two or more dendrons joined to a common core. Dendrons include, but are not limited to, symmetrical and asymmetrical branching dendrimers, cascade molecules, arborols, and the like. Each branch arm of the dendrimer and dendron can be of equal or different in length.

[0040] As used herein, the terms "nucleotide" and "nucleic acid" are used

interchangeably herein and refer to both natural and synthetic nucleotide molecules that can be used in place of naturally occurring bases in nucleic acid synthesis and processing, e.g., enzymatic as well as chemical synthesis and processing. Thus, nucleotide includes modified nucleotides capable of base pairing and optionally synthetic bases that do not comprise adenine, guanine, cytosine, thymidine, uracil or minor bases. For example, "nucleotide" includes, but is not limited to, modified purines and pyrimidines, minor bases, convertible nucleosides, structural analogs of purines and pyrimidines, labeled, derivatized and modified nucleosides and nucleotides, conjugated nucleosides and nucleotides, sequence modifiers, terminus modifiers, spacer modifiers, and nucleotides with backbone modifications, including, but not limited to, ribose-modified nucleotides, phosphoramidates,

phosphorothioates, phosphonamidites, methyl phosphonates, methyl phosphoramidites, methyl phosphonamidites, 5'-P-cyanoethyl phosphoramidites, methylenephosphonates, phosphorodithioates, peptide nucleic acids, achiral and neutral internucleotidic linkages and nonnucleotide bridges such as polyethylene glycol, aromatic polyamides and lipids. In addition, a nucleotide can be a deoxyribonucleotide or ribonucleotide polymer in either single- or double- stranded form, and unless otherwise limited, encompasses known analogs of natural nucleotides that hybridize to nucleic acids in a manner similar to naturally- occurring nucleotides. A "subsequence" or "segment" refers to a sequence of nucleotides that comprise a part of a longer sequence of nucleotides.

[0041] The term "oligonucleotide" refers to a nucleic acid polymer comprising at least two, typically at least five, often at least ten, and more often at least twenty nucleotides. Typically, an oligonucleotide comprises from two to about one thousand nucleotides, often two to about five hundred nucleotides, and more often two to about three hundred

nucleotides.

[0042] As used herein, the terms "solid support" and "solid substrate" are used interchangeably herein and refer to a composition comprising an immobilization matrix such as but not limited to: insolubilized substances; woven or nonwoven fibers; crystals;

membranes; insoluble polymers; plastics; glass; beads; biological or biocompatible or bioerodible or biodegradable polymers or matrix; microparticles; nanoparticles;

semiconductor materials; synthetic (e.g., organic) metals; synthetic semiconductors; metals; alloys; elements; compounds; minerals; synthetic, cleaved, etched, lithographed, printed, machined and microfabricated slides, devices, structures and surfaces; silicon; silicates; ceramics; wood; paper; cardboard; cotton; wool; cloth; woven and nonwoven materials and fabrics; resins; chromatography supports; mica; microspheres; and nanospheres.

Microstructures and nano structures can include, without limitation, microminiaturized, nanometer- scale and supramolecular probes, tips, bars, pegs, plugs, rods, sleeves, wires, filaments, and tubes.

[0043] Unless the context requires otherwise, the term "ligand" refers to any substance that is capable of binding selectively with a probe. A ligand can be an antigen, an antibody, an oligonucleotide, an oligopeptide (including proteins, hormone, etc.), an enzyme, a substrate, a drug, a drug-receptor, cell surface, receptor agonists, partial agonists, mixed agonists, antagonists, response-inducing or stimulus molecules, drugs, hormones, pheromones, transmitters, autacoids, growth factors, cytokines, prosthetic groups, coenzymes, cofactors, substrates, precursors, vitamins, toxins, regulatory factors, antigens, haptens, carbohydrates, molecular mimics, structural molecules, effector molecules, selectable molecules, biotin, digoxigenin, crossreactants, analogs, competitors or derivatives of these molecules as well as library- selected nonoligonucleotide molecules capable of specifically binding to selected targets and conjugates formed by attaching any of these molecules to a second molecule, and any other molecule that binds selectively with a corresponding probe.

[0044] It should be appreciated that the terms "ligand" and "receptor" do not refer to any particular substance or size relationship. These terms are only operational terms that indicate selective binding between the ligand and the corresponding probe where the moiety that is bound to a substrate surface is referred to as a probe and any substance that selectively binds to the probe is referred to as a ligand. Thus, if an antibody is attached to the substrate surface then the antibody is a probe and the corresponding antigen is a ligand. However, if an antigen is attached to the substrate surface then the antigen is a probe and the

corresponding antibody is a ligand.

[0045] The term "complementary" means that one nucleic acid is identical to, or hybridizes selectively to another nucleic acid molecule. Selectivity of hybridization exists when hybridization occurs that is more selective than total lack of specificity. Typically, selective hybridization will occur when there is at least about 55% identity over a stretch of at least 14-25 nucleotides, typically at least 65%, often at least 75%, and more often at least 90%.

