High Throughput Genome Sequencing on DNA Arrays

Abstract

The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.

1 . A method of determining the identification of a first nucleotide at a detection position of a target sequence comprising a plurality of detection positions, said method comprising:
 (a) providing a plurality of concatemers, wherein each concatemer comprises a plurality of monomers and each monomer comprises:
 i) a first target domain of said target sequence comprising a first set of target detection positions; 
 ii) a first adaptor comprising a Type IIs endonuclease restriction site; 
 iii) a second target domain of said target sequence comprising a second set of target detection positions; and 
 iv) a second interspersed adaptor comprising a Type IIs endonuclease restriction site; 
   (b) identifying said first nucleotide.