Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays

• US 7,892,746 B2
• Filed: 03/16/2010
• Issued: 02/22/2011
• Est. Priority Date: 02/09/1996
• Status: Expired due to Fees

• Current Assignee: Cornell Research Foundation Incorporated (Cornell University)
• Original Assignee: Cornell Research Foundation Incorporated (Cornell University)
• Inventors: Kempe, Maria, Blok, Herman, Zirvi, Monib, Barany, George, Barany, Francis, Hammer, Robert P.
• Primary Examiner(s): Martinell; James
• Application Number:
  US12/725,180
• Publication Number:
  US 20100173790A1
• Time in Patent Office: 343 Days
• Field of Search: None
• US Class Current: 435/6.11
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00536 in the shape of disks
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00729 Peptide nucleic acids [PNA]
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6816 : characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6827 : for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• 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 2537/143 : Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2561/125 : Ligase Detection Reaction [LDR]
• CPC Class Codes: C12Q 2565/501 : being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/514 : characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: C12Q 2600/156 : Polymorphic or mutational markers
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries

Abstract

The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.

Claims

1. A method comprising:

providing an array of a plurality of capture oligonucleotides wherein each type of capture oligonucleotide is greater than 16 nucleotides and differs in nucleotide sequence, when aligned to another type of capture oligonucleotide, by at least 25%, wherein said capture oligonucleotides are coupled to a solid support;

providing a sample comprising a plurality of target oligonucleotides, each target oligonucleotide comprising (i) an addressable array-specific portion, (ii) a further nucleotide sequence, and (iii) a detectable reporter label;

contacting the sample comprising the plurality of target oligonucleotides with the array of capture oligonucleotides under uniform hybridization conditions effective to hybridize the addressable array-specific portion of each target oligonucleotide to its complementary capture oligonucleotide; and

detecting the reporter labels of one or more of the plurality of target oligonucleotides hybridized to their complementary capture oligonucleotides on the solid support.

2. The method according to claim 1, wherein each capture oligonucleotide comprises 20-25 nucleotides.

3. The method according to claim 1, wherein the addressable array-specific portions of the target oligonucleotides hybridize to their complementary capture oligonucleotides under highly stringent uniform hybridization conditions.

4. The method according to claim 1, wherein the addressable array-specific portions of the target oligonucleotides hybridize to their complementary capture oligonucleotides with complete complementarity.

5. A method comprising:

providing a collection of capture oligonucleotides wherein each type of capture oligonucleotide in the collection comprises a nucleotide sequence that is greater than sixteen nucleotides and differs from nucleotide sequences of other types of capture oligonucleotides in the collection, when aligned to each other, by at least 25%;

providing a sample comprising a plurality of target oligonucleotides, each oligonucleotide comprising (i) an address-specific portion, (ii) one or more further nucleotide sequence portions, and (iii) a detectable reporter label;

contacting the sample comprising a plurality of target oligonucleotides with the collection of capture oligonucleotides under uniform hybridization conditions effective to hybridize the address-specific portion of each target oligonucleotide to its complementary capture oligonucleotide in the collection with minimal non-specific hybridization; and

detecting the reporter labels of one or more of the plurality of target oligonucleotides hybridized to their complementary capture oligonucleotides.

6. The method according to claim 5, wherein each capture oligonucleotide comprises 20-25 nucleotides.

7. The method according to claim 5, wherein the address-specific portions of the target oligonucleotides hybridize to their complementary capture oligonucleotides under highly stringent uniform hybridization conditions.

8. The method according to claim 5, wherein the address-specific portions of the target oligonucleotides hybridize to their complementary capture oligonucleotide with complete complementarity.

