Annealing control primer and its uses
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Abstract
The present invention relates to an annealing control primer for improving annealing specificity in nucleic acid amplification and its applications to all fields of nucleic acid amplification-involved technology. The present primer comprises (a) a 3′-end portion having a hybridizing nucleotide sequence substantially complementary to a site on a template nucleic acid to hybridize therewith; (b) a 5′-end portion having a pre-selected arbitrary nucleotide sequence; and (c) a regulator portion positioned between said 3′-end portion and said 5′-end portion comprising at least one universal base or non-discriminatory base analog, whereby said regulator portion is capable of regulating an annealing portion of said primer in association with annealing temperature.
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Citations
126 Claims
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1-111. -111. (canceled)
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112. A method for selectively amplifying a target nucleic acid sequence from a deoxyribonucleic acid or a mixture of nucleic acids, comprising the steps of
(a) performing a first-stage amplification of said target nucleic acid sequence at a first annealing temperature, said first-stage amplification comprising at least two cycles of primer annealing, primer extending and nucleic acid denaturing using a first primer pair, each primer of said first primer pair comprising a first 3′ - -end portion and a first 5′
-end portion, and each primer of said first primer pair comprising;(i) a hybridizing sequence at said first 3′
-end portion that is substantially complementary to a region of said target nucleic acid sequence,(ii) a pre-selected arbitrary nucleotide sequence at said first 5′
-end portion that is substantially not complementary to any site of said target nucleic acid sequence, and(iii) a regulator sequence between said first 3′
-end portion and said first 5′
-end portion, comprising at least three contiguous universal bases, said regulator sequence having a melting temperature lower than said hybridizing sequence and said pre-selected arbitrary nucleotide sequence;whereby said regulator sequence restricts primer annealing to said first 3′
-end portion, and whereby an amplification product of said target nucleotide sequence is generated; and(b) performing a second-stage amplification of said amplification product generated from step (a) at a second annealing temperature, said second-stage amplification comprising at least one cycle of primer annealing, primer extending and nucleic acid denaturing using a second primer pair, each primer of said second primer pair comprising a second 3′
-end portion and a second 5′
-end portion, and a pre-selected arbitrary nucleotide sequence corresponding to said first 5′
-end portions of each primer used in step (a), under conditions in which each primer of said second primer pair anneals to 3′
- and 5′
-ends of said amplification product, respectively, whereby said amplification product is re-amplified;wherein the first annealing temperature and the second annealing temperature are different. - View Dependent Claims (113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125)
- -end portion and a first 5′
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126. A method for selectively amplifying a target nucleic acid sequence from a deoxyribonucleic acid or a mixture of nucleic acids, which comprises the steps of
(a) performing a first-stage amplification of said target nucleic acid sequence at a first annealing temperature, said first-stage amplification comprising at least two cycles of primer annealing, primer extending and nucleic acid denaturing using a first primer pair, each primer of said first primer pair comprising a first 3′ - -end portion and a first 5′
-end portion, and each primer of said first primer pair comprising;(i) a hybridizing sequence at said first 3′
-end portion that is substantially complementary to a region of said target nucleic acid sequence,(ii) a pre-selected arbitrary nucleotide sequence at said first 5′
-end portion that is substantially not complementary to any site of said target nucleic acid sequence, and(iii) a regulator sequence between said first 3′
-end portion and said first 5′
-end portion, comprising at least three contiguous universal bases, said regulator sequence having a melting temperature lower than said hybridizing sequence and said pre-selected arbitrary nucleotide sequence;whereby said regulator sequence restricts primer annealing to said first 3′
-end portion, and whereby an amplification product of said target nucleotide sequence is generated; and(b) performing a second-stage amplification of said amplification product generated from step (a) at a second annealing temperature, said second-stage amplification comprising at least one cycle of primer annealing, primer extending and nucleic acid denaturing using a second primer pair, each primer of said second primer pair comprising a second 3′
-end portion and a second 5′
-end portion, and a pre-selected arbitrary nucleotide sequence corresponding to said first 5′
-end portions of each primer used in step (a), under conditions in which each primer of said second primer pair anneals to 3′
- and 5′
-ends of said amplification product, respectively, whereby said amplification product is re-amplified;wherein the first annealing temperature and the second annealing temperature are different; wherein each primer of said first pair and each primer of said second pair has a general formula of 5′
-Xp-Yq-Zr-3′
, wherein Xp represents a 5′
-end portion having said pre-selected arbitrary nucleotide sequence substantially not complementary to any site on said target nucleic acid sequence;
Yq represents said regulator sequence comprising at least three contiguous universal bases to have the lowest melting temperature among the three sequences of each of the primers of said first and second pairs;
Zr represents a 3′
-end portion having a hybridizing nucleotide sequence substantially complementary to a region of said target nucleic acid sequence to hybridize therewith;
wherein p, q and r represent the number of nucleotides; and
wherein each of X, Y and Z is a deoxyribonucleotide or a ribonucleotide.
- -end portion and a first 5′
Specification