Self-assembled single molecule arrays and uses thereof

Abstract

The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.

1 . (canceled) 
     
     
         2 . An ordered nucleic acid array comprising at least 100,000 different DNA species derived from a source nucleic acid, said array comprising:
 a solid substrate comprising a plurality of discrete spaced apart regions separated by inter-regional areas, wherein the spaced apart regions are at predefined positions on the substrate at a density of more than 10 5  per mm 2  and the area of said discrete spaced apart regions is in the range of from 0.04 μm 2  to 1 μm 2 ,   wherein more than 50% of said discrete spaced apart regions on the array contain a single species of said different DNA species, and,   wherein the more than 50% of said discrete spaced apart regions contain multiple copies of the single species.   
     
     
         3 . An ordered nucleic acid array comprising at least 100,000 different DNA species derived from a source nucleic acid, said array comprising:
 a solid substrate comprising a plurality of discrete spaced apart regions separated by inter-regional areas, wherein the spaced apart regions are at predefined positions on the substrate at a density of more than 10 5  per mm 2 , the spaced apart regions are approximately circular or square in shape so that their sizes can be indicated by a single linear dimension, and the single linear dimension is in the range of 125 nm to 250 nm,   wherein more than 50% of said discrete spaced apart regions on the array contain a single species of said different DNA species, and,   wherein the more than 50% of said discrete spaced apart regions contain multiple copies of the single species.   
     
     
         4 . The array of  claim 2  wherein the spaced apart regions are at predefined positions on the substrate at a density of more than 10 6  per mm 2 . 
     
     
         5 . The array of  claim 2  wherein more than 70% of said discrete spaced apart regions on the array have a single species of said different DNA species immobilized therein, and, more than 70% of said discrete spaced apart regions comprise multiple copies of the single species immobilized therein. 
     
     
         6 . The array of  claim 5  wherein more than 90% of said discrete spaced apart regions on the array have a single species of said different DNA species immobilized therein and wherein the more than 90% of said discrete spaced apart regions comprise multiple copies of the single species immobilized therein. 
     
     
         7 . The array of  claim 2  wherein said at least 100,000 different DNA species are genomic DNA fragments. 
     
     
         8 . The array of  claim 2  wherein said at least 100,000 different DNA species each comprise nucleic acid sequence derived from a source nucleic acid also each comprise an adaptor sequence, and all of said species have the same adaptor sequence. 
     
     
         9 . The array of  claim 8  wherein the DNA species are a cDNA or genomic library 
     
     
         10 . The array of  claim 8  wherein the spaced apart regions comprise oligonucleotides attached thereto, wherein the oligonucleotides comprise a sequence complementary to the adaptor sequence. 
     
     
         11 . The array of  claim 2  wherein the DNA species are more than 150 bases in length. 
     
     
         12 . The array of  claim 11  wherein the DNA species are in the range of 300 to 600 nucleotides in length. 
     
     
         13 . The array of  claim 8  wherein the DNA species are more than 150 bases in length. 
     
     
         14 . The array of  claim 13  wherein the DNA species are in the range of 300 to 600 nucleotides in length. 
     
     
         15 . The array of  claim 2  wherein the DNA species are in the range of 1-5 kb. 
     
     
         16 . The array of  claim 2  wherein the discrete spaced apart regions are approximately square in shape so that their sizes can be indicated by a single linear dimension, and the size of the square is size in the range of from 200 nm on a side to 500 nm on a side. 
     
     
         17 . The array of  claim 2  wherein the discrete spaced apart regions are arranged in a rectilinear pattern.