Nucleic acid accessible hybridization sites

Abstract

The present invention relates to methods and compositions for analyzing nucleic acids, and in particular, methods and compositions for detection and characterization of nucleic acid sequences and sequence changes. The present invention also provides methods and compositions for identifying oligonucleotides with desired hybridization properties to nucleic acid targets containing secondary structure.

1 - 49 . (Canceled).  
     
     
         50 . A method for detecting the presence of an HIV target sequence comprising: 
 a. providing: 
 i. a sample suspected of containing an HIV target sequence; and  
 ii. an oligonucleotide selected from the group consisting of SEQ ID NOs: 160-229;  
   b. exposing said sample to said oligonucleotide; and    c. detecting the presence or absence of said hiv target sequence in said sample.    
     
     
         51 . The method of  claim 50 , wherein said exposing step comprises conducting an invasive cleavage assay.  
     
     
         52 . A method, comprising: 
 a. providing: 
 i. a sample suspected of or known to contain an HIV target sequence; and  
 ii. an oligonucleotide, wherein at least a portion of said oligonucleotide hybridizes to a region of said HIV target sequence selected from the group consisting of nucleotides 1084-1088 of SEQ ID NO:158, nucleotides 1107-1112 of SEQ ID NO:158, nucleotides 1159-1162 of SEQ ID NO:158, nucleotides 1326-1332 of SEQ ID NO:158, nucleotides 1411-1414 of SEQ ID NO:158, nucleotides 1467-1469 of SEQ ID NO:158, nucleotides 1484-1491 of SEQ ID NO:158, nucleotides 1710-1714 of SEQ ID NO:158, nucleotides 7224-1728 of SEQ ID NO:158, nucleotides 1740-1743 of SEQ ID NO:158, nucleotides 1805-1813 of SEQ ID NO:158, nucleotides 1846-1849 of SEQ ID NO:158, nucleotides 1853-1855 of SEQ ID NO:158, nucleotides 1929-1935 of SEQ ID NO:158, nucleotides 988-1990 of SEQ ID NO:158, nucleotides 3326-3333 of SEQ ID NO:159, nucleotides 3342-3346 of SEQ ID NO:159, nucleotides 3361-3365 of SEQ ID NO:159, nucleotides 3373-3378 of SEQ ID NO:159, nucleotides 3456-3458 of SEQ ID NO:159, nucleotides 3510-3512 of SEQ ID NO:159, nucleotides 3536-3550 of SEQ ID NO:159, nucleotides 3576-3579 of SEQ ID NO:159, nucleotides 3620-3623 of SEQ ID NO:159, nucleotides 3657-3660 of SEQ ID NO:159, nucleotides 3718-3721 of SEQ ID NO:159, nucleotides 3825-3826 of SEQ ID NO:159, nucleotides 3854-3856 of SEQ ID NO:159, nucleotides 3879-3881 of SEQ ID NO:159, nucleotides 3890-3893 of SEQ ID NO:159, nucleotides 3930-3933 of SEQ ID NO:159, nucleotides 4015-4017 of SEQ ID NO:159, nucleotides 4070-4076 of SEQ ID NO:159, nucleotides 4116-4118 of SEQ ID NO:159, nucleotides 4147-4150 of SEQ ID NO:159, nucleotides 4173-4179 of SEQ ID NO:159, nucleotides 4247-4252 of SEQ ID NO:159, nucleotides 4285-4288 of SEQ ID NO:159, nucleotides 4338-4342 of SEQ ID NO:159, nucleotides 4482-4484 of SEQ ID NO:159, nucleotides 4502-4506 of SEQ ID NO:159, nucleotides 4510-4514 of SEQ ID NO:159, nucleotides 4540-4553 of SEQ ID NO:159, nucleotides 4573-4582 of SEQ ID NO:159, nucleotides 4593-4597 of SEQ ID NO:159, nucleotides 4636-4640 of SEQ ID NO:159, nucleotides 4672-4676 of SEQ ID NO:159, nucleotides 4716-4722 of SEQ ID NO:159, nucleotides 4730-4734 of SEQ ID NO:159, nucleotides 4793-4796 of SEQ ID NO:159, nucleotides 4812-4822 of SEQ ID NO:159, nucleotides 4913-4916 of SEQ ID NO:159, nucleotides 4936-4939 of SEQ ID NO:159, nucleotides 4956-4959 of SEQ ID NO:159, and nucleotides 5004-5008 of SEQ ID NO:159; and  
   b. exposing said sample to one or more of said oligonucleotides.    
     
     
         53 . The method of  claim 52 , further comprising the step of c) detecting the presence or absence of hybridization of said oligonucleotide to said HIV target sequence.  
     
     
         54 . The method of  claim 53 , wherein the presence of said hybridization of said oligonucleotide to said HIV target is indicative of the presence of HIV virus in said sample.  
     
