Methods and apparati using single polymer analysis

Abstract

The invention relates to methods for analyzing and characterizing single polymers such as nucleic acid molecules. In preferred embodiments, the single molecules are analyzed using single molecule detection and analysis systems.

1 .- 30 . (canceled) 
     
     
         31 . A composition comprising
 a unit specific marker attached to a universal linker that is hybridized to a complementary nucleotide sequence attached to a detectable label.   
     
     
         32 . A method for characterizing a polymer sample, comprising
 contacting the polymer sample with a plurality of unit specific markers, each of the plurality having a unique and distinct label,   wherein, when bound to the polymer, individual unit specific markers are spaced apart on the polymer such that, if the labels were not distinct from each other, they would be separated by a distance less than the detection resolution.   
     
     
         33 . The method of  claim 32 , wherein the polymer is a nucleic acid molecule. 
     
     
         34 . The method of  claim 33 , wherein the nucleic acid molecule is free-flowing. 
     
     
         35 . The method of  claim 33 , wherein the nucleic acid molecule is fixed to a solid support. 
     
     
         36 . The method of  claim 33 , wherein the nucleic acid molecule is imaged directly. 
     
     
         37 . The method of  claim 32 , wherein the unique and distinct labels are substrates for an enzymatic reaction. 
     
     
         38 . The method of  claim 37 , wherein the enzymatic reaction is selected from the group consisting of a primer extension reaction and a ligase-mediated reaction. 
     
     
         39 . The method of  claim 33 , wherein the nucleic acid molecule is analyzed using a Gene Engine system. 
     
     
         40 . The method of  claim 32 , wherein the polymer is not pre-amplified. 
     
     
         41 . The method of  claim 32 , wherein the polymer is single stranded. 
     
     
         42 . The method of  claim 37 , wherein the enzymatic reaction produces a detectable product. 
     
     
         43 . The method of  claim 42 , wherein the detectable product is not amplified. 
     
     
         44 . The method of  claim 32 , wherein the polymer is detected using a backbone specific label. 
     
     
         45 . A method for characterizing a polymer, comprising
 fixing the polymer to a solid support,   contacting the polymer sample with a plurality of unit specific markers, each of the plurality having a unique and distinct label, and   determining a pattern of binding of the plurality of unit specific markers to the polymer,   wherein, when bound to the polymer, individual unit specific markers are spaced apart on the polymer such that, if the labels were not distinct from each other, they would be separated by a distance less than the detection resolution.   
     
     
         46 . The method of  claim 45 , wherein the polymer is a nucleic acid molecule. 
     
     
         47 . The method of  claim 46 , wherein the nucleic acid molecule is denatured to a single-stranded form. 
     
     
         48 . The method of  claim 45 , wherein the labels are substrates for enzyme reactions. 
     
     
         49 . The method of  claim 48 , wherein the enzyme reactions produces a detectable product. 
     
     
         50 . The method of  claim 49 , wherein the presence of a detectable product is determined using a single molecule detection system. 
     
     
         51 .- 175 . (canceled)