[0046] The terms "identical" or percent "identity," in the context of two or more nucleic acids, refer to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides that are the same, when compared and aligned for maximum correspondence, as measured using a sequence comparison algorithm such as those described below for example, or by visual inspection.

[0047] The phrase "substantially identical," in the context of two nucleic acids, refers to two or more sequences or subsequences that have at least 75%, typically at least 80% or 85%, often at least 90%, 95% or higher nucleotide identity, when compared and aligned for maximum correspondence, as measured using a sequence comparison algorithm such as those described below for example, or by visual inspection. Generally, the substantial identity exists over a region of the sequences that is at least about 40-60 nucleotides in length, in other instances over a region at least 60-80 nucleotides in length, in still other instances at least 90- 100 nucleotides in length, and in yet other instances the sequences are substantially identical over the full length of the sequences being compared, such as the coding region of a nucleotide for example.

Atomic Force Microscope

[0048] The present invention will be described with regard to immobilizing an oligonucleotide on an Atomic Force Microscope (AFM) tip. However, it should be appreciated that methods of the invention described herein are not limited to attaching oligonucleotide to an AFM tip but rather is generally applicable to attaching a wide number of oligonucleotides to any solid substrate surface.

[0049] Initially, Atomic Force Microscope (AFM) was developed for the observation of solid surface topography. Currently, AFM is used in a wide range of applications including, but not limited to, measuring interactions between biomolecules such as in drug screening. Ability to measure the interaction between biomolecules is a powerful analytical tool that allows identification of various association and dissociation phenomena between biomolecules. For example, AFM is sometimes used to find the position and distribution of a specific ligand on the cell surface. While fluorescence microscope and radioisotope have been used to identify the distribution of ligands on the cell surface, these methods can only show distribution of tens to hundreds of conglomerated ligands in the micron-sized scale. In contrast, measurement of interacting forces between biomolecules with AFM provides more accurate and detailed analysis allowing a possibility of tracking individual position of the nano-sized ligands and observation of individual life phenomena.

[0050] Unfortunately, conventional methods of immobilizing biomolecules onto the

AFM tip typically result in having biomolecules being attached not only on or near the apex of the tip but on various AFM tip locations, thus leading to a relatively low resolution of AFM. To overcome such a limitation, some have used high dilution methods or mixed monolayer methods when introducing the biomolecules onto the AFM tip. Although these methods reduce the relative population density of biomolecules immobilized on the AFM tip, they have not been successful in effectively immobilizing the biomolecules specifically on the apex of the AFM tip and in many instances the biomolecules could not be immobilized on the apex of the AFM tip.

[0051] Besides aforementioned studies on the measurement of interaction between biomolecules by means of AFM, other applications of the AFM have recently been attempted. For example, currently some have attempted to introduce compounds like carbon nanotubes or nanoparticles onto the apex of the AFM tip. But currently available methods are not adapted for selectively modifying the apex of the AFM tip.

[0052] Methods of the invention allow attaching a wide number of oligonucleotides to any solid substrate surface including, but not limited to, on or near the apex of the AFM tip. When applied to attaching oligonucleotides to an AFM tip, methods of the invention can be used to attach five or less, typically three or less, and often a single oligonucleotide molecule on the AFM tip. Moreover, methods of the invention can be used to attach an oligonucleotide near, often at, the apex of AFM tip.

[0053] Single-molecule force spectroscopy has revealed valuable information about the physicochemical properties of individual molecules. In particular, AFM is an important tool because it can sense pN-scale forces, and generate high resolution images of solid surfaces and biological samples, including cells. Additionally, the instrument can be used as a nanomachine to pick up and transport a single molecule to a specific position. For example, using single-molecule fluorescence microscopy, some have shown that AFM could pick a single DNA strand from a depot area and deposit it onto a target area. While the tool has been employed widely, one common challenge is realizing the single molecular interaction while avoiding multimolecular interactions. In the above mentioned DNA transport, it is believed that the AFM tip recognized the single DNA-DNA interaction with about 35% success rate, and the tip was treated at the "trash can" area when multiple DNAs were captured. While carbon nanotube tips have found numerous applications, especially in topographical imaging, double interactions have been observed in some cases. Therefore, the tethering of a single molecule to the apex of an AFM tip is expected to eliminate the common difficulties and to extend the application of this nano-tool.

[0054] The present inventors have previously discovered that the dendron-modified

AFM tip enabled reproducible observation of the binding phenomenon and single peaks in the force-distance curve. This modified AFM tip was used to selectively hybridize a single DNA molecule, and obtained transmission electron microscopy (TEM) images for

visualization. As schematically illustrated in Figure 1, a picker DNA (40-mer) was immobilized on the dendron-modified AFM tip. A probe DNA (35-mer) immobilized on the dendron-modified substrate was hybridized with a target DNA (63-mer) that had a gold nanoparticle at its 5 '-end. A cycle comprising of the approach and the subsequent retraction was expected to transfer the target DNA from the substrate to the tip due to a larger (i.e., stronger) interaction force between the picker DNA and the target DNA.

