Kits containing modified amplification oligonucleotides
First Claim
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.
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Accused Products
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.
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Citations
81 Claims
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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:
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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. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
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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:
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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. - View Dependent Claims (14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29)
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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:
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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, andwherein 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. - View Dependent Claims (31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48)
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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:
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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, andwherein 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. - View Dependent Claims (50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68)
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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:
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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. - View Dependent Claims (70, 71, 72)
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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:
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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. - View Dependent Claims (74, 75, 76, 77, 78)
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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:
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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. - View Dependent Claims (80, 81)
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Specification