WO2001053539A1 - Sensitive, multiplexed diagnostic assays for protein analysis - Google Patents

Sensitive, multiplexed diagnostic assays for protein analysis

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Publication number
WO2001053539A1
WO2001053539A1 PCT/US2001/000291 US0100291W WO0153539A1 WO 2001053539 A1 WO2001053539 A1 WO 2001053539A1 US 0100291 W US0100291 W US 0100291W WO 0153539 A1 WO0153539 A1 WO 0153539A1
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WO
WIPO (PCT)
Prior art keywords
nucleic acid
protein
kit
compound
binding
Prior art date
Application number
PCT/US2001/000291
Other languages
French (fr)
Inventor
Richard Wagner
Original Assignee
Phylos, 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
Application filed by Phylos, Inc. filed Critical Phylos, Inc.
Priority to JP2001553398A priority Critical patent/JP2003520050A/en
Priority to CA002396810A priority patent/CA2396810A1/en
Priority to AU29279/01A priority patent/AU783689B2/en
Priority to DE60118527T priority patent/DE60118527D1/en
Priority to EP01942678A priority patent/EP1250463B1/en
Publication of WO2001053539A1 publication Critical patent/WO2001053539A1/en

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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
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/6825—Nucleic acid detection involving sensors
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1051—Gene trapping, e.g. exon-, intron-, IRES-, signal sequence-trap cloning, trap vectors
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1065—Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags

Definitions

  • the invention relates to diagnostic methods involving multiplex analysis.
  • a variety of methods exist to detect multiple species in a biological sample include ELISA based immunoabsorbent assays, protein biochips, and the like. Each of these methods suffers from limitations in detection sensitivity or selectivity, due, for example, to kinetics of binding or sensitivity of detection reagents. In addition, these techniques are also limited in terms of the number of molecules that can be rapidly detected.
  • the present invention involves a novel multiplex diagnostic approach for the ultra-sensitive detection of molecules in biological samples.
  • binding reagents typically protein binding reagents.
  • Each of these reagents binds to a different target in a sample, facilitating the detection of several targets simultaneously.
  • the targets of the binding reagents are frequently proteins, but they may be any moiety capable of specific binding, including, for example, nucleic acids or sugar moieties.
  • binding reagents may represent naturally-occurring or partially or completely synthetic amino acid sequences.
  • binding reagents include, without limitation, members of the following binding pairs: antigen/antibody pairs, protein/inhibitor pairs, receptor/ligand pairs (for example cell surface receptor/ligand pairs, such as hormone receptor/peptide hormone pairs), enzyme/substrate pairs (for example, kinase/substrate pairs), lectin/carbohydrate pairs, oligomeric or heterooligomeric protein aggregates, DNA binding protein/DNA binding site pairs, RNA/protein pairs, and nucleic acid duplexes, heteroduplexes, or ligated strands, as well as any molecule which is capable of forming one or more covalent or non-covalent bonds (for example, disulfide bonds) with any portion of a nucleic acid-protein fusion.
  • binding reagents may be derived by any technique, for example, by directed evolution approaches using a desired protein as the binding target.
  • binding reagents are utilized in a single diagnostic reaction mixture, they are preferably similar in composition and amino acid length.
  • a common amino acid scaffold or structural motif that displays the binding domain on one face of the molecule, as is the case for an antibody scaffold that displays CDR regions as a binding region of the molecule.
  • a particularly useful binding scaffold is the 10 th domain of type III fibronectin (see, for example, Lipovsek et al., Protein Scaffolds for Antibody Mimics and Other Binding Proteins, U.S.S.N. 09/456,693; U.S.S.N. 09/515,260; U.S.S.N. 09/688,566; WO 00/34784).
  • the compound to be detected by the present approach may be any substance to which a protein may bind, and is preferably itself a protein.
  • target compounds may be present in any sample, for example, any biological sample.
  • Typical biological samples include, without limitation, any fluid or tissue derived from an organism, for example, a plant or a mammal such as a human.
  • each of the binding domains is covalently attached to a nucleic acid that encodes the binding domain.
  • nucleic acid-protein fusion molecules can be produced by any method, for example, by the method of Roberts and Szostak (Szostak et al., U.S.S.N. 09/007,005 and U.S.S.N.
  • peptide acceptor any molecule capable of being added to the C-terminus of a growing protein chain by the catalytic activity of the ribosomal peptidyl transferase function.
  • such molecules contain (i) a nucleotide or nucleotide-like moiety (for example, adenosine or an adenosine analog (di-methylation at the N-6 amino position is acceptable)), (ii) an amino acid or amino acid-like moiety (for example, any of the 20 D- or L-amino acids or any amino acid analog thereof (for example, O-methyl tyrosine or any of the analogs described by Ellman et al., Meth. Enzymol.
  • a nucleotide or nucleotide-like moiety for example, adenosine or an adenosine analog (di-methylation at the N-6 amino position is acceptable
  • an amino acid or amino acid-like moiety for example, any of the 20 D- or L-amino acids or any amino acid analog thereof (for example, O-methyl tyrosine or any of the analogs described by Ellman et al., Meth. Enzymol.
  • Peptide acceptors may also possess a nucleophile, which may be, without limitation, an amino group, a hydroxyl group, or a sulfhydryl group.
  • peptide acceptors may be composed of nucleotide mimetics, amino acid mimetics, or mimetics of the combined nucleotide-amino acid structure.
  • any other unique, PCR-amplifiable nucleic acid for example, RNA, DNA, PNA, or any other nucleic acid which includes two or more covalently bonded, naturally- occurring or modified ribonucleotides or deoxyribonucleotides
  • the protein portions of the fusions are typically, composed of naturally-occurring amino acid residues, but may also include amino acid analogs or derivatives, joined by peptide or peptoid bond(s).
  • each binding domain is associated with (and can therefore be identified by) a unique, amplifiable nucleic acid tag, and that each tag in a multiplex reaction is of identical (or essentially identical) length to avoid amplification (for example, PCR) biases.
  • unique identification tags are nucleic acid sequences that differ sufficiently in sequence from other tags in a given population or reaction mixture that significant cross-hybridization does not occur under the conditions employed.