[0055] Each substrate and AFM tip was treated with N-(3-(triethoxysilyl)propyl)-0- polyethyleneoxide urethane as the first step of the modification. Then, a dendron was introduced on the silylated surface by self-assembly (see Figures 5A and 5B). After introduction of the dendron layer, the DNAs were covalently attached to the dendron apex. The upper 20-bp of the probe DNA were designed to capture the target DNA, and 15-bp of cytosine were added to provide more flexibility and extra space for the gold nanoparticle tethered to the target DNA (Figure IB). Part of the 63-bp target DNA was designed to hybridize with the probe DNA; the other longer part was complementary to the 40-bp picker DNA on the AFM tip. The present inventors have discovered that use of a 9-carboxylic acid terminated dendron is useful for studying DNA-DNA interactions. The present inventors have also discovered that a 27-carboxylic acid terminated dendron is useful for mapping purposes. As discussed in the Example section, AFM tips coated with either 9- or 27-acid were used to investigate the effect of the lateral spacing on the picking. The target DNA was conjugated with a commercially available 5 nm gold nanoparticle (AuNP). To avoid possible complications, particles with one target DNA molecule were isolated through 3% agarose gel electrophoresis (see Figures 6A-C).

[0056] Transmission electron microscopy (TEM) images of 9-acid modified AFM tips and substrates were taken after picking. Two out of the eleven tips had an AuNP at the top when a single cycle of approach and retraction was performed, while one tip had two AuNPs. Five cycles were allowed to increase the success yield, and resulted in three tips with a single AuNP and one tip with two AuNPs out of 9 cases. When five cycles were performed at five different spots (for a total of 25 cycles), further increases in the yield (seven tips with a single AuNP out of 16 cases) were realized, and three tips with two AuNPs and one tip with four AuNPs were observed.

[0057] To identify a condition eliminating or reducing the probability of picking multiple AuNPs, tips and substrates coated with a larger dendron, i.e., 27-carboxylic acid terminated dendon, were employed. Various picking cycles were examined, and tips with multiple AuNPs were not observed. With five cycles at a spot, five out of the 10 tips showed a single AuNP. This yield was increased to 75% (12 out of 16) when the picking was performed with the five cycles at five different spots (see Figure 7). Picking at ten different spots (a total of 50 cycles) also showed a yield of 75% (9/12). While the yield was similar to the former cases (4/9 and 10/16), it was surprising and unexpected that picking multiple DNAs was avoidable with the use of the larger dendron. The observed distance between the AuNP and the top of the tip was about 34 nm or less. Because the DNA could acquire arbitrary conformations in the drying and evacuation steps, and since the maximal distance should be within the combined length of the stretched DNA and the linkers, the observed variation seems reasonable (Figure 2). As control experiments, pickings were performed with aminosilylated tips and substrates; the TEM showed that more than 3 AuNPs were picked at the above optimized condition (see Figure 8).

[0058] Influence of the tip velocity as well as the tip radius to the picking efficiency was also examined. It was observed that a fast (e.g., 10 μιη/s) and a slow tip velocity (e.g., 0.01 μιη/s) reduced the picking yield to 44 % and 22 %, respectively (see Figures 10 and 11). Without being bound by any theory, it is believed that the shortened contact time and the reduced force value difference may be responsible for these observations. TEM images showed that in instances where AFM tips were broad (or dull), picking that produced attachment had either a single AuNP or two AuNPs (see Figure 12). The examination showed that the approach enabled typical AFM tips to pick a single DNA, while there is a chance to pick more than single DNA when the tip radius was unusually large.

[0059] The single strand part of the picked target DNA was utilized for the subsequent chemical conversion (Figure 3). In order to demonstrate a single molecule chemistry with the single DNA picked by AFM, a 50-bp DNA that had a tethered AuNP at its 5'-end and complementary to 20-bp of the target DNA was allowed to hybridize. TEM showed that the AFM tip had two AuNPs near the top, and the distance between them (ca. 10 nm) was within the expected range. The image confirmed the identity of the target DNA picked by the above manipulation and the binding mode between the picker and target DNAs.

[0060] In some embodiments, a second hybridization is applied to covalently conjugate a new single molecule at the apex (see Figure 4). After picking the target DNA, a 20-mer DNA of which sequence is complementary to the single strand part of the target DNA was allowed to hybridize. Through the ligation process, 5'-end of the 20-mer and 3'-end of the picker DNA were covalently linked. Stringent washing removed the target DNA from the tip. To confirm the single presence of the 20-mer DNA at the apex, the force between the tip and a substrate immobilizing the complementary DNA was measured. For this end, commercially available generic aldehyde slides were employed for the substrates, and only single rupture events were expected even with the less controlled substrates. The force- extension curves with a single peak were obtained (see Figure 13). Gaussian fitting gave the probable rupture force of 23 + 1 pN. Such a process can be used to link a single copy of various molecules at the apex of AFM tips as long as the molecules of interest can be conjugated with oligomeric DNA independently.

