Selective terminal tagging of nucleic acids

• US 20050153333A1
• Filed: 12/02/2004
• Published: 07/14/2005
• Est. Priority Date: 12/02/2003
• Status: Abandoned Application

• Current Assignee: Cellscript, LLC
• Original Assignee: Cellscript, LLC
• Inventors: Sooknanan, Roy Rabindranauth
• Application Number:
  US11/000,958
• Publication Number:
  US 20050153333A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12N 15/1096 cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6865 Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
• CPC Class Codes: C12Q 2525/143 incorporating a promoter sequence
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid

Abstract

A method is provided for adding a terminal sequence tag to nucleic acid molecules for use in RNA or DNA amplification. The method involves contacting with a mixture of oligonucleotides, each having a sequence tag template, a random sequence and a blocked 3′ terminus, under conditions such that, the random sequence anneals with the nucleic acid molecules and the nucleic acid molecules are extended using the sequence tag template as template. For synthesis of RNA from DNA molecules having terminal sequence tags, the method includes forming DNA templates having a double stranded promoter sequence and synthesizing RNA from the DNA templates. For amplification of sequences from DNA molecules having terminal sequence tags, the method includes forming DNA templates by extension of one primer having a sequence that is complementary to the terminal sequence tag and another primer having a sequence that is derived form one of the DNA molecules.

Claims

1. A method for adding a terminal sequence tag to nucleic acid molecules, the method comprising:

contacting the nucleic acid molecules with a mixture of oligonucleotides, each oligonucleotide having a sequence tag template, a random sequence and a blocked 3′

terminus, under conditions in which the random sequence anneals with the nucleic acid molecules and the nucleic acid molecules are extended to form first DNA or RNA templates using the sequence tag template as template.

2. The method according to claim 1, wherein the nucleic acid molecules comprise DNA.

3. The method according to claim 2, wherein the DNA is complementary DNA.

4. The method according to claim 2, wherein the DNA is formed by strand separation of double-stranded DNA fragments.

5. The method according to claim 1, wherein each oligonucleotide further comprises a promoter sequence, such that the first DNA templates include a double-stranded promoter sequence.

6. A method for synthesizing RNA from DNA templates, the method comprising synthesizing RNA from a complete or partial double-stranded first DNA template including a double-stranded promoter, the complete or partial double-stranded first DNA template being obtained according to the method of claim 5.

7. The method according to claim 1, wherein the nucleic acid molecules are RNA.

8. The method according to claim 7, wherein the RNA is mRNA.

9. The method according to claim 1, further comprising annealing first RNA templates with a second oligonucleotide having a sequence tag complement to the sequence tag contained in the first RNA templates and extending the first RNA templates using the second oligonucleotide as template to form second RNA templates.

10. The method according to claim 9, wherein the second oligonucleotide contains a promoter sequence.

11. The method according to claim 9, wherein the second oligonucleotide comprises at least one restriction endonuclease site.

12. The method according to claim 9, wherein the second oligonucleotide is capable of serving as a primer for primer extension in an enzymatic DNA polymerization reaction using the first RNA templates as template to form RNA:

DNA hybrids, wherein DNA strands of the RNA;

DNA hybrids are complementary second DNA templates.

13. The method according to claim 12, wherein the complementary second DNA templates are randomly primed in an enzymatic DNA polymerization reaction to form double-stranded DNA templates containing a 3′

double-stranded promoter sequence.

14. A method for synthesizing antisense RNA from DNA templates, the method comprising synthesizing antisense RNA from double-stranded DNA templates including a 3′

double-stranded promoter sequence obtained according to the method of claim 13.

15. The method according to claim 9, wherein the second oligonucleotide contains a blocked 3′

terminus.

16. The method according to claim 1, further comprising annealing first DNA templates with a second oligonucleotide having a sequence tag complement to the sequence tag contained in the first DNA templates, and the first DNA templates are extended using the second oligonucleotide as template to form second DNA templates.