  • These unique identification tags may be present in the protein encoding portion of the fusion (for example, the tag can be a randomized portion of the protein scaffold, such as a randomized loop of the 10 th domain of fibronectin type III).
  • the unique identification tag can be added to the nucleic acid portion of the fusion molecule and be positioned outside of the nucleic acid sequence which encodes the compound binding domain or, if present, its associated scaffold region.
  • unique identification tags may be chosen which most effectively, most selectively, or most conveniently identify the fusion molecule. For example, if binding reagents are deconvoluted on a DNA chip, tag(s) may be chosen which best hybridize to immobilized chip nucleic acid(s) or which are compatible with commercially available chip arrays.
  • DNA chips represent a preferred solid support according to the invention
  • deconvolution may also be carried out on other solid substrates including, without limitation, any other type of chip (for example, silica-based, glass, or gold chip), glass slide, membrane, bead, solid particle (for example, agarose, sepharose, or magnetic bead), column (or column material), membrane (for example, the membrane of a liposome or vesicle), test tube, or microtiter dish.
  • chip for example, silica-based, glass, or gold chip
  • glass slide membrane
  • bead solid particle
  • solid particle for example, agarose, sepharose, or magnetic bead
  • column or column material
  • membrane for example, the membrane of a liposome or vesicle
  • test tube or microtiter dish.
  • the present method may be carried out, in one preferred embodiment, as follows.
  • the high affinity binding reagents each containing a unique affinity binding domain and being present in a mixture of anywhere from 1 to 500,000 (each with equilibrium constants of less than 500 nM), are combined with a sample (for example, a biological sample), under conditions which allow each affinity binding domain to reproducibly recognize a binding partner(s).
  • a sample for example, a biological sample
  • the complex is captured. This can be accomplished through any standard procedure, for example, by biotinylation of the biological sample, followed by capture of biotinylated complexes using immobilized streptavidin (for example, streptavidin immobilized on magnetic beads or a column).
  • the initial protein sample may be preabsorbed onto a membrane and the binding domains mixed with the membrane. Complexes remain bound, while unbound binding reagents are washed away.
  • binding domains that have bound their target(s) in the biological sample are detected simply by performing a PCR reaction using primers which hybridize to the nucleic acid portion of the fusion molecule.
  • the PCR reaction is carried out using standard quantitative methods (for example, using Taq Man by Perkin- Elmer).
  • the isolated pool is then deconvoluted and individual members identified.
  • the identification step may be accomplished through direct sequencing.
  • the isolated pool is deconvoluted and bound analytes identified using DNA chip array detection.
  • the PCR reaction is stopped following predefined cycles, and aliquots extracted. In this way, DNA array detection is performed on each aliquot, allowing for quantitative analysis of amounts of each species present in the pool.
  • a critical feature of the PCR step is that the unique identifiable tag is amplified, and that each amplified segment is the result of using identical primers that generate a DNA product of identical (or essentially identical) size.
  • kits for carrying out any of the methods described herein include at least three important components: (a) a nucleic acid-protein fusion having a protein portion that specifically binds to a desired compound and a nucleic acid portion that both encodes the protein portion and includes a unique identification tag; (b) a PCR primer pair, in which the first primer is designed to hybridize to the nucleic acid portion of the fusion 5' to the unique identification tag and the second primer is designed to hybridize to the nucleic acid portion of the fusion 3' to the unique identification tag and in which hybridization of the primers to the fusion permits amplification of the unique identification tag; and (c) a solid support that includes a nucleic acid that can hybridize to the unique identification tag
  • the kits of the invention may include any of the preferred components discussed above with respect to the preferred methods of the invention.
  • the reagents of the present invention have a multitude of uses in the diagnostic industry and may be substituted for monoclonal antibodies in any use or method for which such antibodies are employed.
  • the molecules described herein may be used for deconvoluting species in complex biological samples.
  • the present approach offers a fast, simple way for detecting species using PCR, a detection technique that is virtually unparalleled in its sensitivity. Coupled with the unique advances for PCR in quantitation of individual species and in DNA array platforms for deconvoluting and detecting low levels of species, the present invention represents the state of the art in the diagnostic area.

