Nucleic acid sequence amplification methods

• US 5,824,518 A
• Filed: 06/06/1995
• Issued: 10/20/1998
• Est. Priority Date: 07/11/1989
• Status: Expired due to Term

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Inventors: Fultz, Timothy J., Kacian, Daniel Louis
• Primary Examiner(s): Zitomer, Stephanie W.
• Application Number:
  US08/469,067
• Time in Patent Office: 1,232 Days
• Field of Search: 435/91.21, 935/77, 935/78
• US Class Current: 435/91.21
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 2521/119 RNA polymerase
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: Y10S 435/975 Kit

Abstract

Methods of synthesizing multiple copies of a target nucleic acid sequence autocatalytically under conditions of substantially constant temperature, ionic strength, and pH are provided in which multiple RNA copies of the target sequence autocatalytically generate additional copies. These methods are useful for generating copies of a nucleic acid target sequence for purposes which include assays to quantitate specific nucleic acid sequences in clinical, environmental, forensic and similar samples, cloning and generating probes.

Claims

1. A block splice templat comprising a first and a second nucleic acid region, wherein said first region is located 3'"'"' of said second region and is blocked at its 3'"'"'-terminus to inhibit primer extension by a DNA polymerase, and said second region comprises a promoter sequence recognized by an RNA polymerase.

2. A kit for synthesizing multiple RNA transcripts comprising:

a primer able to hybridize to a 3'"'"'-terminal portion of a target sequence and be extended to produce a primer extension product containing a complementary target sequence, and

a blocked splice template comprising a first and a second nucleic acid region, wherein said first region is located 3'"'"' of said second region, comprises a nucleotide sequence able to hybridize to a 3'"'"'-terminal portion of a complementary target sequence, and is blocked at its 3'"'"'-terminus to inhibit primer extension by a DNA polymerase, and said second region comprises a promoter sequence recognized by an RNA polymerase.

3. The kit of claim 2, further comprising said RNA polymerase.

4. The kit of claim 3, further comprising a reverse transcriptase.

5. A method for synthesizing multiple RNA transcripts comprising the steps of:

(a) providing a target nucleic acid comprising a target sequence with a first oligonucleotide comprising a primer having a nucleotide sequence able to hybridize to a 3'"'"'-terminal portion of said target sequence, wherein an oligonucleotide;

target sequence hybride is formed and DNA synthesis may be initiated, wherein said target sequence may be initially present or produced by a preliminary procedure;

(b) extending said primer in a primer extension reaction using said target sequence as a template to give a DNA primer extension product comprising a complementary target sequence;

(c) making a 3'"'"'-terminal portion of said complementary target sequence available for hybridization with a second oligonucleotide, wherein said second oligonucleotide is a blocked splice template comprising a first and a second nucleic acid region, wherein said first region is located 3'"'"' of said second region, comprises a nucleotide sequence able to hybridize to said 3'"'"'-terminal protion of said complementary target sequence made available, and is blocked at its 3'"'"'-terminus to inhibit extension by a DAN polymerase, and said second region comprises a promoter sequence recognized by an RNA polymerase;

(d) hybridizing said second oligonucleotide to said DNA primer extension product;

(e) extending the 3'"'"'-end of said DNA primer extension product to form a double-stranded promoter comprising said promoter sequence; and

(f) synthesizing multiple copies of RNA transcripts complementary to said complementary target sequence using said RNA polymerase and DNA priming and nucleic acid synthesizing conditions which include the necessary substrates and buffer conditions for primer extension and production of said RNA transcripts.

6. The method of claim 5, wherein said target nucleic acid is RNA and said step (c) is carried out using an enzyme which selectively degrades said RNA target when present in a RNA:

DNA duplex.

7. The method of claim 6, wherein said enzyme is a reverse transcriptase having RNase H activity.

8. The method of claim 7, wherein said reverse transcriptase alone supplies said RNase H activity.

9. The method of claim 8, wherein said method is carried out under essentially constant temperature.

10. A method for synthesizing multiple RNA transcripts comprising the steps of:

(a) combining;

a target nucleic acid comprising said target sequence, wherein said target sequence may be initially present or produced by a preliminary procedure;

a first oligonucleotide comprising a primer able to hybridize to a 3'"'"'-terminal portion of said target sequence;

a second oligonucleotide which is a blocked splice template comprising a first and a second nucleic acid region, wherein said first region is located 3'"'"' of said second region, comprises a nucleotide sequence able to hybridize to a 3'"'"'-terminal portion of a complementary target sequence, and is blocked at its 3'"'"'-terminus to inhibit extension by a DNA polymerase, and said second region comprises a promoter sequence recognized by an RNA polymerase;

a reverse transcriptase; and

said RNA polymerase;

(b) incubating the mixture of step (a) under DNA priming and nucleic acid synthesizing conditions which include the necessary substrates and buffer conditions for primer extension and production of RNA transcripts; and

(c) synthesizing multiple RNA transcripts.

11. The method of claim 10, wherein said target sequence is RNA and said method is carried out under essentially constant temperature.

12. The method of claim 11, wherein said combining step further comprises an enzyme which selectively degrades the RNA strand of an RNA:

DNA duplex.

13. The method of claim 12, wherein said enzyme is a reverse transcriptase having RNase H activity.

14. The method of claim 13 wherein said reverse transcriptase alone supplies said RNase H activity to degrade said RNA strand.