Kits containing modified amplification oligonucleotides

Abstract

The present invention concerns oligonucleotides containing one or more modified nucleotides which increase the binding affinity of the oligonucleotides to target nucleic acids having a complementary nucleotide base sequence. These modified oligonucleotides hybridize to the target sequence at a faster rate than unmodified oligonucleotides having an identical nucleotide base sequence. Such modified oligonucleotides include oligonucleotides containing at least one 2′-O-methylribofuranosyl moiety joined to a nitrogenous base. Oligonucleotides can be modified in accordance with the present invention to preferentially bind RNA targets. The present invention also concerns methods of using these modified oligonucleotides and kits containing the same.

1 . A kit for amplifying a target nucleic acid sequence contained in a target nucleic acid which may be present in a sample, said kit comprising: 
 an amplification oligonucleotide containing a first base sequence which hybridizes to a second base sequence contained in said target nucleic acid under amplification conditions,    wherein said first base sequence contains a cluster of at least four nucleotides, each nucleotide of said cluster having a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof,    wherein said amplification oligonucleotide does not include a label, and    wherein said amplification oligonucleotide is capable of being extended and forming part of a nucleic acid extension product or directing the synthesis of a nucleic acid transcription product under said amplification conditions; and    a nucleic acid polymerase.    
     
     
         2 . The kit of  claim 1 , wherein the 2′ modification is an alkyl, alkoxy or halide substitution to the ribofuranosyl moiety.  
     
     
         3 . The kit of  claim 2 , wherein the 2′ modification is an alkyl substitution to the ribofuranosyl moiety.  
     
     
         4 . The kit of  claim 1 , wherein said amplification oligonucleotide includes a promoter sequence.  
     
     
         5 . The kit of  claim 1  further comprising an oligonucleotide probe capable of specifically hybridizing to a base sequence contained in said extension product or said transcription product to form a duplex stable for detection in the presence of non-target nucleic acid in said sample under nucleic acid assay conditions.  
     
     
         6 . The kit of  claim 5 , wherein said probe contains one or more nucleotides modified to include a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof.  
     
     
         7 . The kit of  claim 5 , wherein said probe includes a label.  
     
     
         8 . The kit of  claim 1  further comprising a target capture oligonucleotide having a third base sequence, wherein said third base sequence hybridizes to a fourth base sequence contained in said target nucleic acid under nucleic acid assay conditions.  
     
     
         9 . The kit of  claim 8 , wherein said third base sequence contains one or more nucleotides modified to include a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof.  
     
     
         10 . The kit of  claim 8 , wherein the 3′ terminus of said target capture oligonucleotide is capped or blocked to prevent or inhibit its use as a template for nucleic acid polymerase activity.  
     
     
         11 . The kit of  claim 8  further comprising a solid support for directly or indirectly immobilizing said target capture oligonucleotide, wherein said target capture oligonucleotide includes a fifth base sequence which does not hybridize to said target nucleic acid under nucleic acid assay conditions.  
     
     
         12 . The kit of  claim 1  further comprising written instructions for performing a transcription-based method of amplification.  
     
     
         13 . A kit for amplifying a target nucleic acid sequence contained in a target nucleic acid which may be present in a sample, said kit comprising: 
 an amplification oligonucleotide containing a first base sequence which hybridizes to a second base sequence contained in said target nucleic acid under amplification conditions, wherein said first base sequence contains at least one ribonucleotide or deoxyribonucleotide having a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof, and wherein said amplification oligonucleotide is capable of being extended and forming part of a nucleic acid extension product or directing the synthesis of a nucleic acid transcription product under said amplification conditions; and    a labeled oligonucleotide probe capable of specifically hybridizing to a base sequence contained in said extension product or said transcription product to form a duplex stable for detection in the presence of non-target nucleic acid in said sample under nucleic acid assay conditions.    
     
     
         14 . The kit of  claim 13 , wherein the 2′ modification is an alkyl, alkoxy or halide substitution to the ribofuranosyl moiety.  
     
     
         15 . The kit of  claim 13 , wherein the 2′ modification is an alkyl substitution to the ribofuranosyl moiety.  
     
     
         16 . The kit of  claim 13 , wherein said first base sequence contains a cluster of least four nucleotides, each nucleotide of said cluster having a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof.  
     
