Compositions And Methods For Free-Solution Conjugate Nucleic Acid Analysis

Abstract

The present invention provides compositions and methods for performing free-solution conjugate analysis of nucleic acid molecules. For example, the present invention provides multiplexed single-base extension assays for genotyping. In particular, the present invention provides a series of disperse polyamide “drag tags” for use in achieving high-resolution separation of nucleic acid reaction products.

1 . A composition comprising a set of four or more monodisperse uncharged polyamides conjugated to four or more DNA molecules such that the electrophoretic mobility of the DNA-polyamide bioconjugate is modified compared to an unconjugated DNA molecule. 
     
     
         2 . The composition of  claim 2 , wherein said bioconjugate comprises an uncharged polyamide conjugated to one end of said DNA molecule. 
     
     
         3 . The composition of  claim 1 , wherein said bioconjugate comprises uncharged polyamides conjugated to both ends of said DNA molecule. 
     
     
         4 . A method for detection of single nucleotide polymorphisms comprising:
 a) providing one or more DNA samples to be tested,   b) providing four or more DNA-polyamide bioconjugates specific to one or more single nucleotide polymorphisms,   c) contacting said DNA sample with said DNA-polyamide bioconjugates,   d) performing a single nucleotide polymorphism assay under conditions such that a single nucleotide polymorphism in said DNA sample is detected if present,   e) applying the assayed sample to a free solution electrophoretic instrument, and   f) detecting the presence or absence of a single nucleotide polymorphism in said DNA sample.   
     
     
         5 . The method of  claim 4 , further comprising the determination of a disease state in said subject DNA sample based on the detection of the presence of a single nucleotide polymorphism. 
     
     
         6 . The method of  claim 4 , further comprising the diagnosis of a disease state in said subject based on the detection of the presence of a disease state single nucleotide polymorphism in said subject DNA sample.