Compositions and methods of synthesis and use of novel nucleic acid structures

Abstract

The present invention is directed to a method to produce 8-amino-2′deoxyadenosine by treating 8-azido-2′deoxyadenosine with an aqueous solution of methylamine or dimethylamine.

1 - 8 . (canceled)  
     
     
         9 . A triplex-forming oligonucleotide, comprising: 
 (a) a polypyrimidine sequence;    (b) a polypurine sequence complementary to a target sequence and comprising at least one of 8-aminoadenine, 8-aminoguanine or 8-aminohypoxanthine; and    (c) a linker that connects said polypyrimidine sequence with said polypurine sequence so that said polypurine sequence and said polypyrimidine sequence form a parallel double stranded structure.    
     
     
         10 . The oligonucleotide of  claim 9 , wherein said polypyrimidine sequence is in a 5′ to 3′ orientation linked to said polypyrimidine sequence in a 3′ to 5′ orientation.  
     
     
         11 . The oligonucleotide of  claim 9 , wherein said polypyrimidine sequence is in a 3′ to 5′ orientation linked to said polypyrimidine sequence in a 5′ to 3′ orientation.  
     
     
         12 . A method of making a triplex-forming oligonucleotide, comprising synthesizing an oligonucleotide structure comprising a polypyrimidine sequence linked to a polypurine sequence comprising at least one of 8-aminoadenine, 8-aminoguanine, or 8-aminohypoxanthine, wherein said polypurine sequence is complementary to a target sequence and forms a parallel double-stranded structure with said polypyrimidine sequence.  
     
     
         13 . The method of  claim 12 , wherein said polypyrimidine sequence is in a 5′ to 3′ orientation linked to said polypyrimidine sequence in a 3′ to 5′ orientation.  
     
     
         14 . The method of  claim 12 , wherein said polypyrimidine sequence is in a 3′ to 5′ orientation linked to said polypyrimidine sequence in a 5′ to 3′ orientation.  
     
     
         15 . A method for detecting a specific target sequence in a sample comprising: 
 (a) providing at least one oligonucleotide structure comprising a polypyrimidine sequence connected to a linker,    (b) providing a polypurine sequence having at least one 8-aminoadenine, 8-aminoguanine or 8-aminohypoxanthine; and    (c) connecting said polypyrimidine sequence and said polypurine sequence with a linker, said linker is directly or indirectly attached to a capture molecule, said capture molecule capable of attaching to a reporter molecule,    wherein binding of said capture molecule and said reporter molecule detects the presence of a specific target sequence in said sample.    
     
     
         16 . The method of  claim 15 , wherein said polypyrimidine sequence is in a 5′ to 3′ orientation linked to said polypyrimidine sequence in a 3′ to 5′ orientation.  
     
     
         17 . The method of  claim 15 , wherein said polypyrimidine sequence is in a 3′ to 5′ orientation linked to said polypyrimidine sequence in a 5′ to 3′ orientation.