Capturing sequences adjacent to type-IIs restriction sites for genomic library mapping

Abstract

The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.

1 - 12 . (canceled)  
     
     
         13 . A composition comprising at least two oligonucleotide probes, which specifically hybridize to a polymorphism in a DNA sample, and an amplified mixture of DNA isolated from a genome, wherein the amplified mixture of DNA is made by cleaving a genomic DNA sample with at least one restriction enzyme, thereby providing restriction fragments; 
 ligating adapter nucleic acids to the DNA restriction fragments;    providing primers that are complementary to the adapter nucleic acids; and,    amplifying the DNA restriction fragments by the polymerase chain reaction by extending the primers, thereby providing the amplified mixture of DNA.    
     
     
         14 . The composition of  claim 13 , wherein the at least two oligonucleotides are immobilized on a solid support.  
     
     
         15 . A method of characterizing a nucleic acid, comprising: 
 providing at least one oligonucleotide probe which specifically hybridizes to a polymorphic genetic linkage marker in a genomic DNA sample;    amplifying a mixture of nucleic acids comprising a group of genome fragments comprising polymorphisms, thereby providing an amplified nucleic acid mixture of genome fragments; and    hybridizing the at least one oligonucleotide probe to the amplified nucleic acid mixture, thereby detecting at least one nucleic acid fragment in said amplified mixture.    
     
     
         16 . The method of  claim 15 , wherein the oligonucleotide probe is a member of an array of oligonucleotide probes, which array comprises additional oligonucleotide probes which hybridize to one or more polymorphic genetic linkage markers.  
     
     
         17 . The method of  claim 15 , wherein the amplified nucleic acid mixture is made by cleaving a genomic DNA sample with at least one restriction enzyme, thereby providing restriction fragments; 
 ligating adapter nucleic acids to the DNA restriction fragments;    providing primers that are complementary to the adapter nucleic acids; and,    amplifying the DNA restriction fragments by the polymerase chain reaction by extending the primers, thereby providing the amplified nucleic acid mixture.