Abstract

Disclosed herein are methods for detecting multiple compounds in a sample, involving: (a) contacting the sample with a mixture of binding reagents, the binding reagents being nucleic acid-protein fusions, each having (i) a protein portion which is known to specifically bind to one of the compounds and (ii) a nucleic acid portion which encodes the protein portion and which includes a unique identification tag; (b) allowing the protein portions of the binding reagents and the compounds to form complexes; (c) capturing the binding reagent-compound complexes; (d) amplifying the nucleic acid portions of the complexed binding reagents; and (e) detecting the unique identification tag of each of the amplified nucleic acids, thereby detecting the corresponding compounds in the sample. Also disclosed herein are kits for carrying out such methods.

Description

SENSITIVE, MULTIPLEXED DIAGNOSTIC ASSAYS FOR PROTEIN ANALYSIS
Background of the Invention
In general, the invention relates to diagnostic methods involving multiplex analysis.
A variety of methods exist to detect multiple species in a biological sample. These include ELISA based immunoabsorbent assays, protein biochips, and the like. Each of these methods suffers from limitations in detection sensitivity or selectivity, due, for example, to kinetics of binding or sensitivity of detection reagents. In addition, these techniques are also limited in terms of the number of molecules that can be rapidly detected.
Summary of the Invention The present invention involves a novel multiplex diagnostic approach for the ultra-sensitive detection of molecules in biological samples.
According to this approach, one begins with a set of uniquely defined high affinity binding reagents (typically protein binding reagents). Each of these reagents binds to a different target in a sample, facilitating the detection of several targets simultaneously. The targets of the binding reagents are frequently proteins, but they may be any moiety capable of specific binding, including, for example, nucleic acids or sugar moieties. Such binding reagents may represent naturally-occurring or partially or completely synthetic amino acid sequences. Examples of naturally-occurring binding reagents include, without limitation, members of the following binding pairs: antigen/antibody pairs, protein/inhibitor pairs, receptor/ligand pairs (for example cell surface receptor/ligand pairs, such as hormone receptor/peptide hormone pairs), enzyme/substrate pairs (for example, kinase/substrate pairs), lectin/carbohydrate pairs, oligomeric or heterooligomeric protein aggregates, DNA binding protein/DNA binding site pairs, RNA/protein pairs, and nucleic acid duplexes, heteroduplexes, or ligated strands, as well as any molecule which is capable of forming one or more covalent or non-covalent bonds (for example, disulfide bonds) with any portion of a nucleic acid-protein fusion. In addition to naturally-occurring binding partner members, binding reagents may be derived by any technique, for example, by directed evolution approaches using a desired protein as the binding target.
Whether naturally-occurring or synthetic, when mixtures of binding reagents are utilized in a single diagnostic reaction mixture, they are preferably similar in composition and amino acid length. In a particularly preferred approach, one starts with a common amino acid scaffold or structural motif that displays the binding domain on one face of the molecule, as is the case for an antibody scaffold that displays CDR regions as a binding region of the molecule. A particularly useful binding scaffold is the 10th domain of type III fibronectin (see, for example, Lipovsek et al., Protein Scaffolds for Antibody Mimics and Other Binding Proteins, U.S.S.N. 09/456,693; U.S.S.N. 09/515,260; U.S.S.N. 09/688,566; WO 00/34784).
The compound to be detected by the present approach may be any substance to which a protein may bind, and is preferably itself a protein. Such target compounds may be present in any sample, for example, any biological sample. Typical biological samples include, without limitation, any fluid or tissue derived from an organism, for example, a plant or a mammal such as a human. As a central feature of the invention, each of the binding domains is covalently attached to a nucleic acid that encodes the binding domain. Such nucleic acid-protein fusion molecules can be produced by any method, for example, by the method of Roberts and Szostak (Szostak et al., U.S.S.N. 09/007,005 and U.S.S.N. 09/247, 190; Szostak et al., WO 98/31700; Roberts & Szostak, Proc. Natl. Acad. Sci. USA (1997) vol. 94, p. 12297-12302) using a peptide acceptor, such as puromycin, as a covalent linking agent. As used herein, by a "peptide acceptor" is meant any molecule capable of being added to the C-terminus of a growing protein chain by the catalytic activity of the ribosomal peptidyl transferase function. Typically, such molecules contain (i) a nucleotide or nucleotide-like moiety (for example, adenosine or an adenosine analog (di-methylation at the N-6 amino position is acceptable)), (ii) an amino acid or amino acid-like moiety (for example, any of the 20 D- or L-amino acids or any amino acid analog thereof (for example, O-methyl tyrosine or any of the analogs described by Ellman et al., Meth. Enzymol. 202:301, 1991), and (iii) a linkage between the two (for example, an ester, amide, or ketone linkage at the 3' position or, less preferably, the 2' position); preferably, this linkage does not significantly perturb the pucker of the ring from the natural ribonucleotide conformation. Peptide acceptors may also possess a nucleophile, which may be, without limitation, an amino group, a hydroxyl group, or a sulfhydryl group. In addition, peptide acceptors may be composed of nucleotide mimetics, amino acid mimetics, or mimetics of the combined nucleotide-amino acid structure. As noted above, puromycin represents a preferred peptide acceptor for use in the present method. In addition to covalently bonded RNA-protein fusions, any other unique, PCR-amplifiable nucleic acid (for example, RNA, DNA, PNA, or any other nucleic acid which includes two or more covalently bonded, naturally- occurring or modified ribonucleotides or deoxyribonucleotides) can be coupled covalently or non-covalently to each individual binding domain. The protein portions of the fusions are typically, composed of naturally-occurring amino acid residues, but may also include amino acid analogs or derivatives, joined by peptide or peptoid bond(s).