     
         17 . The kit of  claim 16 , wherein the 2′ modification is an alkyl, alkoxy or halide substitution to the ribofuranosyl moiety.  
     
     
         18 . The kit of  claim 16 , wherein the 2′ modification is an alkyl substitution to the ribofuranosyl moiety.  
     
     
         19 . The kit of  claim 13  further comprising a nucleic acid polymerase.  
     
     
         20 . The kit of  claim 19 , wherein said polymerase is an RNA polymerase.  
     
     
         21 . The kit of  claim 13 , wherein said amplification oligonucleotide includes a promoter sequence.  
     
     
         22 . The kit of  claim 13 , wherein said amplification oligonucleotide does not include a label.  
     
     
         23 . The kit of  claim 13 , wherein said probe contains one or more nucleotides modified to include a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof.  
     
     
         24 . The kit of  claim 13  further comprising a target capture oligonucleotide having a third base sequence, wherein said third base sequence hybridizes to a fourth base sequence contained in said target nucleic acid under nucleic acid assay conditions.  
     
     
         25 . The kit of  claim 24 , wherein said third base sequence contains one or more nucleotides modified to include a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof.  
     
     
         26 . The kit of  claim 24 , wherein the 3′ terminus of said target capture oligonucleotide is capped or blocked to prevent or inhibit its use as a template for nucleic acid polymerase activity.  
     
     
         27 . The kit of  claim 24  further comprising a solid support for directly or indirectly immobilizing said target capture oligonucleotide, wherein said target capture oligonucleotide includes a fifth base sequence which does not hybridize to said target nucleic acid under nucleic acid assay conditions.  
     
     
         28 . The kit of  claim 13  further comprising written instructions for performing a polymerase chain reaction method of amplification.  
     
     
         29 . The kit of  claim 13  further comprising written instructions for performing a transcription-based method of amplification.  
     
     
         30 . A kit for amplifying a target nucleic acid sequence contained in a target nucleic acid which may be present in a sample, said kit comprising: 
 a first amplification oligonucleotide containing a first base sequence which hybridizes to a second base sequence contained in said target nucleic acid 5′ to said target sequence under amplification conditions; and    a second amplification oligonucleotide containing a third base sequence which hybridizes to a fourth base sequence contained in a nucleic acid sequence complementary to at least a portion of said target nucleic acid 3′ to said target sequence under said amplification conditions,    wherein at least one of said first and third base sequences contains a cluster of at least four nucleotides, each nucleotide of said cluster having a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof, and    wherein each of said first and second amplification oligonucleotides is capable of being extended and forming part of a nucleic acid extension product or directing the synthesis of a nucleic acid transcription product under said amplification conditions.    
     
     
         31 . The kit of  claim 30 , wherein the 2′ modification is an alkyl, alkoxy or halide substitution to the ribofuranosyl moiety.  
     
     
         32 . The kit of  claim 31 , wherein the 2′ modification is an alkyl substitution to the ribofuranosyl moiety.  
     
     
         33 . The kit of  claim 30 , wherein each of said first and third base sequences contains at least one nucleotide having a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof.  
     
     
         34 . The kit of  claim 33 , wherein the 2′ modification is an alkyl, alkoxy or halide substitution to the ribofuranosyl moiety.  
     
     
         35 . The kit of  claim 34 , wherein the 2′ modification is an alkyl substitution to the ribofuranosyl moiety.  
     
     
         36 . The kit of  claim 30  further comprising a nucleic acid polymerase.  
     
     
         37 . The kit of  claim 36 , wherein said polymerase is an RNA polymerase.  
     
     
         38 . The kit of  claim 30 , wherein at least one of said first and second amplification oligonucleotides includes a promoter sequence.  
     
     
         39 . The kit of  claim 30 , wherein neither of said first and second amplification oligonucleotides includes a label.  
     
     
         40 . The kit of  claim 30  further comprising an oligonucleotide probe capable of specifically hybridizing to a base sequence contained in said extension product or said transcription product to form a duplex stable for detection in the presence of non-target nucleic acid in said sample under nucleic acid assay conditions.  
     
     
         41 . The kit of  claim 40 , wherein said probe contains one or more nucleotides modified to include a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof.  
     
     
         42 . The kit of  claim 40 , wherein said probe includes a label.  
     
