Oligonucleotide population preparation

• US 5,658,736 A
• Filed: 01/16/1996
• Issued: 08/19/1997
• Est. Priority Date: 01/16/1996
• Status: Expired due to Term

• Current Assignee: Genetics Institute LLC (Pfizer Inc.)
• Original Assignee: Genetics Institute LLC (Pfizer Inc.)
• Inventors: Wong, Gordon G.
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): Atzel, Amy
• Application Number:
  US08/586,329
• Time in Patent Office: 581 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/91.4, 435/91.3, 536/24.3, 536/23.1
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2525/131 incorporating a restriction site
• CPC Class Codes: C12Q 2525/143 incorporating a promoter sequence
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2531/143 Promoter based amplification, e.g. NASBA, 3SR, TAS

Abstract

Methods are disclosed for producing a sequence tag from a polynucleotide. In preferred embodiments, the method comprises (a) digesting the polynucleotide with a type II restriction enzyme to produce a first cohesive end; (b) providing a promoter-linker cassette comprising an RNA polymerase promoter, a restriction site for a type IIS restriction enzyme and a second cohesive end which is complementary to the first cohesive end produced by the type II restriction enzyme; (c) ligating the digested polynucleotide to the cassette by joining the first cohesive end and the second cohesive end; (d) digesting the ligated product of step (c) with the type Iis restriction enzyme; and (e) transcribing the resulting construct from the promoter thereby producing a sequence tagged polyribonucleotide.

Claims

1. A method for producing a sequence tag from a polynucleotide, said method comprising:

(a) digesting said polynucleotide with a type II restriction enzyme to produce a first cohesive end;

(b) providing a promoter-linker cassette comprising an RNA polymerase promoter, a restriction site for a type IIs restriction enzyme and a second cohesive end which is complementary to said first cohesive end produced by said type II restriction enzyme;

(c) ligating the digested polynucleotide to the cassette by joining said first cohesive end and said second cohesive end;

(d) digesting the ligated product of step (c) with said type IIs restriction enzyme; and

(e) transcribing the resulting construct from said promoter, thereby producing a sequence tagged polyribonucleotide.

2. A method of analyzing a population of polynucleotides for the presence of a known sequence, said method comprising:

(a) producing sequence tags from said polynucleotides according to the method of claim 1;

(b) combining, said tags with one or more oligonucleotides derived from said known sequence; and

(c) determining whether said tags hybridize to said one or more oligonucleotides.

6. The method of claim 1 or 4 wherein said cassette is digested to produce said second cohesive end prior to combination with said polynucleotide.

7. The method of claim 1 or 4 wherein the ends of the product of the type IIs digestion are blunted prior to transcription.

9. The method of claim 1 or 4 wherein said type II restriction enzyme is selected from the group consisting of an enzyme having a 4-base recognition site, an enzyme having a 5-base recognition site and an enzyme having a 6-base recognition site.

10. The method of claim 1 or 4 wherein said type IIs restriction enzyme is selected from the group consisting of HphI, MboII, BbvI, FokI, HgaI, SfaNI, BspMI, BsmF1, MnlI, AlwI, AlwXI, Alw26I, BbsI, BbvII, BcefI, BccI, BcgI, BinI, BsaI, BsgI, BsmAI, EarI, Eco31I, Eco57I, Esp3I, FauI, GsuI, HinGUII, Ksp632I, MmeI, NgoVIII, PleI, RleAI, SapI, TaqII and Tth111II.

11. The method of claim 1 or 4 wherein the transcribing step is performed by an RNA polymerase.

12. The method of claim 11 wherein said RNA polymerase is selected from the group consisting of T7 polymerase, T3 polymerase and Sp6 polymerase.

3. A promoter-linker cassette oligonucleotide comprising an RNA polymerase promoter which is situated 5'"'"' to a restriction site for a type IIS restriction enzyme which is situated 5'"'"' to a restriction site for a type II restriction enzyme.

4. A method for producing a sequence tag from a polynucleotide, said method comprising:

(a) digesting said polynucleotide with a type II restriction enzyme to produce a first cohesive end;

(b) providing a promoter-linker cassette comprising a polymerase promoter, a restriction site for a type IIs restriction enzyme and a second cohesive end which is complementary to said first cohesive end produced by said type II restriction enzyme;

(c) ligating the digested polynucleotide to the cassette;

(d) digesting the ligated product of step (c) with said type IIs restriction enzyme;

(e) circularizing the product of step (d);

(f) digesting the circularized product with said type II restriction enzyme; and

(g) transcribing the resulting construct, thereby producing a sequence tagged polynucleotide.

5. The method of claim 4 wherein said cassette further comprises a clamp sequence at the 5'"'"' end of said promoter.

8. The method of claim 4 wherein the ends of the product of the type IIs digestion are blunted prior to circularization.

13. A method for producing a sequence tag from a polynucleotide, said method comprising:

(a) shearing said polynucleotide;

(b) providing a promoter-linker cassette comprising an RNA polymerase promoter and a restriction site for a type IIs restriction enzyme;

(c) blunting said polynucleotide;

(d) ligating the sheared polynucleotide to the cassette;

(e) digesting the ligated product of step (d) with said type IIs restriction enzyme; and

(f) transcribing the resulting construct from said promoter, thereby producing a sequence tagged polyribonucleotide.

14. A method for producing a unique sequence tag from a polynucleotide, said method comprising:

(a) digesting said polynucleotide with a type II restriction enzyme;

(b) ligating the digested polynucleotide to a promoter-linker cassette comprising an RNA polymerase promoter and a cohesive end complementary to cohesive ends produced by said type II restriction enzyme, such that the ligated product contains a recognition site for a type IIs restriction enzyme;

(c) digesting the ligated product of step (b) with said type IIs restriction enzyme; and

(d) transcribing the resulting construct from said promoter, thereby producing a sequence tagged polyribonucleotide.

15. The method of claim 14 wherein the recognition site for the type IIs restriction enzyme is formed upon ligation.

16. A method for producing a sequence tag from a polynucleotide, said method comprising:

(a) digesting said polynucleotide with a type II restriction enzyme to produce a first cohesive end;

(b) providing a promoter-linker cassette comprising an RNA polymerase promoter, a restriction site for a type IIs restriction enzyme and a second cohesive end which is complementary to said first cohesive end produced by said type II restriction enzyme, wherein said cassette is digested to produce said second cohesive end;

(c) ligating the digested polynucleotide to the cassette by joining said first cohesive end and said second cohesive end;

(d) digesting the ligated product of step (c) with said type IIs restriction enzyme;

(e) blunting the ends of the product of the type IIs digestion; and

(f) transcribing the resulting construct from said promoter, thereby producing a sequence tagged polyribonucleotide.

17. A method for producing a sequence tag from a polynucleotide, said method comprising:

(a) digesting said polynucleotide with a type II restriction enzyme to produce a first cohesive end;

(b) providing a promoter-linker cassette comprising an RNA polymerase promoter, a restriction site for a type IIs restriction enzyme and a second cohesive end which is complementary to said first cohesive end produced by said type II restriction enzyme, wherein said cassette is digested to produce said second cohesive end;

(c) ligating the digested polynucleotide to the cassette;

(d) digesting the ligated product of step (c) with said type IIs restriction enzyme;

(e) blunting the ends of the product of the type IIs digestion;

(f) circularizing the product of step (e);

(g) digesting the circularized product with said type II restriction enzyme;

(h) blunting the ends of the product of the type II digestion; and

(i) transcribing the resulting construct from said promoter, thereby producing a sequence tagged polyribonucleotide.