Multiple displacement amplification

• US 6,642,034 B2
• Filed: 07/23/2001
• Issued: 11/04/2003
• Est. Priority Date: 10/08/1997
• Status: Expired due to Term

• Current Assignee: Yale University
• Original Assignee: Yale University
• Inventors: Lizardi, Paul M.
• Primary Examiner(s): Whisenant, Ethan
• Assistant Examiner(s): Tung, Joyce
• Application Number:
  US09/911,226
• Publication Number:
  US 20030143536A1
• Time in Patent Office: 834 Days
• Field of Search: 435/6, 435/91.2, 435/91.52, 435/91.51, 435/91.1, 536/24.3
• US Class Current: 435/91.1
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2531/119 Strand displacement amplification [SDA]
• CPC Class Codes: C12Q 2531/125 Rolling circle
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis

Abstract

Disclosed are compositions and a method for amplification of nucleic acid sequences of interest. The method is based on stand displacement replication of the nucleic acid sequences of interest by multiple primers. In one preferred form of the method, referred to as multiple strand displacement amplification, two sets of primers are used, a right set and a left set. The primers in the right set are complementary to one strand of the nucleic acid molecule to be amplified and the primers in the left set are complementary to the opposite strand. The 5′ end of primers in both sets are distal to the nucleic acid sequence of interest when the primers have hybridized to the nucleic acid sequence molecule to be amplified. Amplification proceeds by replication initiated at each primer and continuing through the nucleic acid sequence of interest. A key feature of this method is the displacement of intervening primers during replication by the polymerase. In another preferred form of the method, referred to as whole genome strand displacement amplification, a random set of primers is used to randomly prime a sample of genomic nucleic acid (or another sample of nucleic acid of high complexity). By choosing a set of primers which are sufficiently random, the primers in the set will be collectively, and randomly, complementary to nucleic acid sequences distributed throughout nucleic acid in the sample. Amplification proceeds by replication with a highly processive polymerase initiated at each primer and continuing until spontaneous termination. A key feature of this method is the displacement of intervening primers during replication by the polymerase. In this way, multiple overlapping copies of the entire genome to be synthesized in a short time.

Claims

1. A method of amplifying a target nucleic acid sequence, the method comprising,

bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence,

wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand, wherein the set of primers has 3 or more primers complementary to the same strand of the target sequence.

2. The method of claim 1 wherein the DNA polymerase is φ

29 DNA polymerase.

3. The method of claim 1 wherein the target sequence comprises two strands, wherein the set of primers has 3 or more primers complementary to one of the strands of the target sequence and the set of primers also has at least one primer complementary to the other strand of the target sequence.

4. The method of claim 1 wherein the target sequence comprises an amplification target and a hybridization target, wherein the hybridization target flanks the amplification target,

wherein the set of primers comprises a plurality of primers,

wherein each primer comprises a complementary portion, wherein the complementary portions of the primers are each complementary to a different portion of the hybridization target.

5. The method of claim 1 further comprising incubating the polymerase-target sample mixture under conditions that promote strand displacement.

6. The method of claim 1 wherein the set of primers has 4 or more primers complementary to the same strand of the target sequence.

7. The method of claim 1 wherein the set of primers has 4 or more primers.

8. The method of claim 7 wherein the set of primers has 5 or more primers.

9. The method of claim 1 wherein the conditions that promote replication of the target sequence are substantially isothermic.

10. The method of claim 1 wherein the conditions that promote replication of the target sequence do not involve thermal cycling.

11. The method of claim 1 wherein the conditions do not include thermal cycling.

12. The method of claim 4 wherein the set of primers comprises a right set of primers and a left set of primers,

wherein the target sequence is double-stranded, having a first and a second strand,

wherein the hybridization target comprises a right and left hybridization target, wherein the right hybridization target flanks the amplification target on one end and the left hybridization target flanks the amplification target on the other end,

wherein the complementary portions of the right set primers are (i) all complementary to the first strand of the target sequence and (ii) each complementary to a different portion of the right hybridization target, and

wherein the complementary portions of the left set primers are (i) all complementary to the second strand of the target sequence and (ii) each complementary to a different portion of the left hybridization target.

13. The method of claim 12 wherein the right and left set of primers each have 3 or more primers.

14. The method of claim 13 wherein the right and left set of primers each have 4 or more primers.

15. The method of claim 14 wherein the right and left set of primers each have 5 or more primers.

16. The method of claim 12 wherein the right and left set of primers each have the same number of primers.

17. The method of claim 1 wherein the target sequence is a nucleic acid sample of substantial complexity, and wherein the set of primers comprises primers having random nucleotide sequences.

18. The method of claim 17 wherein the target sequence is a sample of genomic nucleic acid.

19. The method of claim 17 wherein the primers are from 12 to 60 nucleotides in length.

20. The method of claim 19 wherein the primers are from 12 to 40 nucleotides in length.

21. The method of claim 20 wherein the primers are from 15 to 40 nucleotides in length.

22. The method of claim 21 wherein the primers are from 15 to 25 nucleotides in length.

23. The method of claim 17 wherein the primers are all of the same length.

24. The method of claim 17 wherein each primer comprises a constant portion and a random portion, wherein the constant portion of each primer has the same nucleotide sequence and the random portion of each primer has a random nucleotide sequence.

25. The method of claim 1 wherein the target sequence is concatenated DNA.

26. The method of claim 25 wherein the concatenated DNA is concatenated with linkers.

27. The method of claim 26 wherein each linker comprises a primer complement portion, wherein each primer comprises a complementary portion, wherein the complementary portion of each primer is complementary to the complementary portion of the linkers.