[0061] Dendron surface modification of the tips and substrates allows the AFM to pick a single DNA reproducibly. The successful conjugation of a new DNA at the apex of the tip through the specific hybridization and the subsequent ligation provide a novel approach for introducing a single copy of various molecules at the tip.

Linker [0062] As stated herein, the present inventors have discovered that using a dendron as a linker allows a sufficient spacing to attach five or less, typically three or less, and often a single oligonucleotide on an AFM tip. Suitable dendrons comprise a plurality of functional groups (i.e., substrate bound functional groups) that are used to attach the dendron to a solid substrate surface and a linker functional group (i.e., oligonucleotide bound functional group) that is used to attach an oligonucleotide moiety. Generally, useful dendrons comprise at least nine, typically at least eighteen, often twenty seven substrate bound functional groups.

Suitable substrate bound functional groups include, but are not limited to, carboxylates, amines, hydroxyl groups, thiol groups, carbamides, and other suitable functional groups well known to one skilled in the art.

[0063] In many instances, the linker is of the formula:

Figure imgf000016_0001

I

wherein

each of m, a, b, and c is independently 0 or 1;

x is 1 when c is 0 or when c is 1, x is an integer from 1 to the oxidation state of Q4-l; y is 1 when b is 0 or when b is 1, y is an integer from 1 to the oxidation state of Q -1; z is 1 when a is 0 or when a is 1, z is an integer from 1 to the oxidation state of Q -1; n is an integer from 1 to the oxidation state of Qx-1;

Q1 is a central atom having the oxidation state of at least 3;

each of Q 2 , Q 3 and Q 4 is independently a branch atom having the oxidation state of at least 3;

each of R1, R2, R3, R4, and R5 is independently a linker;

Z is the functional group that is attached to an oligonucleotide; and

each of Y is independently a substrate bound functional group,

provided the product of n, x, y, and z is at least 3.

[0064] It should be appreciated that when a, b or c is 1 and the corresponding z, y or x is less than the oxidation state of Q 2-l, Q 3-l or Q 4-l, respectively, the remaining atoms attached to Q 2 , Q 3 , or Q 4 , respectively, is hydrogen. As used herein, "Q" refers to any one of or all of Q1, Q2, Q3, Q4. Typically, Q is any atom in group IVA or VA of the periodic table. Exemplary atoms for Q include, but are not limited to, N, P, C, Si, Ge, and the like. Often, Q is N, P, C, or Si. [0065] As can be seen in Formula I, Z is attached to the central atom optionally through a linker R1. Often a is 1 such that Z is attached to the central atom through a linker R1.

[0066] Yet in other embodiments, Z comprises a heteroatom selected from the group consisting of N, O, S, P, and a combination thereof.

[0067] Each Y can be independently a substrate bound function group. That is, each

Y can be independent of the other Y group. Often, however, all of the Y's are the same functional group. However, in general Z and Y are different functional groups. In some instances, Z and Y can be the same functional group, but one or the other is in a protected form. Such differences in functional group and/or the presence of a protecting group allow one to distinguish the reactivity of Z and Y, thereby allowing one to attach the dendron to the solid support via a plurality of Y's and allows attachment of an oligonucleotide on Z.

[0068] Each of linkers R1, R2, R3, R4, and R5 can be the same or different. As used herein, when "R" is used to denote a linker generically, it can refer to R1, R2, R3, R4, R5, or any combination thereof. Typically, each linker is a repeating unit, a linear or branched organic moiety. However, it is also understood that not all the linkers need to be the same repeating unit. Nor do all valence positions for a linker need be filled with a repeating unit.

For example, all of the R 2 can be the same repeating units. Or one or two of the R 2 may be a repeating unit, and the remaining R 's may be H or other chemical entities. Likewise, one or two of each of R3, R4, or R5 may be, independently, a repeating unit, H or any other chemical entity. Thus, a variety of polymers are within the scope of the invention. Accordingly, it is possible that a dendron can have from about 3 to about 81 Y functional groups. Generally, the dendron has from about 6 to about 81 Y functional groups, typically from about 6 to about 54 Y functional groups, often from about 6 to about 27 Y functional groups, and more often from about 9 to about 27 Y functional groups.

[0069] Table 1 below lists various types of exemplified dendrons. However, it is to be understood that variations in Za, R1, Q, R and Ya are encompassed by the present invention. It should be noted that in Table 1, the term Za refers to a protected form of oligonucleotide bound functional group and Ya refers to a substrate bound functional group prior to being bound to the solid substrate surface. Accordingly, in some instances Za and /or Ya need to be deprotected prior to being bound to an oligonucleotide and the solid substrate surface, respectively.

