Optimized real-time nucleic acid detection processes

Abstract

This invention provides for compositions for use in real time nucleic acid detection processes. Such real time nucleic acid detection processes are carried out with energy transfer elements attached to nucleic acid primers, nucleotides, nucleic acid probes or nucleic acid binding agents. Real time nucleic acid detection allows for the qualitative or quantitative detection or determination of single-stranded or double-stranded nucleic acids of interest in a sample. Other processes are provided by this invention including processes for removing a portion of a homopolymeric sequence, e.g., poly A sequence or tail, from an analyte or library of analytes. Compositions useful in carrying out such removal processes are also described and provided. Paneling and multiplex analyses of more than one nucleic acid analyte using one sample are also provided.

What is claimed is: 
     
         1 . A composition of matter comprising:
 a first set of two adjacent oligonucleotides complementary to a target nucleic acid strand,
 wherein one or both of the two adjacent oligonucleotides of the first set comprises a first energy transfer element of an energy transfer element pair, and 
 wherein in the presence of the target nucleic strand and a ligase, the two oligonucleotides of the first set are ligatable to each other to form a first ligation product complementary to the target nucleic acid strand; and 
   a second set of two adjacent oligonucleotides complementary to the first ligation product,
 wherein one or both of the two adjacent oligonucleotides of the second set comprises a second energy transfer element of the energy transfer element pair, and 
 wherein in the presence of the first ligation product and a ligase, the two adjacent oligonucleotides of the second set are ligatable to each other to form a second ligation product complementary to the first ligation product, 
   wherein either (i) the first energy transfer element is an energy donor and the second energy transfer element is an energy acceptor, or (ii) the first energy transfer element is an energy acceptor and the second energy transfer element is an energy donor.   
     
     
         2 . The composition of  claim 1 , further comprising the target nucleic acid strand. 
     
     
         3 . The composition of matter of  claim 2 , further comprising a ligase. 
     
     
         4 . The composition of matter of  claim 1 , further comprising a ligase. 
     
     
         5 . The composition of matter of  claim 1 , wherein
 one of the two adjacent oligonucleotides of the first set comprises the first energy transfer element of the energy transfer element pair, and   one of the two adjacent oligonucleotides of the second set comprises the second energy transfer element of the energy transfer element pair.   
     
     
         6 . The composition of  claim 5 , further comprising the target nucleic acid strand. 
     
     
         7 . The composition of matter of  claim 6 , further comprising the ligase. 
     
     
         8 . The composition of matter of  claim 5 , further comprising the ligase.