Nucleic acid quantification products and processes

Abstract

Described herein are products and processes for nucleic acid quantification, which are in part useful for detecting and determining the nucleotide sequence of rare nucleic acids (i.e., low copy number nucleic acids) in a sample. Such products and processes are useful for reducing the dynamic range among different nucleic acid species.

1 - 21 . (canceled) 
     
     
         22 . A method for quantifying the amount of a target nucleic acid of a biological sample, which comprises:
 (a) contacting (i) a target nucleic acid of a biological sample with (ii) a known amount of a counterpart nucleic acid for the target,   where the counterpart comprises (i) a nucleotide sequence substantially identical to its target nucleic acid, and (ii) a feature that distinguishes the counterpart nucleic acid from the target nucleic acid, under conditions in which the target hybridizes to the counterpart nucleic acid;   (b) amplifying the target and the counterpart nucleic acid to form a mixture comprising the amplified target nucleic acid and the amplified counterpart nucleic acid;   (c) determining the amount of the amplified target nucleic acid and the amplified counterpart nucleic acid; and   (d) quantifying the amount of the target nucleic acid based on the ratio of the amount of the amplified target nucleic acid and the amount of the amplified counterpart nucleic acid.   
     
     
         23 . The method of  claim 22 , wherein the target nucleic acid is contacted with differing predetermined amounts of the counterpart nucleic acid. 
     
     
         24 . The method of  claim 22 , wherein the feature in the counterpart is a one nucleotide substitution in the sequence substantially identical to its target. 
     
     
         25 . The methods of  claim 22 , wherein the method step (b) further comprises contacting the mixture with a capture nucleic acid, and wherein the capture agent is a capture nucleic acid that comprises a polynucleotide sequence complementary to a nucleotide sequence of a target. 
     
     
         26 . The methods of  claim 25 , wherein the capture agent is on a solid support. 
     
     
         27 . The methods of  claim 25 , wherein the capture agent interacts with the target and the counterpart with substantially equal affinity. 
     
     
         28 . The method of  claim 25 , wherein the capture agent melting temperature differs from the counterpart-capture agent melting temperature by less than or equal to one degree Celsius. 
     
     
         29 . The method of  claim 25 , wherein the counterpart nucleic acid or target nucleic acid comprises a capture moiety that binds to the capture agent. 
     
     
         30 . The method of  claim 22 , wherein the ratio of the amount of target nucleic acid to the amount of its counterpart nucleic acid is between 1:10 and 10:1. 
     
     
         31 . A system for quantifying the amount of a target nucleic acid of a biological sample, wherein the system comprises:
 (a) a target nucleic acid of the biological sample,   (b) a known amount of a counterpart nucleic acid for the target nucleic acid,   (c) a device configured for
 (i) amplifying the target nucleic acid, 
 (ii) quantifying the amplified target nucleic acid and the counterpart nucleic acid, and 
 (iii) determining the ratio of the amount of the amplified target nucleic acid and the counterpart nucleic acid.