Arrays for detecting nucleic acids

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.

What is claimed is:  
     
         1 . A composition comprising a plurality of positionally distinguishable sequence specific reagents attached to a solid substrate, which reagents are capable of specifically binding to a predetermined subunit sequence of a preselected multi-subunit length having at least three subunits, said reagents representing substantially all possible sequences of said preselected length.  
     
     
         2 . A composition of  claim 1 , wherein said subunit sequence is a polynucleotide or a polypeptide.  
     
     
         3 . A composition of  claim 1 , wherein said preselected multi-subunit length is five subunits and said subunit sequence is a polynucleotide sequence.  
     
     
         4 . A composition of  claim 1 , wherein said specific reagent is an oligonucleotide of at least about five nucleotides.  
     
     
         5 . A composition of  claim 1 , wherein said specific reagent is a monoclonal antibody.  
     
     
         6 . A composition of  claim 1 , wherein said specific reagents are all attached to a single solid substrate.  
     
     
         7 . A composition of  claim 1 , wherein said reagents comprise about 3000 different sequences.  
     
     
         8 . A composition of  claim 1 , wherein said reagents represents at least about 25% of the possible subsequences of said preselected length.  
     
     
         9 . A composition of  claim 1 , wherein said reagents are localized in regions of the substrate having a density of at least 25 regions per square centimeter.  
     
     
         10 . A composition of  claim 6 , wherein said substrate has a surface area of less than about 4 square centimeters.  
     
     
         11 . A method of analyzing a sequence of a polynucleotide or a polypeptide, said method comprising the step of: 
 a) exposing said polynucleotide or polypeptide to a composition of  claim 1 .    
     
     
         12 . A method of identifying or comparing a target sequence with a reference, said method comprising the step of: 
 a) exposing said target sequence to a composition of  claim 1;     b) determining the pattern of positions of said reagents which specifically interact with said target sequence; and    c) comparing said pattern with the pattern exhibited by said reference when exposed to said composition.    
     
     
         13 . A method for sequencing a segment of a polynucleotide comprising the steps of: 
 a) combining: 
 i) a substrate comprising a plurality of chemically synthesized and positionally distinguishable oligonucleotides capable of recognizing defined oligonucleotide sequences; and  
 ii) a target polynucleotide; thereby forming high fidelity matched duplex structures of complementary subsequences of known sequence; and  
   b) determining which of said reagents have specifically interacted with subsequences in said target polynucleotide.    
     
     
         14 . A method of  claim 13 , wherein said segment is substantially the entire length of said polynucleotide.  
     
     
         15 . A method for sequencing a polymer, said method comprising the steps of: 
 a) preparing a plurality of reagents which each specifically bind to a subsequence of preselected length;    b) positionally attaching each of said reagents to one or more solid phase substrates, thereby producing substrates of positionally definable sequence specific probes;    c) combining said substrates with a target polymer whose sequence is to be determined; and    d) determining which of said reagents have specifically interacted with subsequences in said target polymer.    
     
     
         16 . A method of  claim 15 , wherein said substrates are beads.  
     
     
         17 . A method of claim is, wherein said plurality of reagents comprise substantially all possible subsequences of said preselected length found in said target.  
     
     
         18 . A method of  claim 15 , wherein said solid phase substrates are a single substrate having attached thereto reagents recognizing substantially all possible subsequences of preselected length found in said target.  
     
     
         19 . A method of  claim 15 , further comprising the step of analyzing a plurality of said recognized subsequences to assemble a sequence of said target polymer.  
     
     
         20 . A method of  claim 16 , wherein at least some of said plurality of substrates have on e subsequence specific reagent attached thereto, and said substrates are coded to indicate the specificity of said reagent.  
     
     
         21 . A method of using a fluorescent nucleotide to detect interactions with oligonucleotide probes of known sequence, said method comprising: 
 a) attaching said nucleotide to a target unknown polynucleotide sequence, and    b) exposing said target polynucleotide sequence to a collection of positionally defined oligonucleotide probes of known sequences to determine the sequences of said probes which interact with said target.    
     
     
         22 . A method of  claim 21 , further comprising the step of: 
 a) collating said known sequences to determine the overlaps of said known sequences to determine the sequence of said target sequence.    
     
     
         23 . A method of mapping a plurality of sequences relative to one another, said method comprising: 
 a) preparing a substrate having a plurality of positionally attached sequence specific probes;    b) exposing each of said sequences to said substrate, thereby determining the patterns of interaction between said sequence specific probes and said sequences; and    c) determining the relative locations of said sequence specific probe interactions on said sequences to determine the overlaps and order of said sequences.    
     
     
         24 . A method of  claim 23 , wherein said sequence specific probes are oligonucleotides.  
     
     
         25 . A method of  claim 23 , wherein said sequences are nucleic acid sequences.