Methods for detecting nucleic acid sequence variations

Abstract

The invention employs an unlabeled signal primer comprising a 5′ adapter sequence for detection of variations in nucleic acid target sequences. The detection system further comprises a reporter probe, the 3′ end of which hybridizes to the complement of the 5′ adapter sequence of the signal primer to produce a 5′ overhang. Polymerase is used to fill in the overhang and synthesize the complement of the 5′ overhang of the reporter probe. Synthesis of the reporter probe complement is detected, either directly or indirectly, as an indication of the presence of the target.

1 - 23 . (canceled) 
     
     
         24 . A set of oligonucleotides for detecting a target sequence comprising: a) a first unlabeled signal primer comprising a single oligonucleotide having a 3′ target binding sequence and a 5′ adapter sequence, b) a second signal primer having an adapter sequence which is substantially identical to an adapter sequence of the first signal primer: and; c) a reporter probe comprising a 5′ reporter moiety and 3′ sequence which is substantially identical to the adapter sequence. 
     
     
         25 . The set of oligonucleotides of  claim 24 , wherein the reporter moiety is labeled. 
     
     
         26 . The set of oligonucleotides of  claim 25 , wherein the reporter moiety is labeled with a fluorescent donor/quencher dye pair. 
     
     
         27 . The set of oligonucleotides of  claim 24 , wherein the reporter moiety is selected from the group consisting of secondary structures and specialized sequences. 
     
     
         28 . The set of oligonucleotides of  claim 27 , wherein the reporter moiety is selected from the group consisting of G-quartets and restriction endonuclease recognition sites. 
     
     
         29 . The set of oligonucleotides of  claim 24 , wherein the reporter probe is non-extendible. 
     
     
         30 . A set of oligonucleotides for detecting a target sequence comprising: a) an unlabeled signal primer comprising a single oligonucleotide having a 3′ target-binding sequence and a 5′ adapter sequence, b) a second signal primer having an adapter sequence which is different from an adapter sequence of a first signal primer; and b) a reporter probe comprising a 5′ reporter moiety and 3′ sequence which is substantially identical to the adapter sequence.