     
         43 . The kit of  claim 30  further comprising a target capture oligonucleotide having a fifth base sequence, wherein said fifth base sequence hybridizes to a sixth base sequence contained in said target nucleic acid under nucleic acid assay conditions.  
     
     
         44 . The kit of  claim 43 , wherein said fifth base sequence contains one or more nucleotides modified to include a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof.  
     
     
         45 . The kit of  claim 43 , wherein the 3′ terminus of said target capture oligonucleotide is capped or blocked to prevent or inhibit its use as a template for nucleic acid polymerase activity.  
     
     
         46 . The kit of  claim 43  further comprising a solid support for directly or indirectly immobilizing said target capture oligonucleotide, wherein said target capture oligonucleotide includes a seventh base sequence which does not hybridize to said target nucleic acid under nucleic acid assay conditions.  
     
     
         47 . The kit of  claim 30  further comprising written instructions for performing a polymerase chain reaction method of amplification.  
     
     
         48 . The kit of  claim 30  further comprising written instructions for performing a transcription-based method of amplification.  
     
     
         49 . A kit for amplifying a target nucleic acid sequence contained in a target nucleic acid which may be present in a sample, said kit comprising: 
 a first amplification oligonucleotide containing a first base sequence which hybridizes to a second base sequence contained in said target nucleic acid 5′ to said target sequence under amplification conditions;    a second amplification oligonucleotide containing a third base sequence which hybridizes to a fourth base sequence contained in a nucleic acid sequence complementary to at least a portion of said target nucleic acid 3′ to said target sequence under said amplification conditions,    wherein at least one of said first and third base sequences contains one or more ribonucleotides or deoxyribonucleotide having a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof, and    wherein each of said first and second amplification oligonucleotides is capable of being extended and forming part of a nucleic acid extension product or directing the synthesis of a nucleic acid transcription product under said amplification conditions; and    a labeled oligonucleotide probe capable of specifically hybridizing to a base sequence contained in said extension product or said transcription product to form a duplex stable for detection in the presence of non-target nucleic acid in said sample under nucleic acid assay conditions.    
     
     
         50 . The kit of  claim 49 , wherein the 2′ modification is an alkyl, alkoxy or halide substitution to the ribofuranosyl moiety.  
     
     
         51 . The kit of  claim 50 , wherein the 2′ modification is an alkyl substitution to the ribofuranosyl moiety.  
     
     
         52 . The kit of  claim 49 , wherein each of said first and third base sequences contains at least one ribonucleotide or deoxyribonucleotide having a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof.  
     
     
         53 . The kit of  claim 52 , wherein the 2′ modification is an alkyl, alkoxy or halide substitution to the ribofuranosyl moiety.  
     
     
         54 . The kit of  claim 53 , wherein the 2′ modification is an alkyl substitution to the ribofuranosyl moiety.  
     
     
         55 . The kit of  claim 49 , wherein at least one of said first and third base sequences includes a cluster of at least four nucleotides, each nucleotide of said cluster having a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof.  
     
     
         56 . The kit of  claim 55 , wherein the 2′ modification is an alkyl, alkoxy or halide substitution to the ribofuranosyl moiety.  
     
     
         57 . The kit of  claim 56 , wherein the 2′ modification is an alkyl substitution to the ribofuranosyl moiety.  
     
     
         58 . The kit of  claim 49  further comprising a nucleic acid polymerase.  
     
     
         59 . The kit of  claim 58 , wherein said polymerase is an RNA polymerase.  
     
     
         60 . The kit of  claim 49 , wherein at least one of said first and second amplification oligonucleotides includes a promoter sequence.  
     
     
         61 . The kit of  claim 49 , wherein neither of said first and second amplification oligonucleotides includes a label.  
     
     
         62 . The kit of  claim 49 , wherein said probe contains one or more ribonucleotides modified to include a 2′-O-methyl substitution to the ribofuranosyl moiety.  
     
     
         63 . The kit of  claim 49  further comprising a target capture oligonucleotide having a fifth base sequence, wherein said fifth base sequence hybridizes to a sixth base sequence contained in said target nucleic acid under nucleic acid assay conditions.  
     
     
         64 . The kit of  claim 63 , wherein said fifth base sequence contains one or more ribonucleotides modified to include a 2′-O-methyl substitution to the ribofuranosyl moiety.  
     
