Dna array

Abstract

Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer.

1 - 73 . (canceled) 
     
     
         74 . A random DNA array comprising
 a) a support,   b) a plurality of individual DNA binding regions arranged in a pattern at predetermined locations on the support, and   c) individual DNA molecules disposed on the support and immobilized at the individual DNA binding regions,
 wherein the individual DNA binding regions comprise capture oligonucleotides for immobilizing individual DNA molecules, and all of the individual DNA binding regions of the DNA array comprise the same capture oligonucleotides, 
 wherein the individual DNA molecules are immobilized on the individual DNA binding regions by a covalent or non-covalent interaction with the capture oligonucleotides, 
 wherein the individual DNA molecules each comprise a DNA target sequence, 
 wherein a majority of the individual DNA binding regions on the support each comprise a plurality of individual DNA molecules immobilized thereon, 
 wherein, in each individual DNA binding region of the majority of the individual DNA binding regions on the support, multiple individual DNA molecules of the plurality of individual DNA molecules immobilized thereon comprise the same DNA target sequence, 
 wherein the DNA target sequences of the multiple individual DNA molecules immobilized on the individual DNA binding regions are not known, 
 wherein said individual DNA binding regions of the majority of the individual DNA binding regions on the support do not all comprise the same multiple individual DNA molecules, and 
 wherein the random DNA array is not a bead array. 
   
     
     
         75 . The random DNA array of  claim 74  wherein the individual DNA molecules comprise a target sequence and an adaptor sequence, and the individual DNA molecules are immobilized on the individual DNA binding regions by base pairing between the capture oligonucleotide and the adaptor sequence. 
     
     
         76 . The random DNA array of  claim 74  wherein the capture oligonucleotides are 20 to 100 bases in length. 
     
     
         77 . The random DNA array of  claim 74  wherein the immobilized individual DNA molecules comprise two different adaptor sequences. 
     
     
         78 . The random DNA array of  claim 77  wherein the individual DNA molecules are immobilized by an association between the two different adaptor sequences and two different capture oligonucleotide sequences in the individual DNA binding regions. 
     
     
         79 . The random DNA array of  claim 74 , wherein the individual DNA molecules are immobilized by a capture oligonucleotide at the 5′ terminus, wherein the capture oligonucleotide is immobilized on the individual DNA binding regions, whereby the individual DNA molecules are immobilized on the individual DNA binding regions by a covalent interaction with a capture oligonucleotide. 
     
     
         80 . The random DNA array of  claim 74 , wherein the DNA target sequences are from a cDNA or genomic DNA library. 
     
     
         81 . The random DNA array of  claim 74 , wherein the DNA target sequences are genomic DNA sequences. 
     
     
         82 . The random DNA array of  claim 81 , wherein the DNA target sequences are human genomic sequences. 
     
     
         83 . The random DNA array of  claim 74 , wherein the DNA target sequences are cDNA sequences. 
     
     
         84 . The random DNA array of  claim 83 , wherein the DNA target sequences are human cDNA sequences. 
     
     
         85 . The DNA array of  claim 79  wherein at least some of the individual DNA molecules comprise one copy of the DNA target sequence. 
     
     
         86 . The DNA array of  claim 74  wherein the pattern is a rectilinear pattern. 
     
     
         87 . The DNA array of  claim 74  wherein the pattern is a grid pattern. 
     
     
         88 . The random DNA array of  claim 74  wherein said individual DNA molecules disposed on the support comprise at least 10,000 different DNA target sequences. 
     
     
         89 . The DNA array of  claim 74  wherein the individual DNA binding regions are substantially circular or square in shape so that their sizes can be indicated by a single linear dimension, which is in the range of 125-250 nm. 
     
     
         90 . The DNA array of  claim 74  wherein the individual DNA binding regions are substantially circular or square in shape so that their sizes can be indicated by a single linear dimension, which is in the range of 200-500 nm. 
     
     
         91 . The random DNA array of  claim 74  wherein said individual DNA binding regions in (b) are at a density greater than 10,000 per mm 2 . 
     
     
         92 . The random DNA array of  claim 76  wherein said individual DNA binding regions in (b) are at a density in the range of 1 million to 10 million per mm 2 .