Photolithographic and other means for manufacturing arrays
First Claim
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1. A method of using a fluorescent label to detect binding with polypeptide probes of known sequence, said method comprising:
- (a) attaching said label to a target polypeptide to form a labeled polypeptide;
(b) contacting said labeled target polypeptide with a collection of polypeptide probes of known sequences wherein said polypeptide probes are attached to a substrate at positionally defined locations; and
(c) determining the sequences of the probes that bind with said target, said collection comprising at least 100 different probes per square centimeter of substrate.
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Abstract
The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.
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Citations
44 Claims
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1. A method of using a fluorescent label to detect binding with polypeptide probes of known sequence, said method comprising:
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(a) attaching said label to a target polypeptide to form a labeled polypeptide;
(b) contacting said labeled target polypeptide with a collection of polypeptide probes of known sequences wherein said polypeptide probes are attached to a substrate at positionally defined locations; and
(c) determining the sequences of the probes that bind with said target, said collection comprising at least 100 different probes per square centimeter of substrate. - View Dependent Claims (2, 4, 5, 6, 7, 8, 9, 10, 11)
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3. A method of using a fluorescent label to detect binding with polypeptide probes of known sequence, said method comprising:
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(a) attaching said label to a target polypeptide to form a labeled polypeptide;
(b) contacting said labeled target polypeptide with a collection of polypeptide probes of known sequences wherein said polypeptide probes are attached to a substrate at positinally defined locations; and
(c) identifying the probes that bind with said target, said collection comprising more than 100 different probes per square centimeter of substrate.
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12. A method of mapping a plurality of polypeptides relative to one another, said method comprising:
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(a) preparing a substrate having attached thereto at positionally defined locations a plurality of sequence specific probes comprising at least about 100 probes per square centimeter of substrate;
(b) subjecting each of said polypeptides to contact with the probes attached to said substrate under binding conditions; and
(c) determining the relative locations of said binding of said polypeptides to determine the overlap of said plurality of polypeptides. - View Dependent Claims (13, 14, 15, 16, 17, 18, 19, 20, 21)
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22. A method for identifying polypeptide probes, said method comprising:
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(a) binding non-identical polypeptide probes attached to a substrate at a density of at least 100 of said probes per square centimeter with target polypeptides;
(b) identifying a first polypeptide probe that binds in step (a) with said target polypeptide;
(c) further identifying other polypeptide probes which binds in step (a) beginning with a second polypeptide probe; and
(d) continuing said identification to identify at least about 100 probes that bind with said target polypeptides. - View Dependent Claims (23, 24, 25, 26, 27, 28, 29, 30, 31, 32)
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33. A method for detecting sequences in two or more collections of polypeptides, the method comprising:
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(a) providing an array of polypeptides bound to a solid surface, each said polypeptide comprising a determinable sequence;
(b) sequentially or simultaneously contacting the array of polypeptides with;
(i) a first collection of labeled polypeptides comprising a sequence that will bind to a polypeptide of said array, and (ii) at least a second collection of labeled polypeptide comprising a sequence that will bind to a polypeptide of said array;
wherein the first and second labels are distinguishable from each other; and
(c) detecting binding of the first and second labeled polypeptides to polypeptides of said arrays. - View Dependent Claims (34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44)
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Specification