Table 1 - Representative and Exemplified Macromolecule Compounds

Figure imgf000017_0001
A-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OH

A-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OMe

Boc-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OH

Boc-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OMe

A-NH- -(CH2CH20)2CH2C(0)NH C CH20(CH2)2C(0) OH

A-NH- -(CH2CH20)2CH2C(0)NH C CH20(CH2)2C(0) OMe

A-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OH

Boc-NH- -(cyclohexyl)(CO)CH2 C (CH2)2-(cyclohexyl)-C(0) NH2

Boc-NH- -(CH2CH20)2CH2C(0)NH C CH20(CH2)2C(0) OH

Fmoc-NH- -(CH2)6NHC(0)NH C CH2-C=C-CH2C(0) OH

Fmoc-NH- -(CH2)7C(0)0 C CH2-C=C-CH2C(0) OMe

Ns-NH- -(cyclohexyl)(CO)0 C CH20(CH2)2C(0) NH2

Ns-NH- -(CH2)6NHC(0)NH C (CH2)7 NH2

A-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OH

Boc-NH- -(CH2)7C(0)NH C (CH2)2C(0) OH

Ns-NH- -(CH2)6 (CO)NH C (CH2)2-(cyclohexyl)-C(0) OH

Fmoc-NH- -(CH2)6 (CO)O C CH2-C=C-CH2C(0) NH2

Fmoc-NH- -(CH2)6NH(CO)0 C (CH2)2-(cyclohexyl)-C(0) OH

Ns-NH- -(cyclohexyl)(CO)0 C CH2OCH(CH3)CH2C(0) NH2

Boc-NH- -(cyclopropyl)(CO)0 C CH2-C=C-CH2C(0) NH2

A-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OH

A-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OMe

A-NH- -(CH2CH20)2CH2C(0)NH C CH20(CH2)2C(0) OH

A-NH- -(CH2CH20)2CH2C(0)NH C CH20(CH2)2C(0) OMe

Fmoc-NH- -(CH2)6C(0)NH C CH20(CH2)2C(0) OH

Fmoc-NH- -(CH2)6C(0)NH C CH20(CH2)2C(0) OMe

Boc-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OH

Boc-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OMe

Ns-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OH

Ns-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OMe

A-NH- -(CH2)6NHC(0)CH2CH2 C (CH2)7 OBzl

A-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OH

Fmoc-NH- -(CH2)6NHC(0)NH C (CH2)2-(cyclohexyl)-C(0) NH2

Boc-NH- -(cyclohexyl)(CO)0 C CH2-C=C-CH2C(0) OMe

Boc-NH- -(CH2)5NH C CH2OCH(CH3)CH2C(0) NH2

Ns-NH- -(cyclopropyl)(CO)CH2 C (CH2)2 NH2

Ns-NH- -(CH2)6C(0)0 C CH2OCH2CH(CH3)C(0) NH2

Fmoc-NH- -(CH2)6NHC(0)0 C CH2OCH(CH3)CH2C(0) NH2

Boc-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) NH2

Boc-NH- -(cyclohexyl)(CO)CH2 C (CH2)2-(cyclohexyl)-C(0) OH

Fmoc-NH- -(CH2CH20)2CH2C(0)0 C CH20(CH2)2C(0) OH

Fmoc-NH- -(CH2)6NHC(0)NH C (CH2)2-(cyclohexyl)-C(0) NH2

Ns-NH- -(cyclohexyl)(CO)NH C CH2-C=C-CH2C(0) OH

Ns-NH- -(cyclopropyl)(CO)CH2 C CH20(CH2)2C(0) OMe

A-NH- -(cyclopropyl)(CO)CH2 C CH2OCH(CH3)CH2C(0) OH

A-NH- -(cyclopropyl)(CO)CH2 C CH2OCH2CH(CH3)C(0) NH2 A-NH- -(CH2)50 C CH2OCH2CH(CH3)C(0) OH

A-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OH

Fmoc-NH- -(cyclohexyl)(CO)0 C CH2OCH(CH3)CH2C(0) NH2

Boc-NH- -(cyclopropyl)(CO)0 C CH2OCH2CH(CH3)C(0) NH2

Fmoc-NH- -(CH2)6NHC(0)CH2NH C (CH2)2-(cyclohexyl)-C(0) OH

Ns-NH- -(CH2)6NHC(0)CH2 C CH2-C=C-CH2C(0) OMe

Boc-NH- -(CH2)50 C CH2OCH2CH(CH3)C(0) NH2

A-NH- -(CH2)3C(0)NH C CH20(CH2)2C(0) OH

A-NH- -(CH2)6NHC(0)CH2CH2 C (CH2)7 OH

Fmoc-NH- -(CH2CH20)2CH2C(0)0 C (CH2)2-(cyclohexyl)-C(0) NH2

Ns-NH- -(cyclopropyl)(CO)NH C (CH2)2-(cyclohexyl)-C(0) NH2

Boc-NH- -(cyclohexyl)(CO)CH2 C CH2OCH(CH3)CH2C(0) OMe

Fmoc-NH- -(CH2)50 C CH2OCH2CH(CH3)C(0) NH2 where A = anthracenemethyl, Fmoc = 9-fluorenylmethyloxycarbonyl, Boc = tert- butoxycarbonyl, and Ns = 2-nitrophenylsulfonyl.

