Competitive probes for engineering signal generation

Abstract

A method of identifying a first target nucleic acid comprising, providing a sample comprising the first target nucleic acid, providing a first set of paired oligonucleotides with complementarity to the first target nucleic acid, the first set of paired oligonucleotides comprising a first ratio of (a) first competitive oligonucleotides to (b) first signal oligonucleotides comprising a signal tag, wherein the competitive oligonucleotides compete with the signal oligonucleotides for binding to the first target nucleic acid, amplifying the first target nucleic acid with the polymerase chain reaction, thereby degrading the first signal oligonucleotide and permitting generation of a first signal, generating the first signal, measuring intensity of the first signal, and correlating the intensity of the first signal to the first ratio, thereby identifying the first target nucleic acid.

What is claimed is: 
     
         1 - 28 . (canceled) 
     
     
         29 . A method of altering an amplification level of a target nucleic acid comprising, 
 providing a sample comprising the target nucleic acid,   providing a set of paired oligonucleotides able to hybridize to the target nucleic acid, the set of paired oligonucleotides comprising a ratio of (a) competitive oligonucleotides to (b) functional oligonucleotides,   wherein the competitive oligonucleotides compete with the functional oligonucleotides for binding to the target nucleic acid and are not extendible by a nucleic acid polymerase,   wherein the functional oligonucleotides are extendible by the nucleic acid polymerase as primers for amplifying the target nucleic acid; and   subjecting the target nucleic acid to an amplification reaction.   
     
     
         30 . The method of  claim 29 , wherein the competitive oligonucleotides comprise at least one modified end. 
     
     
         31 . The method of  claim 30 , wherein the at least one modified end comprises a 3′ end lacking a hydroxyl group. 
     
     
         32 . The method of  claim 30 , wherein the at least one modified end comprises a 5′ end lacking a phosphate group. 
     
     
         33 . The method of  claim 30 , wherein the at least one modified end comprises a 5′ capped end. 
     
     
         34 . The method of  claim 30 , wherein the at least one modified end comprises a 3′ capped end. 
     
     
         35 . The method of any of  claims 29 , wherein a total number of molecules during the amplification reaction remains constant. 
     
     
         36 . The method of any of  claims 29 , wherein the amplification reaction is a polymerase chain reaction (PCR). 
     
     
         37 . The method of any one of  claims 29 , wherein the method comprises detecting the presence of the target nucleic acid. 
     
     
         38 . The method of any one of  claim 29 , wherein the method comprises quantifying the target nucleic acid. 
     
     
         39 . The method of any one of  claims 29 , wherein the method comprises altering an amplification level of a second target nucleic acid comprising:
 a second set of paired oligonucleotides with complementarity to a second target nucleic acid, the set of paired oligonucleotides comprising a second ratio of (c) competitive oligonucleotides to (d) functional oligonucleotides,   wherein the first ratio and the second ratio are different, and   wherein the sample comprises the first target nucleic acid and the second target nucleic acid.   
     
     
         40 . The method of  claim 39 , wherein the method comprises detecting a presences of the first nucleic acid target and detecting a presence of the second nucleic acid target. 
     
     
         41 . A composition comprising:
 a set of paired oligonucleotides able to hybridize to a target nucleic acid, said set of paired oligonucleotides comprising a ratio of (a) competitive oligonucleotides to (b) functional oligonucleotides,   wherein the competitive oligonucleotides are configured to compete with the functional oligonucleotides for binding to the nucleic acid target during amplification of the first target nucleic acid during an amplification reaction and are not extendible by a nucleic acid polymerase.   
     
     
         42 . The composition of  claim 41 , wherein the competitive oligonucleotides comprise at least one modified end. 
     
     
         43 . The composition of  claim 42 , wherein the at least one modified end comprises a 3′ end lacking a hydroxyl group. 
     
     
         44 . The composition of  claim 42 , wherein the at least one modified end comprises a 5′ end lacking a phosphate group. 
     
     
         45 . The composition of  claim 42 , wherein the at least one modified end comprises a 5′ capped end. 
     
     
         46 . The composition of  claim 42 , wherein the at least one modified end comprises a 3′ capped end. 
     
     
         47 . The composition of any of  claims 41 , wherein the amplification reaction is a polymerase chain reaction (PCR). 
     
     
         48 . The composition of  claim 41 , wherein the composition comprises:
 a second set of paired oligonucleotides able to hybridize to a second target nucleic acid, said second set of paired oligonucleotides comprising a second ratio of (c) competitive oligonucleotides to (d) functional oligonucleotides.