     
         55 . The method of  claim 52 , wherein said exposing comprises conducting an invasive cleavage assay.  
     
     
         56 . The method of  claim 52 , wherein said oligonucleotide is an oligonucleotide for performing an invasive cleavage assay.  
     
     
         57 . The method of  claim 52 , wherein said oligonucleotide is an antisense oligonucleotide.  
     
     
         58 . The method of  claim 57 , wherein said antisense oligonucleotide is single stranded.  
     
     
         59 . The method of  claim 52 , wherein said exposing results in inhibition of expression of one or more genes from said HIV target sequence.  
     
     
         60 . A kit comprising one or more oligonucleotides, wherein at least a portion of said one or more oligonucleotides hybridize to a region of a HIV target sequence selected from the group consisting of nucleotides 1084-1088 of SEQ ID NO:158, nucleotides 1107-1112 of SEQ ID NO:158, nucleotides 1159-1162 of SEQ ID NO:158, nucleotides 1326-1332 of SEQ ID NO:158, nucleotides 1411-1414 of SEQ ID NO:158, nucleotides 1467-1469 of SEQ ID NO:158, nucleotides 1484-1491 of SEQ ID NO:158, nucleotides 1710-1714 of SEQ ID NO:158, nucleotides 7224-1728 of SEQ ID NO:158, nucleotides 1740-1743 of SEQ ID NO:158, nucleotides 1805-1813 of SEQ ID NO:158, nucleotides 1846-1849 of SEQ ID NO:158, nucleotides 1853-1855 of SEQ ID NO:158, nucleotides 1929-1935 of SEQ ID NO:158, nucleotides 988-1990 of SEQ ID NO:158, nucleotides 3326-3333 of SEQ ID NO:159, nucleotides 3342-3346 of SEQ ID NO:159, nucleotides 3361-3365 of SEQ ID NO:159, nucleotides 3373-3378 of SEQ ID NO:159, nucleotides 3456-3458 of SEQ ID NO:159, nucleotides 3510-3512 of SEQ ID NO:159, nucleotides 3536-3550 of SEQ ID NO:159, nucleotides 3576-3579 of SEQ ID NO:159, nucleotides 3620-3623 of SEQ ID NO:159, nucleotides 3657-3660 of SEQ ID NO:159, nucleotides 3718-3721 of SEQ ID NO:159, nucleotides 3825-3826 of SEQ ID NO:159, nucleotides 3854-3856 of SEQ ID NO:159, nucleotides 3879-3881 of SEQ ID NO:159, nucleotides 3890-3893 of SEQ ID NO:159, nucleotides 3930-3933 of SEQ ID NO:159, nucleotides 4015-4017 of SEQ ID NO:159, nucleotides 4070-4076 of SEQ ID NO:159, nucleotides 4116-4118 of SEQ ID NO:159, nucleotides 4147-4150 of SEQ ID NO:159, nucleotides 4173-4179 of SEQ ID NO:159, nucleotides 4247-4252 of SEQ ID NO:159, nucleotides 4285-4288 of SEQ ID NO:159, nucleotides 4338-4342 of SEQ ID NO:159, nucleotides 4482-4484 of SEQ ID NO:159, nucleotides 4502-4506 of SEQ ID NO:159, nucleotides 4510-4514 of SEQ ID NO:159, nucleotides 4540-4553 of SEQ ID NO:159, nucleotides 4573-4582 of SEQ ID NO:159, nucleotides 4593-4597 of SEQ ID NO:159, nucleotides 4636-4640 of SEQ ID NO:159, nucleotides 4672-4676 of SEQ ID NO:159, nucleotides 4716-4722 of SEQ ID NO:159, nucleotides 4730-4734 of SEQ ID NO:159, nucleotides 4793-4796 of SEQ ID NO:159, nucleotides 4812-4822 of SEQ ID NO:159, nucleotides 4913-4916 of SEQ ID NO:159, nucleotides 4936-4939 of SEQ ID NO:159, nucleotides 4956-4959 of SEQ ID NO:159, and nucleotides 5004-5008 of SEQ ID NO:159.  
     
     
         61 . The kit of  claim 60 , further comprising reagents for using said one or more oligonucleotides for detecting the presence or absence of said HIV target sequence in a sample.  
     
     
         62 . The kit of  claim 60 , further comprising instructions for using said kit for detecting the presence or absence of said HIV target sequence in a sample.  
     
     
         63 . The kit of  claim 60 , wherein said one or more oligonucleotides are antisense oligonucleotides.  
     
     
         64 . The kit of  claim 63 , wherein said antisense oligonucleotides are singe stranded.  
     
     
         65 . The kit of  claim 60 , further comprising instructions for using said kit for inhibiting expression of one or more genes from said HIV target sequence.