Separtion of tagged fragments

Abstract

Methods of separating tagged nucleic acid fragments from populations of fragments are provided. The fragments are produced from a population of tagged nucleic acids. In some cases, the population of tagged nucleic acids comprises a population of clonal nucleic acids.

1 .- 5 . (canceled) 
     
     
         6 . A method comprising:
 providing a population of tagged nucleic acids, wherein the nucleic acids have a tag at only one end;   fragmenting the population of tagged nucleic acids to produce a population of fragments, wherein only the fragments having a tag at one end are tagged; and   using the tags on the tagged fragments as a tool to separate the tagged fragments from the population.   
     
     
         7 . The method of  claim 6  wherein the population of tagged nucleic acids is a clonal population. 
     
     
         8 . The method of  claim 6  wherein the tag comprises a DNA-binding protein, a modified nucleotide, or an oligonucleotide having a specific sequence. 
     
     
         9 . The method of  claim 6  wherein the tag comprises biotin. 
     
     
         10 . The method of  claim 6  wherein the tag comprises an oligonucleotide having a specific sequence, and the specific sequence comprises a nucleotide hybridization site or a protein binding site. 
     
     
         11 . The method of  claim 6  wherein the population of tagged nucleic acids is produced using a ligase to attach the tags. 
     
     
         12 . The method of  claim 6  wherein the fragmenting comprises enzymatic digestion, sonication, mechanical shearing, nebulization, hydroshearing, or electrochemical cleavage. 
     
     
         13 . The method of  claim 6  further comprising amplifying the tagged fragments. 
     
     
         14 . The method of  claim 13  wherein the amplifying comprises linear amplification. 
     
     
         15 . The method of  claim 6  further comprising circularizing the tagged fragments.