28. The method of claim 25 wherein the set of primers comprises primers having random nucleotide sequences.

29. The method of claim 28 wherein each primer comprises a constant portion and a random portion, wherein the constant portion of each primer has the same nucleotide sequence and the random portion of each primer has a random nucleotide sequence.

30. The method of claim 25 wherein the concatenated DNA is formed by ligating DNA fragments together.

31. The method of claim 30 wherein the DNA fragments are cDNA made from mRNA.

32. The method of claim 31 wherein the mRNA comprises a mixture of mRNA isolated from cells.

33. The method of claim 1 wherein the target sequence is not a nucleic acid molecule made up of multiple tandem repeats of a single sequence that was synthesized by rolling circle replication.

34. A method of amplifying a target nucleic acid sequence, the method comprising,

(a) mixing a set of primers with a target sample, to produce a primer-target sample mixture, and incubating the primer-target sample mixture under conditions that promote hybridization between the primers and the target sequence in the primer-target sample mixture,

(b) mixing DNA polymerase with the primer-target sample mixture, to produce a polymerase-target sample mixture, and incubating the polymerase-target sample mixture under conditions that promote replication of the target sequence, wherein the DNA polymerase is φ

29 DNA polymerase,

wherein the set of primers comprises a right set of primers and a left set of primers,

wherein the target sequence is double-stranded, having a first and a second strand,

wherein the right set primers are all complementary to the first strand of the target sequence and the left set primers are all complementary to the second strand of the target sequence,

wherein the right set of primers has 4 or more primers and the left set of primers has 4 or more primers,

wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.

35. A method of amplifying a target nucleic acid sequence, the method comprising,

(a) mixing a set of primers with a target sample, to produce a primer-target sample mixture, and incubating the primer-target sample mixture under conditions that promote hybridization between the primers and the target sequence in the primer-target sample mixture,

(b) mixing DNA polymerase with the primer-target sample mixture, to produce a polymerase-target sample mixture, and incubating the polymerase-target sample mixture under conditions that promote replication of the target sequence, wherein the DNA polymerase is φ

29 DNA polymerase,

wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand,

wherein the target sequence is a nucleic acid sample of substantial complexity, and wherein the set of primers comprises primers having random nucleotide sequences.

36. A method of amplifying a target nucleic acid sequence, the method comprising,

(a) mixing a set of primers with a target sample, to produce a primer-target sample mixture, and incubating the primer-target sample mixture under conditions that promote hybridization between the primers and the target sequence in the primer-target sample mixture,

(b) mixing DNA polymerase with the primer-target sample mixture, to produce a polymerase-target sample mixture, and incubating the polymerase-target sample mixture under conditions that promote replication of the target sequence, wherein the DNA polymerase is φ

29 DNA polymerase,

wherein all of the primers in the set of primers are complementary to the same strand in the target sequence, wherein the set of primers has 3 or more primers,

wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.

37. A method of amplifying a target nucleic acid sequence, the method comprising,

(a) mixing a set of primers with a target sample, to produce a primer-target sample mixture, and incubating the primer-target sample mixture under conditions that promote hybridization between the primers and the target sequence in the primer-target sample mixture,

(b) mixing DNA polymerase with the primer-target sample mixture, to produce a polymerase-target sample mixture, and incubating the polymerase-target sample mixture under conditions that promote replication of the target sequence, wherein the DNA polymerase is φ

29 DNA polymerase,

wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand,

wherein the target sequence is a nucleic acid sample of substantial complexity, and wherein the set of primers comprises primers having random nucleotide sequences,

wherein each primer comprises a constant portion and a random portion, wherein the constant portion of each primer has the same nucleotide sequence and the random portion of each primer has a random nucleotide sequence.

38. A method of amplifying a target nucleic acid sequence, the method comprising,

(a) mixing a set of primers with a target sample, to produce a primer-target sample mixture, and incubating the primer-target sample mixture under conditions that promote hybridization between the primers and the target sequence in the primer-target sample mixture,

(b) mixing DNA polymerase with the primer-target sample mixture, to produce a polymerase-target sample mixture, and incubating the polymerase-target sample mixture under conditions that promote replication of the target sequence, wherein the DNA polymerase is φ

29 DNA polymerase,

wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand,

wherein the conditions that promote replication of the target sequence do not involve thermal cycling, and

wherein the target sequence is concatenated DNA.

39. A method of amplifying a target nucleic acid sequence, the method comprising,

bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence,

wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand, wherein the target sequence is a nucleic acid sample of substantial complexity, and wherein the set of primers comprises primers having random nucleotide sequences.

40. A method of amplifying a target nucleic acid sequence, the method comprising,

bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence,

wherein all of the primers in the set of primers are complementary to the same strand in the target sequence, wherein the set of primers has 3 or more primers,

wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand.

41. A method of amplifying a target nucleic acid sequence, the method comprising,

bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence,

wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand,

wherein the target sequence is a nucleic acid sample of substantial complexity, and wherein the set of primers comprises primers having random nucleotide sequences,

wherein each primer comprises a constant portion and a random portion, wherein the constant portion of each primer has the same nucleotide sequence and the random portion of each primer has a random nucleotide sequence.

42. A method of amplifying a target nucleic acid sequence, the method comprising,

bringing into contact a set of primers, DNA polymerase, and a target sample, and incubating the target sample under conditions that promote replication of the target sequence,

wherein replication of the target sequence results in replicated strands, wherein during replication at least one of the replicated strands is displaced from the target sequence by strand displacement replication of another replicated strand,

wherein the conditions that promote replication of the target sequence do not involve thermal cycling, and

wherein the target sequence is concatenated DNA.