Of particular importance is that each binding domain is associated with (and can therefore be identified by) a unique, amplifiable nucleic acid tag, and that each tag in a multiplex reaction is of identical (or essentially identical) length to avoid amplification (for example, PCR) biases. Such unique identification tags are nucleic acid sequences that differ sufficiently in sequence from other tags in a given population or reaction mixture that significant cross-hybridization does not occur under the conditions employed. These unique identification tags may be present in the protein encoding portion of the fusion (for example, the tag can be a randomized portion of the protein scaffold, such as a randomized loop of the 10th domain of fibronectin type III). Alternatively, the unique identification tag can be added to the nucleic acid portion of the fusion molecule and be positioned outside of the nucleic acid sequence which encodes the compound binding domain or, if present, its associated scaffold region. In the latter case, unique identification tags may be chosen which most effectively, most selectively, or most conveniently identify the fusion molecule. For example, if binding reagents are deconvoluted on a DNA chip, tag(s) may be chosen which best hybridize to immobilized chip nucleic acid(s) or which are compatible with commercially available chip arrays. Although DNA chips represent a preferred solid support according to the invention, deconvolution may also be carried out on other solid substrates including, without limitation, any other type of chip (for example, silica-based, glass, or gold chip), glass slide, membrane, bead, solid particle (for example, agarose, sepharose, or magnetic bead), column (or column material), membrane (for example, the membrane of a liposome or vesicle), test tube, or microtiter dish.
Using the affinity binding reagents described above, the present method may be carried out, in one preferred embodiment, as follows. The high affinity binding reagents, each containing a unique affinity binding domain and being present in a mixture of anywhere from 1 to 500,000 (each with equilibrium constants of less than 500 nM), are combined with a sample (for example, a biological sample), under conditions which allow each affinity binding domain to reproducibly recognize a binding partner(s). Following complex formation, the complex is captured. This can be accomplished through any standard procedure, for example, by biotinylation of the biological sample, followed by capture of biotinylated complexes using immobilized streptavidin (for example, streptavidin immobilized on magnetic beads or a column). Alternatively, the initial protein sample may be preabsorbed onto a membrane and the binding domains mixed with the membrane. Complexes remain bound, while unbound binding reagents are washed away.
Following capture of bound complexes, binding domains that have bound their target(s) in the biological sample are detected simply by performing a PCR reaction using primers which hybridize to the nucleic acid portion of the fusion molecule. Preferably, the PCR reaction is carried out using standard quantitative methods (for example, using Taq Man by Perkin- Elmer).
If multiple complexes are isolated, the isolated pool is then deconvoluted and individual members identified. The identification step may be accomplished through direct sequencing. Alternatively, in a preferred feature of the invention, the isolated pool is deconvoluted and bound analytes identified using DNA chip array detection. In one preferred method, the PCR reaction is stopped following predefined cycles, and aliquots extracted. In this way, DNA array detection is performed on each aliquot, allowing for quantitative analysis of amounts of each species present in the pool. Again, a critical feature of the PCR step is that the unique identifiable tag is amplified, and that each amplified segment is the result of using identical primers that generate a DNA product of identical (or essentially identical) size.
In addition, the present invention includes kits for carrying out any of the methods described herein. Typically, these kits include at least three important components: (a) a nucleic acid-protein fusion having a protein portion that specifically binds to a desired compound and a nucleic acid portion that both encodes the protein portion and includes a unique identification tag; (b) a PCR primer pair, in which the first primer is designed to hybridize to the nucleic acid portion of the fusion 5' to the unique identification tag and the second primer is designed to hybridize to the nucleic acid portion of the fusion 3' to the unique identification tag and in which hybridization of the primers to the fusion permits amplification of the unique identification tag; and (c) a solid support that includes a nucleic acid that can hybridize to the unique identification tag In preferred embodiments, the kits of the invention may include any of the preferred components discussed above with respect to the preferred methods of the invention.
Use
The reagents of the present invention have a multitude of uses in the diagnostic industry and may be substituted for monoclonal antibodies in any use or method for which such antibodies are employed. In addition, the molecules described herein may be used for deconvoluting species in complex biological samples. In addition, the present approach offers a fast, simple way for detecting species using PCR, a detection technique that is virtually unparalleled in its sensitivity. Coupled with the unique advances for PCR in quantitation of individual species and in DNA array platforms for deconvoluting and detecting low levels of species, the present invention represents the state of the art in the diagnostic area.
Other Embodiments
Other embodiments are within the claims. All publications mentioned in this specification are hereby incorporated by reference to the same extent as if each independent publication or patent application was specifically and individually indicated to be incorporated by reference.
What is claimed is:

