Method of Detection of Nucleic Acids With a Specific Sequence Composition

Abstract

This invention is a novel method for detecting and localizing specific nucleic acid sequences in a sample with a high degree of sensitivity and specificity. The method and novel compositions used in the method involve the use of Probe Nucleic Acids, the production of nucleic acid binding regions and the use of nucleic acid Target Binding Assemblies to detect and localize specific Target Nucleic Acids. The detection and localization of the Target Nucleic Acid is accomplished even in the presence of nucleic acids which have similar sequences. The method provides for a high degree of amplification of the signal produced by each specific binding event. In particular, methods and compositions are presented for the detection of HIV and HPV nucleic acid in samples. These methods and compositions find use in diagnosis of disease, genetic monitoring, forensics, and analysis of nucleic acid mixtures. Some of the novel compositions used in the detection method are useful in preventing or treating pathogenic conditions.

1 . A method of using a target binding assembly (TBA) wherein said TBA comprises a plurality of nucleic acid recognition units, wherein each of said nucleic acid recognition units binds to a specific nucleic acid sequence on a target double stranded nucleic acid molecule; and wherein the combined affinity of said plurality of nucleic acid recognition units is such that said TBA specifically binds to the target double stranded nucleic acid molecule but does not bind to non-target molecules; and wherein said method comprises contacting said TBA, or nucleic acid which codes for and produces said TBA, with said target double stranded nucleic acid molecule such that the TBA binds to the target double stranded nucleic acid molecule, and wherein the TBA comprises a nucleic acid recognition unit from at least one of the group consisting of NF-kB, NF-1L6, NE-AT, rel, TBP, the papilloma virus' E2 protein, sp1, cro and CI. 
     
     
         2 . The method, according to  claim 1 , wherein said TBA is selected from the group consisting of SEQ ID NO. 109, SEQ ID NO. 110, SEQ ID NO. 111, SEQ ID NO. 112, SEQ ID NO. 113, SEQ ID NO. 114, SEQ ID NO. 115, and SEQ ID NO. 116. 
     
     
         3 . The method, according to  claim 1 , wherein said TBA has a sequence selected from the group consisting of:
 A. I+II+III;   B. IV+V+III; and   C. IV+III   
       wherein I-V are defined as follows: 
       
         
           
                 
                 
                 
               
                     
                     
                 
                     
                   Group 
                   Sequence 
                 
                     
                     
                 
                     
                   I 
                   Any of SEQ ID NOS. 85-92; 
                 
                     
                   II 
                   Met Ser, linked to any of SEQ ID NOS 104-106, 
                 
                     
                     
                   each of which is linked to SEQ ID NO. 99; 
                 
                     
                   III 
                   SEQ ID NO 100 linked to any of SEQ ID NOS. 75-84 
                 
                     
                     
                   or 94-98; SEQ ID NO. 101 linked to either SEQ ID 
                 
                     
                     
                   NO 74 or SEQ ID NO. 93; or SEQ ID NO 102 linked 
                 
                     
                     
                   to SEQ ID NO. 74 or SEQ ID NO. 93; or any of 
                 
                     
                     
                   SEQ ID NOS. 72, 103, 73, or 63-71; 
                 
                     
                   IV 
                   Any of SEQ ID NOS. 104-106; and 
                 
                     
                   V 
                   SEQ ID NO. 99. 
                 
                     
                     
                 
             
                
                
                
               
               
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
     
     
         4 . The method, according to  claim 3 , wherein said TBA comprises a sequence selected from the group consisting of SEQ ID NOS:104-106. 
     
     
         5 . The method, according to  claim 3 , wherein said TBA has a sequence selected from Group B or Group C. 
     
     
         6 . The method, according to  claim 1 , wherein said TBA has SEQ ID NO: 114. 
     
     
         7 . The method, according to  claim 1 , wherein the target nucleic acid is from HIV or HPV. 
     
     
         8 . The method, according to  claim 1 , wherein the binding affinity is 10 −5  to 10 −12 .