9. The method according to claim 5, wherein said detecting is carried out on a solid support.

10. A method for identifying one or more target nucleotide sequences in a sample, said method comprising:

providing a sample potentially containing one or more target nucleotide sequences;

providing a plurality of oligonucleotide probe sets, each set characterized by (a) a first oligonucleotide probe, having a target-specific portion and an addressable array-specific portion and (b) a second oligonucleotide probe, having a target-specific portion;

providing a ligase;

blending the sample, the plurality of oligonucleotide probe sets, and the ligase to form a mixture;

subjecting the mixture to one or more ligase detection reaction cycles to form a ligated product sequence containing (a) the addressable array-specific portion and (b) the target-specific portions, if their respective target nucleotide is present in the sample;

providing a solid support with a plurality of types of capture oligonucleotides immobilized at particular sites, wherein the plurality of types of capture oligonucleotides, each having greater than 16 nucleotides, comprise nucleotide sequences that are complementary to the addressable array-specific portions, and wherein each type of capture oligonucleotide differs in nucleotide sequence, when aligned to each other, by at least 25% to reduce non-specific hybridization between non-complementary capture oligonucleotides and addressable array-specific portions;

contacting the mixture, after said subjecting, with the solid support under uniform hybridization conditions effective to hybridize the addressable array-specific portions to their complementary capture oligonucleotides in a base-specific manner, thereby capturing the addressable array-specific portions on the solid support at the site with the complementary capture oligonucleotide; and

detecting the ligated product sequences captured to the solid support at particular sites, thereby indicating the presence of one or more target nucleotide sequences in the sample.

11. The method according to claim 10, wherein the first and second oligonucleotide probes hybridize at adjacent positions in a base-specific manner to their respective target nucleotide sequence, if present in the sample, to form a ligation junction and ligate to one another due to perfect complementarity at the ligation junction, but, when the first and second oligonucleotide probes in the set are hybridized to any other nucleotide sequence present in the sample, there is a mismatch at a base at the ligation junction which interferes with such ligation.

12. The method according to claim 11, wherein the mismatch is at the 3′

base at the ligation junction.

13. The method according to claim 10, wherein the first and second oligonucleotide probes hybridize at adjacent positions in a base-specific manner to their respective target nucleotide sequence, if present in the sample, to form a ligation junction and ligate to one another due to perfect complementarity at the ligation junction, but, when the first and second oligonucleotide probes in the set are hybridized to any other nucleotide sequence present in the sample, there is a mismatch at a base adjacent to a base at the ligation junction which interferes with such ligation.

14. The method according to claim 13, wherein the mismatch is at the base adjacent to the 3′

base at the ligation junction.

15. The method according to claim 10, wherein a ligation detection reaction cycle comprises a denaturation treatment, wherein any hybridized oligonucleotide probes are separated from their target nucleotide sequences, and a hybridization treatment, wherein the target-specific oligonucleotide probe portions hybridize in a base-specific manner to their respective target nucleotide sequences, if present in the sample, and ligate to one another.

16. The method according to claim 15, wherein each cycle, comprising a denaturation treatment and a hybridization treatment, is from about 30 seconds to about five minutes long.

17. The method according to claim 16, wherein the denaturation treatment is at a temperature of about 80°

-105°

C.

18. The method according to claim 10, wherein said subjecting is repeated for 2 to 50 cycles.

19. The method according to claim 10, wherein total time for said subjecting is 1 to 250 minutes.

20. The method according to claim 10, wherein the target-specific portions of the oligonucleotide probes each have a hybridization temperature of 20-85°

C.

21. The method according to claim 10, wherein the target-specific portions of the oligonucleotide probes are 20 to 28 nucleotides long.

22. The method according to claim 10 further comprising:

amplifying the target nucleotide sequences in the sample prior to said blending.

23. The method according to claim 22, wherein said amplifying is carried out by subjecting the sample to a polymerase-based amplifying procedure.

24. The method according to claim 23, wherein said polymerase-based amplifying procedure is carried out with DNA polymerase.

25. The method according to claim 22, wherein said amplifying is carried out by subjecting the target nucleotide sequences in the sample to a ligase chain reaction process.

26. The method according to claim 10, wherein the target-specific portions of the oligonucleotide probe sets are configured to be successfully ligated in the presence of their target sequences under a single set of ligase reaction conditions.

27. The method according to claim 10, wherein the ligase is selected from the group consisting of Thermus aquaticus ligase, Thermus thermophilus ligase, E. coli ligase, T4 ligase, and Pyrococcus ligase.