Claims

Claims
1. A method for detecting multiple compounds in a sample, said method comprising:
(a) contacting said sample with a mixture of binding reagents, said binding reagents being nucleic acid-protein fusions, each having (i) a protein portion which is known to specifically bind to one of said compounds and (ii) a nucleic acid portion which encodes said protein portion and which includes a unique identification tag;
(b) allowing said protein portions of said binding reagents and said compounds to form complexes;
(c) capturing said binding reagent-compound complexes;
(d) amplifying said nucleic acid portions of said complexed binding reagents; and
(e) detecting said unique identification tag of each of said amplified nucleic acids, thereby detecting the corresponding compounds in said sample.
2. The method of claim 1, wherein said sample is a biological sample.
3. The method of claim 1, wherein said nucleic acid-protein fusion is an RNA-protein fusion.
4. The method of claim 1, wherein said nucleic acid-protein fusion is covalently bound.
5. The method of claim 4, wherein said nucleic acid-protein fusion is covalently bound through a peptide acceptor.
6. The method of claim 5, wherein said peptide acceptor is puromycin.
7. The method of claim 1, wherein said binding reagents do not bind said compounds through compound-specific antibody domains.
8. The method of claim 1, wherein each of said binding reagents comprises a scaffold domain.
9. The method of claim 8, wherein each of said binding reagents comprises a fibronectin scaffold domain.
10. The method of claim 9, wherein said fibronectin scaffold domain is the 10th domain of fibronectin type III.
11. The method of claim 8, wherein each of said binding reagents comprises an antibody scaffold domain.
12. The method of claim 1, wherein said binding reagents bind said compounds with equilibrium constants of less than about 500 nM.
13. The method of claim 1, wherein said unique identification tags are detected using a solid support to which are immobilized nucleic acids specific for said unique identification tags and said detection is accomplished by hybridization of said unique identification tags to said immobilized nucleic acids.
14. The method of claim 1, wherein said amplifying step (d) is carried out using quantitative PCR.
15. The method of claim 1, wherein said compounds are proteins.
16. The method of claim 1, wherein said mixture of binding reagents comprises at least 5 different nucleic acid-protein fusions, each specifically binding to a different compound.
17. The method of claim 16, wherein said mixture of binding reagents comprises at least 100 different nucleic acid-protein fusions, each specifically binding to a different compound.
18. The method of claim 17, wherein said mixture of binding reagents comprises at least 40,000 different nucleic acid-protein fusions, each specifically binding to a different compound.
19. The method of claim 18, wherein said mixture of binding reagents comprises at least 500,000 different nucleic acid-protein fusions, each specifically binding to a different compound.
20. A method for detecting a compound in a sample, said method comprising:
(a) contacting said sample with a binding reagent, said binding reagent being a nucleic acid-protein fusion having (i) a protein portion which is known to specifically bind to said compound and (ii) nucleic acid portion which encodes said protein portion and which includes a unique identification tag;
(b) allowing said protein portion of said binding reagent and said compound to form a complex; (c) capturing said binding reagent-compound complex;
(d) amplifying said nucleic acid portion of said complexed binding reagent; and
(e) detecting said unique identification tag of said amplified nucleic acid, thereby detecting the corresponding compound in said sample.
21. A kit for carrying out compound detection, said kit comprising:
(a) a nucleic acid-protein fusion, wherein said protein portion of said fusion specifically binds said compound and said nucleic acid portion of said fusion encodes said protein portion and includes a unique identification tag;
(b) a PCR primer pair, wherein the first of said primers hybridizes to said nucleic acid portion of said fusion 5' to said unique identification tag and the second of said primers hybridizes to said nucleic acid portion of said fusion 3' to said unique identification tag and hybridization of said primers to said nucleic acid fusion permits amplification of said unique identification tag; and
(c) a solid support comprising a nucleic acid which can hybridize to said unique identification tag.
22. The kit of claim 21, wherein said kit further comprises Taq polymerase.
23. The kit of claim 21, wherein said nucleic acid-protein fusion is an RNA-protein fusion.
24. The kit of claim 21, wherein said nucleic acid-protein fusion is covalently bound.
25. The kit of claim 24, wherein said nucleic acid-protein fusion is covalently bound through a peptide acceptor.
26. The kit of claim 25, wherein said peptide acceptor is puromycin.
27. The kit of claim 21, wherein said nucleic acid-protein fusion does not bind said compound through a compound-specific antibody domain.
28. The kit of claim 21, wherein said nucleic acid-protein fusion comprises a scaffold domain.
29. The kit of claim 28, wherein nucleic acid-protein fusion comprises a fibronectin scaffold domain.
30. The kit of claim 29, wherein said fibronectin scaffold domain is the 10th domain of fibronectin type III.
31. The kit of claim 28, wherein said nucleic acid-protein fusion comprises an antibody scaffold domain.
32. The kit of claim 21, wherein said nucleic acid-protein fusion binds said compound with an equilibrium constant of less than about 500 nM.
33. The kit of claim 21, wherein said solid support is a chip.
34. The kit of claim 21, wherein said solid support comprises an ordered array of single-stranded nucleic acids on its surface, each of said single-stranded nucleic acids being capable of hybridizing to a different said unique identification tag.
35. The kit of claim 21, wherein said compound is a protein.
36. The kit of claim 21, wherein said kit comprises at least 5 different nucleic acid-protein fusions, each specifically binding to a different compound.
37. The kit of claim 36, wherein said kit comprises at least 100 different nucleic acid-protein fusions, each specifically binding to a different compound.
38. The kit of claim 37, wherein said kit comprises at least 40,000 different nucleic acid-protein fusions, each specifically binding to a different compound.
39. The kit of claim 38, wherein said kit comprises at least 500,000 different nucleic acid-protein fusions, each specifically binding to a different compound.
PCT/US2001/000291 2000-01-24 2001-01-04 Sensitive, multiplexed diagnostic assays for protein analysis WO2001053539A1 (en)

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JP2001553398A JP2003520050A (en) 2000-01-24 2001-01-04 Sensitive multiplexed diagnostic assays for protein analysis
CA002396810A CA2396810A1 (en) 2000-01-24 2001-01-04 Sensitive, multiplexed diagnostic assays for protein analysis
AU29279/01A AU783689B2 (en) 2000-01-24 2001-01-04 Sensitive, multiplexed diagnostic assays for protein analysis
DE60118527T DE60118527D1 (en) 2000-01-24 2001-01-04 SENSITIVE AND MULTIPLEXED DIAGNOSTIC TESTS FOR PROTEIN ANALYSIS
EP01942678A EP1250463B1 (en) 2000-01-24 2001-01-04 Sensitive, multiplexed diagnostic assays for protein analysis