17. The method according to claim 16, wherein the second oligonucleotide contains a promoter sequence.

18. The method according to claim 16, wherein the second oligonucleotide further comprises at least one restriction endonuclease site.

19. The method according to claim 16, wherein the second oligonucleotide contains a blocked 3′

terminus.

20. A method for synthesizing RNA from DNA templates, the method comprising synthesizing RNA from a complete or partial double-stranded second DNA template including a double-stranded promoter, the complete or partial double-stranded second DNA template being obtained according to the method of claim 16.

28. A method for amplifying terminal sequences of DNA molecules comprising,

forming first DNA templates by contacting the DNA molecules with a mixture of oligonucleotides, each having a sequence tag template, a random sequence and a blocked 3′

terminus, under conditions such that, the DNA templates anneal with the random sequence and are extended using the sequence tag template as template;

forming double-stranded DNA templates by contacting the first DNA templates with a first primer having a sequence complementary to the sequence tag contained in the first DNA templates, under conditions such that, the sequence of the first primer anneals with the sequence tag contained in the first DNA templates and is extended using the first DNA templates as template to form double-stranded DNA templates;

amplifying the double-stranded DNA templates by contacting with said first primer and a second primer containing a sequence complementary to a sequence from the complementary strand of the first DNA templates, under conditions such that the primers anneal to complementary templates and are extended repeatedly; and

forming complementary second DNA templates according to claim 12 and amplifying said complementary second DNA templates by contacting with a second primer containing a sequence that is complementary to the complementary second DNA templates and a first primer having a sequence of similar sense to the sequence tag contained in the complementary second DNA templates, under conditions such that the primers anneal to complementary templates and are extended repeatedly.

29. The method according to claim 28, wherein the DNA molecules are formed by contacting a mixture containing mRNA with a primer having a sequence complementary to the mRNA, under conditions such that, the sequence of the primer anneals with the mRNA and is extended using the mRNA as template.

30. The method according to claim 28, wherein the second primer further comprises at least one sequence that is specific for at least one sequence in a mixture of double-stranded DNA templates, wherein a limited number of sequences in the mixture are amplified.

21. A method for adding a terminal sequence tag to the 3′

-end of a first nucleic acid molecule, the method comprising;

contacting the first nucleic acid molecule with a mixture of oligonucleotides, each oligonucleotide having a sequence tag template, and a blocked random sequence at its 3′

terminus, under conditions in which the random sequence of at least one of the oligonucleotides anneals with the first nucleic acid molecule and the first nucleic acid molecule is extended to form a first extended nucleic acid molecule using the sequence tag template as template.

22. The method of claim 21, further comprising:

separating the annealed first extended nucleic acid molecule and the oligonucleotide from each other and contacting the first extended nucleic acid molecule with an oligonucleotide having at least a portion of said sequence tag template and being unblocked at its 3′

-terminus under conditions in which the at least a portion of said tag template anneals to its complement in the first extended nucleic acid molecule and the 3′

-end of the unblocked oligonucleotide is extended to form a second extended nucleic acid molecule using the first extended nucleic acid molecule as template.

23. The method of claim 22, wherein the sequence tag template unblocked at its 3′

-terminus further comprises a promoter sequence at its 5′

-end, and the first extended nucleic acid molecule is extended at its 3′

-end using the promoter sequence as template.

