Annealing control primer and its uses

• US 8,124,346 B2
• Filed: 07/21/2009
• Issued: 02/28/2012
• Est. Priority Date: 12/08/2001
• Status: Expired due to Term

• Current Assignee: Seegene, Inc.
• Original Assignee: Seegene, Inc.
• Inventors: Chun, Jong-Yoon
• Primary Examiner(s): WOOLWINE, SAMUEL C
• Application Number:
  US12/458,702
• Publication Number:
  US 20100291634A1
• Time in Patent Office: 952 Days
• Field of Search: None
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine

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.

Claims

1. 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 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.

2. The method according to claim 1, wherein the second annealing temperature is higher than the first annealing temperature.

3. The method according to claim 1, wherein the first annealing temperature is between 30°

C. and 68°

C.

4. The method according to claim 1, wherein the second annealing temperature is between 50°

C. and 72°

C.

5. The method according to claim 1, each primer of said first primer pair and each primer of said second primer pair comprising a general formula of 5′

-X_p-Y_q-Z_r-3′

, wherein X_p represents a 5′

-end portion having said pre-selected arbitrary nucleotide sequence substantially not complementary to any site on said target nucleic acid sequence;

Y_q 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 primer pairs;

Z_r 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.

6. The method according to claim 5, wherein each of said at least three contiguous universal bases is selected from the group consisting of deoxyinosine, inosine, 7-deaza-2′

-deoxyinosine, 2-aza-2′

-deoxyinosine, 2′

-OMe inosine, 2′

-F inosine, deoxy 3-nitropyrrole, 3-nitropyrrole, 2′

-OMe 3-nitropyrrole, 2′

-F 3-nitropyrrole, 1-(2′

-deoxy-beta-D-ribofuranosyl) -3-nitropyrrole, deoxy 5-nitroindole, 5-nitroindole, 2′

-OMe 5-nitroindole, 2′

-F 5nitroindole, deoxy 4-nitrobenzimidazole, 4-nitrobenzimidazole, deoxy 4-aminobenzimidazole, 4-aminobenzimidazole, deoxy nebularine, 2′

-F nebularine, 2′

-F 4-nitrobenzimidazole, PNA-5-introindole, PNA-nebularine, PNA-inosine, PNA-4-nitrobenzimidazole, PNA-3-nitropyrrole, morpholino-5-nitroindole, morpholino-nebularine, morpholino-inosine, morpholino-4-nitrobenzimidazole, morpholino-3-nitropyrrole, phosphoramidate-5-nitroindole, phosphoramidate-nebularine, phosphoramidate-inosine, phosphoramidate-4- nitrobenzimidazole, phosphoramidate-3-nitropyrrole, 2′

-0-methoxyethyl inosine, 2′

0-methoxyethyl nebularine, 2′

-0-methoxyethyl 5-nitroindole, 2′

-0-methoxyethyl 4-nitro-benzimidazole, 2′

-0-methoxyethyl 3-nitropyrrole, and combinations thereof.

7. The method according to claim 5, wherein each of said at least three contiguous universal bases is deoxyinosine, 1-(2′

-deoxy-beta-D-ribofuranosyl)-3nitropyrrole or 5-nitroindole.

8. The method according to claim 5, wherein p represents an integer of 15 to 60.

9. The method according to claim 5, wherein q is an integer of 3 to 15.

10. The method according to claim 5, wherein r is an integer of 6 to 50.

11. The method according to claim 5, wherein p is an integer of 15 to 60, q is an integer of 3 to 15 and r is an integer of 6 to 30.

12. The method according to claim 1, wherein said second-stage amplification is repeated at least 5 times.

13. The method according to claim 1, wherein said first-stage amplification and said second-stage amplification reactions are a polymerase chain reaction.

14. 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 having 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′

-X_p-Y_q-Z_r-3′

, wherein X_p represents a 5′

-end portion having said pre-selected arbitrary nucleotide sequence substantially not complementary to any site on said target nucleic acid sequence;

Y_q 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;

Z_r 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.