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US60/177,873 2000-01-24

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Publication number Priority date Publication date Assignee Title
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Families Citing this family (30)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7045311B2 (en) * 2001-10-25 2006-05-16 Monogram Biosciences, Inc. Whole cell assay systems for cell surface proteases
AU2002365404A1 (en) * 2001-11-27 2003-06-10 Compound Therapeutics, Inc. Solid-phase immobilization of proteins and peptides
WO2003061570A2 (en) * 2002-01-16 2003-07-31 Zyomyx, Inc. Engineered binding proteins
US20030166010A1 (en) * 2002-02-25 2003-09-04 Affholter Joseph A. Custom ligand design for biomolecular filtration and purification for bioseperation
US20030198973A1 (en) * 2002-04-23 2003-10-23 The Molecular Sciences Institute, Inc. Chimeric fusion molecule for analyte detection and quantitation
US20040229294A1 (en) * 2002-05-21 2004-11-18 Po-Ying Chan-Hui ErbB surface receptor complexes as biomarkers
US7402397B2 (en) 2002-05-21 2008-07-22 Monogram Biosciences, Inc. Detecting and profiling molecular complexes
WO2004094456A2 (en) 2003-04-18 2004-11-04 Becton, Dickinson And Company Immuno-amplification
WO2004104229A2 (en) * 2003-05-16 2004-12-02 Vickery Michael C L Internal control nucleic acid molecule for nucleic acid amplification systems
US7713923B2 (en) * 2003-06-25 2010-05-11 Massachusetts Institute Of Technology Self-assembling peptides incorporating modifications and methods of use thereof
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US7785843B2 (en) * 2004-06-23 2010-08-31 Sequenom, Inc. Target-specific compomers and methods of use
US20060110724A1 (en) 2004-11-19 2006-05-25 Burkhardt William Iii Quantitative real-time assay for noroviruses and enteroviruses with built in quality control standard
US20060204999A1 (en) * 2005-03-14 2006-09-14 Stephen Macevicz Detecting molecular complexes
EP2283851B1 (en) 2005-04-25 2023-06-07 Massachusetts Institute of Technology Compositions for promoting hemostasis
WO2007059312A2 (en) 2005-11-16 2007-05-24 Ambrx, Inc. Methods and compositions comprising non-natural amino acids
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CN104645329A (en) 2007-11-30 2015-05-27 Abbvie公司 Protein formulations and methods of making same
US8883146B2 (en) 2007-11-30 2014-11-11 Abbvie Inc. Protein formulations and methods of making same
KR20110036638A (en) 2008-07-25 2011-04-07 리차드 더블유. 와그너 Protein screening methods
WO2011072482A1 (en) 2009-12-14 2011-06-23 The University Of Hong Kong Nano cancer barrier device(ncbd) to immobilize and inhibit the division of metastic cancer stem cells
ES2926988T3 (en) 2011-03-15 2022-10-31 X Body Inc Antibody screening methods
EP3421592B1 (en) 2011-04-28 2023-09-13 The Board of Trustees of the Leland Stanford Junior University Identification of polynucleotides associated with a sample
EP2788379B1 (en) 2011-12-05 2020-02-05 X-Body, Inc. Pdgf receptor beta binding polypeptides
SG11201510312RA (en) 2013-06-28 2016-01-28 X Body Inc Target antigen discovery, phenotypic screens and use thereof for identification of target cell specific target epitopes
US10519436B2 (en) 2013-09-23 2019-12-31 X-Body, Inc. Methods and compositions for generation of binding agents against cell surface antigens
AU2015271324B2 (en) * 2014-06-06 2019-09-12 Herlev Hospital Determining antigen recognition through barcoding of MHC multimers
EP3155426B1 (en) 2014-06-13 2023-07-19 Immudex ApS General detection and isolation of specific cells by binding of labeled molecules

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1998031700A1 (en) * 1997-01-21 1998-07-23 The General Hospital Corporation Selection of proteins using rna-protein fusions
WO1999051773A1 (en) * 1998-04-03 1999-10-14 Phylos, Inc. Addressable protein arrays