28. A method for identifying one or more target nucleotide sequences in a sample, said method comprising:

providing a sample potentially containing one or more target nucleotide sequences;

providing a plurality of oligonucleotide probe sets, each set characterized by (a) a first oligonucleotide probe, having a target-specific portion and an address-specific portion and (b) a second oligonucleotide probe, having a target-specific portion;

providing a ligase;

blending the sample, the plurality of oligonucleotide probe sets, and the ligase to form a mixture;

subjecting the mixture to one or more ligase detection reaction cycles to form a ligated product sequence containing (a) the address-specific portion and (b) the target-specific portions, if their respective target nucleotide is present in the sample;

providing a collection of capture oligonucleotides wherein each type of capture oligonucleotide in the collection comprises greater than 16 nucleotides and comprises a nucleotide sequence complementary to an address-specific portion, wherein each type of capture oligonucleotide in the collection differs in nucleotide sequence, when aligned to another type of capture oligonucleotide in the collection, by at least 25% of their nucleotides to reduce non-specific hybridization between non-complementary capture oligonucleotides and address-specific portions;

contacting the mixture, after said subjecting, with the collection of capture oligonucleotides under uniform hybridization conditions effective to hybridize the address-specific portion of each ligation product sequence to its capture oligonucleotide comprising a complementary nucleotide sequence in a base-specific manner; and

detecting the ligated product sequences hybridized to their complementary capture oligonucleotides, thereby indicating the presence of one or more target nucleotide sequences in the sample.

29. The method according to claim 28, wherein the first and second oligonucleotide probes hybridize at adjacent positions in a base-specific manner to their respective target nucleotide sequence, if present in the sample, to form a ligation junction and ligate to one another due to perfect complementarity at the ligation junction, but, when the first and second oligonucleotide probes in the set are hybridized to any other nucleotide sequence present in the sample, there is a mismatch at a base at the ligation junction which interferes with such ligation.

30. The method according to claim 29, wherein the mismatch is at the 3′

base at the ligation junction.

31. The method according to claim 28, wherein the first and second oligonucleotide probes hybridize at adjacent positions in a base-specific manner to their respective target nucleotide sequence, if present in the sample, to form a ligation junction and ligate to one another due to perfect complementarity at the ligation junction, but, when the first and second oligonucleotide probes in the set are hybridized to any other nucleotide sequence present in the sample, there is a mismatch at a base adjacent to a base at the ligation junction which interferes with such ligation.

32. The method according to claim 31, wherein the mismatch is at the base adjacent to the 3′

base at the ligation junction.

33. The method according to claim 28, wherein a ligation detection reaction cycle comprises a denaturation treatment, wherein any hybridized oligonucleotide probes are separated from their target nucleotide sequences, and a hybridization treatment, wherein the target-specific oligonucleotide probe portions hybridize in a base-specific manner to their respective target nucleotide sequences, if present in the sample, and ligate to one another.

34. The method according to claim 33, wherein each cycle, comprising a denaturation treatment and a hybridization treatment, is from about 30 seconds to about five minutes long.

35. The method according to claim 34, wherein the denaturation treatment is at a temperature of about 80°

-105°

C.

36. The method according to claim 28, wherein said subjecting is repeated for 2 to 50 cycles.

37. The method according to claim 28, wherein total time for said subjecting is 1 to 250 minutes.

38. The method according to claim 28, wherein the target-specific portions of the oligonucleotide probes each have a hybridization temperature of 20-85°

C.

39. The method according to claim 28, wherein the target-specific portions of the oligonucleotide probes are 20 to 28 nucleotides long.

40. The method according to claim 28 further comprising:

amplifying the target nucleotide sequences in the sample prior to said blending.

41. The method according to claim 40, wherein said amplifying is carried out by subjecting the sample to a polymerase-based amplifying procedure.

42. The method according to claim 41, wherein said polymerase-based amplifying procedure is carried out with DNA polymerase.

43. The method according to claim 40, wherein said amplifying is carried out by subjecting the target nucleotide sequences in the sample to a ligase chain reaction process.

44. The method according to claim 28, wherein the target-specific portions of the oligonucleotide probe sets are configured to be successfully ligated in the presence of their target sequences under a single set of ligase reaction conditions.

45. The method according to claim 28, wherein the ligase is selected from the group consisting of Thermus aquaticus ligase, Thermus thermophilus ligase, E. coli ligase, T4 ligase, and Pyrococcus ligase.

46. The method according to claim 28, wherein said detecting is carried out on a solid support.