[0070] Additional objects, advantages, and novel features of this invention will become apparent to those skilled in the art upon examination of the following examples thereof, which are not intended to be limiting. In the Examples, procedures that are constructively reduced to practice are described in the present tense, and procedures that have been carried out in the laboratory are set forth in the past tense.

EXAMPLES

General Methods

[0071] The silane coupling agent N-(3-(triethoxysilyl)propyl)-0-polyethyleneoxide urethane was purchased from Gelest (Morrisville, Pennsylvania, USA). All other chemicals, including a 5-nm AuNP colloid solution, are of reagent grade purchased from Sigma- Aldrich (St Louis, MO). UV-grade fused silica plates were purchased from CVI Laser. Polished Si (100) wafers (dopant: phosphorus; resistivity: 1.5-2.1 -cm) were purchased from MEMC Electronic Materials (St. Peters, Missouri, USA). Deionized water (18 M-cm) was obtained by passing distilled water through a Barnstead E-pure 3-Module system. All oligonucleotides were purchased from Bionics (Korea). The AFM probes for TEM imaging were purchased from Applied NanoStructures (SICON, k = 0.2 N/m) (Santa Clara, California, USA) and Umasch (Portland, Oregon, USA) (CSC38, CSC17/Si3N4/noAl, fc = 0.1~0.3 N/m). Tips from Applied Nanostructures were used for optimizing the picking condition and investigating the influence of the tip velocity. Tips from were used for investigating the influence of the tip radius. For the force measurement, silicon nitride AFM probes were purchased from Nanolnk, Inc. (Skokie, Illinois, USA) (PEN-0012-03, k = 0.004 N/m). The aldehyde- terminated slides were purchased from Arrayit Corporation (Super Aldehyde). (Sunnyvale, California, USA)T4 DNA ligase was purchased from Takara Inc (Otsu, Shiga, Japan).

Transmittance Electron Microscopy (JEM-1011, JEOL, Japan) was used to image the silicon tips.

Preparation of the tips and substrates

[0072] AFM probes and silicon wafers were treated as described previously (see

Figures 5A-B). See, for example, Jung et al., /. Am. Chem. Soc. 2007, 129, 9349-9355; and Jung et al., Nucleic Acids Res. 2009, 37, elO.

Gold-labeled DNA

[0073] The previously reported preparation method was adopted to prepare the DNA-

AuNP conjugates. See, for example, Zanchet et al., Nano Lett. 2001, 1, 32-35. Briefly, bis(para-sulfonatophenyl)phenylphosphine dehydrate dipotassium salt (1.0 mg) was added to the gold nanoparticle (AuNP) solution (10 mL), and the solution was incubated at 22 °C overnight. The AuNPs were then precipitated by adding solid NaCl until the solution color turned blue. After centrifugation, the supernatant was removed, and the AuNPs were redispersed in 0.5x TBE buffer. The resulting concentration of the AuNPs was 2 μΜ. The AuNP solution was then mixed with a DNA solution at a molar ratio of 1: 1 and incubated at 22 °C overnight. Subsequently, the sample was injected into 3% agarose gel, and

electrophoresis was performed with 0.5x TBE running buffer (see Figure 7). The band corresponding to the AuNPs conjugated with a single DNA was cut from the gel, and the gel pad was placed in a dialysis tube filled with 0.5x TBE buffer. After applying a voltage (100 V/15 cm) for 20 min, the solution was transferred to a centrifugation tube, and the volume was adjusted to 11.5 mL with the running buffer. After centrifugation, the supernatant was discarded, and DNA- AuNP conjugates were redispersed in a 0.5x TBE buffer containing 50 mM NaCl. UV-vis spectroscopy showed that the concentration of the resulting solution was 1 x 102 nM.

Hybridization of DNA -AuNP conjugates with probe DNAs

[0074] Substrates immobilizing the probe DNA were incubated overnight in the above conjugate solution at room temperature. The substrates were then washed with 20 ml of a 0.5x TBE buffer solution (pH 8.0) containing 50 mM NaCl and shaken gently in a 0.5 x TBE buffer solution at 37 °C. After washing, the substrates were stored in a 0.5x TBE buffer solution (pH 8.0) containing 50 mM NaCl until the picking experiment.

Materials for control experiments [0075] Silicon wafers and AFM probes were treated with (3-aminopropyl)diethoxy- methylsilane (APDES) as described previously by Jung et al. in /. Am. Chem. Soc. 2007, 129, 9349-9355. Subsequent treatment with a linker, N,N'-disuccinimidyl carbonate, and conjugation with DNAs were performed as described elsewhere. See, for example, Jung et al., /. Am. Chem. Soc. 2007, 129, 9349-9355.