Family Cites Families (37)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4587044A (en) 1983-09-01 1986-05-06 The Johns Hopkins University Linkage of proteins to nucleic acids
DE3590766C2 (en) 1985-03-30 1991-01-10 Marc Genf/Geneve Ch Ballivet
US5223409A (en) 1988-09-02 1993-06-29 Protein Engineering Corp. Directed evolution of novel binding proteins
US5424186A (en) 1989-06-07 1995-06-13 Affymax Technologies N.V. Very large scale immobilized polymer synthesis
EP0494955B1 (en) 1989-10-05 1998-07-15 Optein, Inc. Cell-free synthesis and isolation of novel genes and polypeptides
US5270163A (en) 1990-06-11 1993-12-14 University Research Corporation Methods for identifying nucleic acid ligands
US5723286A (en) 1990-06-20 1998-03-03 Affymax Technologies N.V. Peptide library and screening systems
US5650489A (en) 1990-07-02 1997-07-22 The Arizona Board Of Regents Random bio-oligomer library, a method of synthesis thereof, and a method of use thereof
WO1992002536A1 (en) 1990-08-02 1992-02-20 The Regents Of The University Of Colorado Systematic polypeptide evolution by reverse translation
US5264563A (en) 1990-08-24 1993-11-23 Ixsys Inc. Process for synthesizing oligonucleotides with random codons
US5795747A (en) 1991-04-16 1998-08-18 Evotec Biosystems Gmbh Process for manufacturing new biopolymers
DE4112440C1 (en) 1991-04-16 1992-10-22 Diagen Institut Fuer Molekularbiologische Diagnostik Gmbh, 4000 Duesseldorf, De
AU2313392A (en) 1991-08-01 1993-03-02 University Research Corporation Systematic polypeptide evolution by reverse translation
US5639603A (en) 1991-09-18 1997-06-17 Affymax Technologies N.V. Synthesizing and screening molecular diversity
US5733731A (en) 1991-10-16 1998-03-31 Affymax Technologies N.V. Peptide library and screening method
US5270170A (en) 1991-10-16 1993-12-14 Affymax Technologies N.V. Peptide library and screening method
US5541061A (en) 1992-04-29 1996-07-30 Affymax Technologies N.V. Methods for screening factorial chemical libraries
US5565324A (en) 1992-10-01 1996-10-15 The Trustees Of Columbia University In The City Of New York Complex combinatorial chemical libraries encoded with tags
US6087186A (en) 1993-07-16 2000-07-11 Irori Methods and apparatus for synthesizing labeled combinatorial chemistry libraries
US5635602A (en) 1993-08-13 1997-06-03 The Regents Of The University Of California Design and synthesis of bispecific DNA-antibody conjugates
WO1995011922A1 (en) 1993-10-29 1995-05-04 Affymax Technologies N.V. In vitro peptide and antibody display libraries
US5561043A (en) 1994-01-31 1996-10-01 Trustees Of Boston University Self-assembling multimeric nucleic acid constructs
DE69531148T2 (en) 1994-01-31 2004-04-29 Trustees Of Boston University, Boston LIBRARIES MADE OF POLYCLONAL ANTIBODIES
US5605793A (en) 1994-02-17 1997-02-25 Affymax Technologies N.V. Methods for in vitro recombination
EP0763202A4 (en) 1994-05-23 1998-12-09 Smithkline Beecham Corp Encoded combinatorial libraries
US5627024A (en) 1994-08-05 1997-05-06 The Scripps Research Institute Lambdoid bacteriophage vectors for expression and display of foreign proteins
US5559000A (en) 1995-01-18 1996-09-24 The Scripps Research Institute Encoded reaction cassette
US5751629A (en) 1995-04-25 1998-05-12 Irori Remotely programmable matrices with memories
DE19646372C1 (en) 1995-11-11 1997-06-19 Evotec Biosystems Gmbh Conjugates of polypeptide and encoding nucleic acid
JP3683282B2 (en) 1996-10-17 2005-08-17 三菱化学株式会社 Genotype-phenotype mapping molecule and use thereof
US6261804B1 (en) * 1997-01-21 2001-07-17 The General Hospital Corporation Selection of proteins using RNA-protein fusions
GB9703369D0 (en) * 1997-02-18 1997-04-09 Lindqvist Bjorn H Process
GB9712512D0 (en) 1997-06-16 1997-08-20 Bioinvent Int Ab A method for in vitro molecular evolution of protein function
US5985575A (en) 1998-05-20 1999-11-16 Wisconsin Alumni Research Foundation Tethered function assay for protein function
PT1105360E (en) 1998-08-17 2009-09-30 Bristol Myers Squibb Co Identification of compound-protein interactions using libraries of protein-nucleic acid fusion molecules
KR20010099821A (en) * 1998-12-02 2001-11-09 추후기재 Dna-protein fusions and uses thereof
ATE439592T1 (en) 1998-12-10 2009-08-15 Bristol Myers Squibb Co PROTEIN SCAFFOLDS FOR ANTIBODY MIMICS AND OTHER BINDING PROTEINS

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1998031700A1 (en) * 1997-01-21 1998-07-23 The General Hospital Corporation Selection of proteins using rna-protein fusions
WO1999051773A1 (en) * 1998-04-03 1999-10-14 Phylos, Inc. Addressable protein arrays

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
ROBERTS ET AL.: "RNA-peptide fusions for the in vitro selection of peptides and proteins", PROC. NATL. ACAD. SCI. USA, vol. 94, November 1997 (1997-11-01), pages 12297 - 12302, XP002940042 *

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