Methods and Reagents for Detecting Target Binding by Nucleic Acid Ligands
First Claim
1. A method for detecting the presence of a target molecule suspected of being contained in a test mixture, wherein said target molecule is a protein, the method comprising;
- a) providing a solid support, said solid support comprising a photoreactive nucleic acid ligand having specific affinity for said target protein, said photoreactive nucleic acid ligand binding specifically to said target molecule through non-Watson-Crick interactions;
b) contacting said solid support with said test mixture suspected of containing said target molecule, wherein a nucleic acid ligand-target molecule complex is formed if said target molecule is present;
c) irradiating said solid support, wherein said nucleic acid ligand-target molecule complex photocrosslinks;
d) removing non-specifically bound material from said solid support;
e) contacting said solid support with a Universal Protein Stain (UPS), said UPS comprising one or more reagents that label proteins with a detectable moiety; and
f) detecting the presence of said target molecule by detecting the presence of said detectable moiety on said solid support.
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Abstract
The present invention provides novel methods and reagents for detecting the binding of protein targets to nucleic acid ligands. Using Universal Protein Stains (UPS), proteins bound by nucleic acid ligands may be labeled with a detectable moiety. The methods and reagents are particularly useful for the detection of protein targets bound to multiplexed arrays of nucleic acid ligands. The present invention also provides novel methods for the multiplexed evaluation of photocrosslinking nucleic acid ligands. The methods allow one simultaneously to: (1) evaluate the performance (dynamic range) of a plurality of photocrosslinking nucleic acid ligands; and (2) assess the specificity of each photocrosslinking nucleic acid ligand for its cognate target protein. Photocrosslinking nucleic acid ligands with the most desirable properties can then be selected for use in diagnostic and prognostic medical assays. The present invention also provides a photocrosslinking nucleic acid ligand that binds specifically to HIV gp120MN.
124 Citations
41 Claims
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1. A method for detecting the presence of a target molecule suspected of being contained in a test mixture, wherein said target molecule is a protein, the method comprising;
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a) providing a solid support, said solid support comprising a photoreactive nucleic acid ligand having specific affinity for said target protein, said photoreactive nucleic acid ligand binding specifically to said target molecule through non-Watson-Crick interactions; b) contacting said solid support with said test mixture suspected of containing said target molecule, wherein a nucleic acid ligand-target molecule complex is formed if said target molecule is present; c) irradiating said solid support, wherein said nucleic acid ligand-target molecule complex photocrosslinks; d) removing non-specifically bound material from said solid support; e) contacting said solid support with a Universal Protein Stain (UPS), said UPS comprising one or more reagents that label proteins with a detectable moiety; and f) detecting the presence of said target molecule by detecting the presence of said detectable moiety on said solid support. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31)
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32. A method for detecting the presence of a target molecule suspected of being contained in a test mixture, wherein said target molecule to be detected is a protein, the method comprising;
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a) providing a biochip comprising a solid support, said solid support comprising a plurality of spatially defined addresses, each said address comprising at least one copy of a single species of nucleic acid ligand attached thereto, each said species of nucleic acid ligand having specific affinity for one of said target molecules suspected of being contained in said test mixture, and each said species of nucleic acid ligand binding specifically to said target molecule through non-Watson-Crick interactions; b) contacting said biochip with said test mixture suspected of containing said target molecule; c) removing non-specifically bound material from said biochip; d) contacting said solid support with a Universal Protein Stain (UPS), said UPS comprising one or more reagents that label proteins with a detectable moiety; and e) detecting the presence of said target molecule by detecting the presence of said detectable moiety at the appropriate address on said biochip.
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33. A method for detecting the presence of a target molecule suspected of being contained in a test mixture, wherein said target molecule is a protein, the method comprising;
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a) providing a solid support, said solid support comprising a nucleic acid ligand having specific affinity for said target protein, said nucleic acid ligand binding specifically to said target protein through non-Watson-Crick interactions; b) contacting said solid support with said test mixture suspected of containing said target molecule; c) removing non-specifically bound material from said solid support; d) contacting said solid support with a Universal Protein Stain (UPS), said UPS comprising one or more reagents that label proteins with a detectable moiety; and e) detecting the presence of said target molecule by detecting the presence of said detectable moiety at the appropriate address on said biochip.
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34. A method for detecting the presence of a target molecule suspected of being contained in a test mixture, wherein said target molecule be to detected is a protein, the method comprising;
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a) providing a biochip comprising a solid support, said solid support comprising a plurality of spatially defined addresses, each said address comprising at least one copy of a single species of nucleic acid ligand attached thereto, each said species of nucleic acid ligand having specific affinity for one of said target molecules suspected of being contained in said test mixture, each said species of nucleic acid ligand binding specifically to said target molecule through non-Watson-Crick interactions, and wherein said nucleic acid ligand having specific affinity for said target molecule to be detected is a photoreactive nucleic acid ligand; b) contacting said biochip with said test mixture suspected of containing said target molecule, wherein a nucleic acid ligand-target molecule complex is formed if said target molecule is present; c) irradiating said biochip, wherein said nucleic acid ligand-target molecule complex photocrosslinks; d) removing non-specifically bound material from said biochip; e) contacting said biochip with a reagent that reacts covalently with proteins and not with nucleic acids; and f) detecting the presence of said target molecule by detecting the presence of said detectable moiety at the appropriate address on said biochip.
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35. A biochip comprising an array of a plurality of nucleic acid ligands attached to a solid support, wherein a plurality of said nucleic acid ligands are specifically associated with a target molecule through non-Watson-Crick interactions, and wherein said target molecules are labeled with a detectable moiety.
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36. A method for attaching a nucleic acid ligand to a solid support comprising:
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a) derivatizing said nucleic acid ligand with a poly(ethylene glycol) (PEG); b) attaching said PEG to said solid support. - View Dependent Claims (37)
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38. A method for simultaneously measuring the dose-response characteristics of a plurality of species of photocrosslinking nucleic acid ligands, each said species of photocrosslinking nucleic acid ligands having specific affinity for a cognate target protein, the method comprising:
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a) providing a plurality of arrays, each said array comprising a plurality of spatially defined addresses, each said address having at least one copy of a single species of photocrosslinking nucleic acid ligand attached thereto; b) providing a plurality of target protein mixtures, wherein each mixture comprises a unique target protein concentration profile; c) contacting each said array with a different one of said mixtures; and d) measuring the amount of target protein bound to each said address on each said array; whereby the dose-response characteristics of each said species of photocrosslinking nucleic acid ligands are measured simultaneously. - View Dependent Claims (39, 40, 41)
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Specification