     
         65 . The kit of  claim 63  wherein the 3′ terminus of said target capture oligonucleotide is capped or blocked to prevent or inhibit its use as a template for nucleic acid polymerase activity.  
     
     
         66 . The kit of  claim 63  further comprising a solid support for directly or indirectly immobilizing said target capture oligonucleotide, wherein said target capture oligonucleotide includes a seventh base sequence which does not hybridize to said target nucleic acid under nucleic acid assay conditions.  
     
     
         67 . The kit of  claim 49  further comprising written instructions for performing a polymerase chain reaction method of amplification.  
     
     
         68 . The kit of  claim 49  further comprising written instructions for performing a transcription-based method of amplification.  
     
     
         69 . A kit for amplifying a target nucleic acid sequence contained in a target nucleic acid which may be present in a sample, said kit comprising: 
 an amplification oligonucleotide containing a first base sequence which hybridizes to a second base sequence contained in said target nucleic acid under amplification conditions, wherein said first base sequence contains a cluster of at least four nucleotides, each nucleotide of said cluster having a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof, and wherein said amplification oligonucleotide is capable of being extended and forming part of a nucleic acid extension product or directing the synthesis of a nucleic acid transcription product under said amplification conditions;    an oligonucleotide probe capable of specifically hybridizing to a base sequence contained in said extension product or said transcription product to form a duplex stable for detection in the presence of non-target nucleic acid in said sample under nucleic acid assay conditions; and    a nucleic acid polymerase.    
     
     
         70 . The kit of  claim 69 , wherein the 2′ modification is an alkyl, alkoxy or halide substitution to the ribofuranosyl moiety.  
     
     
         71 . The kit of  claim 70 , wherein the 2′ modification is an alkyl substitution to the ribofuranosyl moiety.  
     
     
         72 . The kit of  claim 69 , wherein said probe contains one or more nucleotides modified to include a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof.  
     
     
         73 . A kit for amplifying a target nucleic acid sequence contained in a target nucleic acid which may be present in a sample, said kit comprising: 
 an amplification oligonucleotide containing a first base sequence which hybridizes to a second base sequence contained in said target nucleic acid under amplification conditions, wherein said first base sequence contains a cluster of at least four nucleotides, each nucleotide of said cluster having a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof, and wherein said amplification oligonucleotide is capable of being extended and forming part of a nucleic acid extension product or directing the synthesis of a nucleic acid transcription product under said amplification conditions;    a target capture oligonucleotide having a third base sequence, wherein said third base sequence hybridizes to a fourth base sequence contained in said target nucleic acid under nucleic acid assay conditions; and    a nucleic acid polymerase.    
     
     
         74 . The kit of  claim 73 , wherein the 2′ modification is an alkyl, alkoxy or halide substitution to the ribofuranosyl moiety.  
     
     
         75 . The kit of  claim 74 , wherein the 2′ modification is an alkyl substitution to the ribofuranosyl moiety.  
     
     
         76 . The kit of  claim 73 , wherein said third base sequence contains one or more nucleotides modified to include a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof.  
     
     
         77 . The kit of  claim 73 , wherein the 3′ terminus of said target capture oligonucleotide is capped or blocked to prevent or inhibit its use as a template for nucleic acid polymerase activity.  
     
     
         78 . The kit of  claim 73  further comprising a solid support for directly or indirectly immobilizing said target capture oligonucleotide, wherein said target capture oligonucleotide includes a fifth base sequence which does not hybridize to said target nucleic acid under nucleic acid assay conditions.  
     
     
         79 . A kit for amplifying a target nucleic acid sequence contained in a target nucleic acid which may be present in a sample, said kit comprising: 
 an amplification oligonucleotide containing a first base sequence which hybridizes to a second base sequence contained in said target nucleic acid under amplification conditions, wherein said first base sequence contains a cluster of at least four nucleotides, each nucleotide of said cluster having a 2′ modification to the ribofuranosyl or deoxyribofuranosyl moiety thereof, and wherein said amplification oligonucleotide contains a promoter sequence; and    a nucleic acid polymerase.    
     
     
         80 . The kit of  claim 79 , wherein the 2′ modification is an alkyl, alkoxy or halide substitution to the ribofuranosyl moiety.  
     
     
         81 . The kit of  claim 80 , wherein the 2′ modification is an alkyl substitution to the ribofuranosyl moiety.