Picking AuNP-DNA conjugates

[0076] All picking experiments were performed with a NanoWizard AFM (JPK

Instrument) (Berlin, Germany), and carried out in a fresh 0.5x TBE buffer solution (pH 8.0) containing NaCl (50 mM) at room temperature. The tip velocity was fixed at 0.2 μιη/s, the z- range was set to 500 nm, and it took 5 s to complete a cycle. The picking was carried out in autoscan mode, and for every case the picking process took < 5 min. To investigate an influence of tip velocity, velocities of 0.01 μητ/s and 10 μητ/s were also examined.

Second hybridization with the AFM tips

[0077] The sequence of another thiolated DNA was selected to hybridize with the ss

DNA part (20-bp) of the picked AuNP-DNA conjugate. For proper isolation, an oligocytosine (30-bp) was added to the 5' position of the new thiolated DNA (see Figure 7). The new AuNP-DNA conjugate was prepared and isolated using the same method as described above. After picking the first AuNP-DNA conjugate, the tip was immediately transferred to a solution containing the second AuNP-DNA conjugates, and incubated for 1 h at room temperature. Subsequently, the tip was washed with 20 ml of a 0.5x TBE buffer solution (pH 8.0) containing 50 mM of NaCl, then shaken gently in a 0.5 x TBE buffer solution at 37 °C. Tip images were taken with TEM.

Ligation

[0078] The tips picked up the target DNA from the substrate were placed in a solution containing the 20 mer DNA (40 μΜ, Tris-HCl buffer from Takara Inc. (pH7.6)) for 1 hr at room temperature. Subsequently, T4 DNA ligase (10 units) was added into the solution, and 12 h at room temperature were allowed. After the ligation, the tips were placed in deionized water heated at 90 °C for 1 h. The tips were rinsed with deionized water at room temperature and dried under vacuum.

AFM force measurement

[0079] All force measurements were performed with the NanoWizard AFM (JPK instrument). The spring constant of each tip was calibrated using the thermal fluctuation method right before each experiment. The spring constants of the cantilevers employed varied between 0.006 and 0.008 N/m. All measurements were carried out in PBS buffer and the loading rate was 0.54 μιη sec"1. More than 100 force-distance curves were recorded per spot and more than 5 spots were examined for each tip.

[0080] The foregoing discussion of the invention has been presented for purposes of illustration and description. The foregoing is not intended to limit the invention to the form or forms disclosed herein. Although the description of the invention has included description of one or more embodiments and certain variations and modifications, other variations and modifications are within the scope of the invention, e.g., as may be within the skill and knowledge of those in the art, after understanding the present disclosure. It is intended to obtain rights which include alternative embodiments to the extent permitted, including alternate, interchangeable and/or equivalent structures, functions, ranges or steps to those claimed, whether or not such alternate, interchangeable and/or equivalent structures, functions, ranges or steps are disclosed herein, and without intending to publicly dedicate any patentable subject matter.