24. The method of claim 23, wherein the first nucleic acid molecule is DNA.

25. A method for synthesizing sense RNA from DNA molecules comprising forming first DNA templates by contacting the DNA molecules with a mixture of oligonucleotides, each having a sequence tag template, a random sequence and a blocked 3′

terminus, under conditions such that, the DNA molecules anneal with the random sequence and are extended using the sequence tag template as template;

forming first DNA templates having a 5′

double-stranded promoter sequence by contacting the DNA molecules with a mixture of oligonucleotides, each having a promoter sequence, a sequence tag template, a random sequence and a blocked 3′

terminus, under conditions such that, the DNA molecules anneal with the random sequence and are extended using the promoter sequence and the sequence tag templates as template;

forming second DNA templates having a 5′

double-stranded promoter sequence by contacting the first DNA templates with a second oligonucleotide, containing a sequence tag complement to the sequence tag contained in the first DNA templates and a promoter sequence, under conditions such that, the first DNA templates anneal with the second oligonucleotide and are extended using the promoter sequence as template;

forming second DNA templates having a 5′

double-stranded promoter sequence by contacting first DNA templates with a second oligonucleotide, containing a sequence tag complement to the sequence tag contained in the first DNA templates, a promoter sequence and a blocked 3′

terminus, under conditions such that, the first DNA templates anneal with the second oligonucleotide and are extended using the promoter sequence as template; and

synthesizing RNA from the first or second DNA templates having a 5′

double-stranded promoter sequence.

26. The method according to claim 25, wherein the DNA molecules are formed by contacting a mixture containing mRNA with a primer having a terminal sequence complementary to the mRNA, under conditions such that, the terminal sequence of the primer anneals with the mRNA and is extended using the mRNA as template.

27. The method according to claim 25, wherein the method further comprises extending the second oligonucleotide using the first DNA templates as template to form complete double-stranded second DNA templates

31. A composition comprising a nucleic acid molecule having annealed at its 3′

-end an oligonucleotide blocked from replication at its 3′

-end and a sequence tag template at its 5′

-end, the sequence tag template extending past the 3′

-end of the nucleic acid molecule.

32. The composition of claim 31, wherein the nucleic acid molecule is DNA.

33. The composition of claim 31, wherein the nucleic acid molecule is RNA.

34. The composition of claim 31, wherein the oligonucleotide further comprises a promoter sequence.

35. The composition of claim 31, wherein the nucleic acid molecule further comprises a double-stranded promoter sequence.

36. A kit for selective terminal tagging of nucleic acid molecules in a sample, the kit comprising:

(a) an oligonucleotide sequence tag template further comprising a tag sequence, and a random sequence for binding terminally said nucleic acid molecules, wherein the 3′

-end of said oligonucleotide sequence tag template is blocked to preclude extension thereof;

(b) a DNA polymerase and reagents for extending the 3′

terminal ends of said nucleic acid molecules;

(c) size selection columns and buffers for removal of unused oligonucleotide sequence tag template; and

(d) instructions for hybridizing said oligonucleotide sequence tag template to nucleic molecules of said sample, extending said nucleic acid molecules with the DNA polymerase using the oligonucleotide sequence tag templates as template, and creating first DNA or RNA templates with double-stranded regions corresponding in sequence to at least a sequence tag region.

37. The kit of claim 36, further comprising a second oligonucleotide sequence tag template having a sequence tag complement to the oligonucleotide sequence tag contained in the first RNA or DNA templates and a promoter sequence, wherein the first RNA or DNA templates are extended according to instructions included using the second oligonucleotide sequence tag template as template to form second DNA templates or second RNA templates containing a complementary promoter sequence.

38. The kit of claim 37, wherein the second oligonucleotide sequence tag template contains a blocked 3′

terminus.

39. The kit of claim 36, wherein the oligonucleotide sequence tag template further comprises a promoter sequence on it'"'"'s 5′

-end.

40. The kit of claim 36, further comprising a reverse transcriptase, at least one enzyme for RNA hydrolysis and an oligonucleotide complementary to mRNA molecules.

41. The kit of claim 40, further comprising a RNA polymerase matching a functional promoter and reagents, and cofactors for in vitro RNA synthesis from said promoter.

42. The kit of claim 40, further comprising a first primer corresponding to the sequence tag and at least one second primer for exponential amplification of at least one sequence contained in nucleic acid mixture of said sample, wherein the primers anneal to complementary templates and are extended repeatedly.