Claims

What is Claimed is:
1. A method for producing a surface bound oligonucleotide on a solid substrate, said method comprising:
contacting a target oligonucleotide with a first oligonucleotide bound to a surface of a first solid substrate under conditions sufficient to produce a partially hybridized oligonucleotide complex, wherein the target oligonucleotide comprises an oligonucleotide sequence that is complementary to the first oligonucleotide sequence;
contacting a second oligonucleotide with the partially hybridized oligonucleotide complex under conditions sufficient to produce a segmented hybridized oligonucleotide complex, wherein the second oligonucleotide comprises an oligonucleotide sequence that is complementary to an unhybridized portion of the target oligonucleotide of the partially hybridized oligonucleotide complex; and
contacting the segmented hybridized oligonucleotide complex with a ligase under conditions sufficient to covalently link the first oligonucleotide and the second oligonucleotide to produce a surface bound oligonucleotide complex comprising a surface bound oligonucleotide which comprises a nucleotide sequence that is complementary to the nucleotide sequence of the target oligonucleotide.
2. The method of Claim 1, wherein said step of contacting the target
oligonucleotide with the first substrate surface comprises contacting the first oligonucleotide with the target oligonucleotide that is bound to a surface of a second solid substrate under conditions sufficient to hybridize the first oligonucleotide to a portion of the target oligonucleotide.
3. The method of Claim 1, wherein the second oligonucleotide further comprises an additional oligonucleotide such that the segmented hybridized oligonucleotide complex comprises at least a portion of the second oligonucleotide that is not hybridized to the target oligonucleotide.
4. The method of Claim 3 further comprising the step of ligating at least a portion of the second oligonucleotide that is not hybridized to the target oligonucleotide prior to said step of forming a covalent link between the first oligonucleotide and the second oligonucleotide.
5. The method of Claim 1 further comprising a step of subjecting the surface bound oligonucleotide complex under conditions sufficient to remove the target
oligonucleotide from the surface bound oligonucleotide complex to produce the first substrate surface bound oligonucleotide that comprises a complementary nucleotide sequence of the target oligonucleotide.
6. The method of Claim 1, wherein the first oligonucleotide is bound to the first substrate surface by a first linker.
7. The method of Claim 6, wherein the first linker comprises a dendron.
8. The method of Claim 7, wherein the dendron is of the formula:
-Z-[Rl]m-Ql-{ [R2-Q2]a-{ (R3-Q3)b-[(R4-Q4)c-(R5-Y)x]y }z}„
I
wherein
each of m, a, b, and c is independently 0 or 1;
x is 1 when c is 0 or when c is 1, x is an integer from 1 to the oxidation state of Q4-l; y is 1 when b is 0 or when b is 1, y is an integer from 1 to the oxidation state of Q -1; z is 1 when a is 0 or when a is 1, z is an integer from 1 to the oxidation state of Q -1; n is an integer from 1 to the oxidation state of Qx-1;
Q1 is a central atom having the oxidation state of at least 3;
each of Q 2 , Q 3 and Q 4 is independently a branch atom having the oxidation state of at least 3;
each of R1, R2, R3, R4, and R5 is independently a linker;
Z is a functional group linked to the first oligonucleotide; and
each of Y is independently a functional group, wherein a plurality of Y are attached to the first solid substrate surface,
provided the product of n, x, y, and z is at least 3.
9. The method of Claim 8, wherein Z comprises a heteroatom selected from the group consisting of N, O, S, P, and a combination thereof.
10. The method of Claim 8, wherein Z comprises a functional group selected from the group consisting of -NR-C(=X) -0-, -0-C(=X) -0-, -NR-C(=X) -, -0-C(=X) -, wherein X is N, O, or S, and R is hydrogen, alkyl, cycloalkyl, aralkyl, aryl, or
(cycloalkyl) alkyl .
11. The method of Claim 8, wherein each of R1, R2, R3, R4, and R5 is
independently a linker comprising 4 to 20 linker chain atoms, wherein each linker chain atom is independently selected from the group consisting of C, O, N, S, and P.
12. The method of Claim 1, wherein the first solid substrate is an atomic force microscope tip.
13. The method of Claim 1, wherein the first oligonucleotide comprises at least 10 oligonucleotide sequence.
14. The method of Claim 1, wherein the second oligonucleotide comprises at least 10 oligonucleotide sequence.
15. The method of Claim 1, wherein said method produces a single surface bound oligonucleotide which comprises a nucleotide sequence that is complementary to the nucleotide sequence of the target oligonucleotide.
16. The method of Claim 15, wherein the solid substrate is an AFM tip.
17. The method of Claim 1, wherein the surface bound oligonucleotide complex further comprises a tethered moiety.
18. The method of Claim 17, wherein the tethered moiety comprises a label, a probe, a ligand, a peptide, or a combination thereof.
19. A method for attaching a single- stranded oligonucleotide on a first solid substrate surface, said method comprising:
contacting a single- stranded target oligonucleotide with a first single-stranded
oligonucleotide bound to a surface of a first solid substrate under conditions sufficient to produce a first hybridized partially double- stranded oligonucleotide complex, wherein the target oligonucleotide comprises a nucleotide sequence that is complementary to the nucleotide sequence of the first single stranded oligonucleotide;
contacting a second oligonucleotide with the first hybridized partially double-stranded oligonucleotide complex under conditions sufficient to produce a segmented hybridized double-stranded oligonucleotide complex, wherein the second oligonucleotide comprises a nucleotide sequence that is complementary to an unhybridized portion of the target oligonucleotide of the first hybridized partially double-stranded oligonucleotide complex;
contacting the segmented hybridized double- stranded oligonucleotide complex with a ligase under conditions sufficient to covalently link the first oligonucleotide and the second oligonucleotide to produce a first solid substrate surface bound double-stranded oligonucleotide complex comprising a nucleotide sequence that is complementary to the nucleotide sequence of the target oligonucleotide; and subjecting the first solid substrate surface bound double-stranded oligonucleotide complex to conditions sufficient to denature the first solid substrate surface bound double- stranded oligonucleotide complex to produce a first solid substrate surface bound single- stranded oligonucleotide, wherein the first solid substrate surface bound single- stranded oligonucleotide comprises nucleotide sequence that is complementary to the nucleotide sequence of the target oligonucleotide.
20. A method for determining the presence of a particular oligonucleotide in a sample, said method comprising:
contacting the sample with a probe oligonucleotide bound to a solid substrate surface under conditions sufficient to produce a probe-ligand hybridized complex when the sample comprises a particular oligonucleotide having a nucleotide sequence that is complementary to the nucleotide sequence of the probe oligonucleotide, wherein the probe oligonucleotide comprises a single- stranded oligonucleotide bound to the solid substrate surface produced by a method of Claim 19; and
determining the presence of the probe-ligand hybridized complex on the solid
substrate surface,
wherein the presence of the probe-ligand hybridized complex on the solid substrate surface is indication that the particular oligonucleotide is present in the sample.
21. The method of Claim 20, wherein the first solid substrate is an atomic force microscope tip.
PCT/US2009/064556 2009-11-16 2009-11-16 Methods for producing surface bound oligonucleotide on solid substrate and uses thereof WO2011059453A1 (en)

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