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

• US 9,206,477 B2
• Filed: 10/14/2014
• Issued: 12/08/2015
• 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: Barany, Francis, Barany, George, Hammer, Robert P., Kempe, Maria, Blok, Herman, Zirvi, Monib
• Primary Examiner(s): Martinell, James
• Application Number:
  US14/513,906
• Publication Number:
  US 20150038374A1
• Time in Patent Office: 420 Days
• Field of Search: None
• US Class Current: 1/1
• 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 group of beads, wherein each bead of the group comprises one type of capture oligonucleotide from a collection of capture oligonucleotides, wherein each type of capture oligonucleotide is 20-24 nucleotides in length, and wherein each type of capture oligonucleotide comprises a nucleotide sequence that differs from the nucleotide sequence of other types of capture oligonucleotides of the collection by at least 25% when aligned, and wherein each capture oligonucleotide in the collection hybridizes to a nucleic acid molecule comprising a complementary nucleotide sequence under uniform hybridization conditions, wherein hybridized capture oligonucleotides comprise a melting temperature (T_m) that is >

55°

C. when calculated using the formula T_m=4(G+C)+2(A+T) °

C.

2. The group of beads of claim 1, wherein each type of capture oligonucleotide hybridizes to the nucleic acid molecule comprising a complementary nucleotide sequence at a temperature of 60°

C.

3. The group of beads of claim 1, wherein each type of capture oligonucleotide hybridizes to the nucleic acid molecule comprising a complementary nucleotide sequence at a temperature of 65°

C.

4. The group of beads of claim 1, wherein each type of capture oligonucleotide hybridizes to the nucleic acid molecule comprising a complementary nucleotide sequence at a temperature of 70°

C.

5. The group of beads of claim 1, wherein each type of capture oligonucleotide is 24 nucleotides in length.

6. The group of beads of claim 1, wherein the beads are configured on an addressable array.

7. The group of beads of claim 1, wherein each type of capture oligonucleotide within the collection of oligonucleotides exhibits minimal cross-hybridization to a complement of another type of capture oligonucleotide within the collection at 35°

C.

8. The group of beads of claim 1, wherein each type of capture oligonucleotide has a sequence configured to hybridize to the nucleic acid molecule having a complementary nucleotide sequence when incubated for 15 minutes at 60°

C. in a solution comprising 0.5 M Na₂HPO₄ having a pH of 7.2, 1% BSA, 1 mM EDTA, and 7% SDS.

9. The group of beads of claim 8, wherein each type of capture oligonucleotide has a sequence configured to remain hybridized to its complementary nucleic acid molecule following washing at 60°

C. in a low stringency wash buffer comprising 300 mM sodium chloride, 30 mM sodium citrate, and 0.1% SDS, and washing at 60°

C. in a high stringency wash buffer comprising 30 mM sodium chloride, 3 mM sodium citrate, and 0.1% SDS.

10. The group of beads of claim 8, wherein each type of capture oligonucleotide has a sequence configured to remain hybridized to its complementary nucleic acid molecule following washing at 65°

C. in a low stringency wash buffer comprising 300 mM sodium chloride, 30 mM sodium citrate, and 0.1% SDS, and washing at 65°

C. in a high stringency wash buffer comprising 30 mM sodium chloride, 3 mM sodium citrate, and 0.1% SDS.

11. The group of beads of claim 8, wherein each type of capture oligonucleotide has a sequence configured to remain hybridized to its complementary nucleic acid molecule following washing at 70°

C. in a low stringency wash buffer comprising 300 mM sodium chloride, 30 mM sodium citrate, and 0.1% SDS, and washing at 70°

C. in a high stringency wash buffer comprising 30 mM sodium chloride, 3 mM sodium citrate, and 0.1% SDS.

12. The group of beads of claim 1, wherein each type of capture oligonucleotide has a sequence configured to hybridize to the nucleic acid molecule having a complementary nucleotide sequence when incubated for 15 minutes at 65°

C. in a solution comprising 0.5 M Na₂HPO₄ having a pH of 7.2, 1% BSA, 1 mM EDTA, and 7% SDS.

13. The group of beads of claim 1, wherein each type of capture oligonucleotide has a sequence configured to hybridize to the nucleic acid molecule having a complementary nucleotide sequence when incubated for 15 minutes at 70°

C. in a solution comprising 0.5 M Na₂HPO₄ having a pH of 7.2, 1% BSA, 1 mM EDTA, and 7% SDS.

14. A group of beads, wherein each bead of the group comprises one type of capture oligonucleotide from a collection of capture oligonucleotides, wherein each type of capture oligonucleotide is 20-24 nucleotides in length and comprises a guanosine/cytosine (GC) content that is >

50%, and wherein each type of capture oligonucleotide comprises a nucleotide sequence that differs from the nucleotide sequence of other types of capture oligonucleotides of the collection by at least 25% when aligned, and wherein each capture oligonucleotide in the collection hybridizes to a nucleic acid molecule comprising a complementary nucleotide sequence under uniform hybridization conditions.

15. The group of beads of claim 14, wherein each type of capture oligonucleotide hybridizes to the nucleic acid molecule comprising a complementary nucleotide sequence at a temperature of 60°

C.

16. The group of beads of claim 14, wherein each type of capture oligonucleotide hybridizes to the nucleic acid molecule comprising a complementary nucleotide sequence at a temperature of 65°

C.

17. The group of beads of claim 14, wherein each type of capture oligonucleotide hybridizes to the nucleic acid molecule comprising a complementary nucleotide sequence at a temperature of 70°

C.

18. The group of beads claim 14, wherein each type of capture oligonucleotide is 24 nucleotides in length.

19. The group of beads of claim 14, wherein the beads are configured on an addressable array.

20. The group of beads of claim 14, wherein each type of capture oligonucleotide within the collection of oligonucleotides exhibits minimal cross-hybridization to a complement of another type of capture oligonucleotide within the collection at 35°

C.

21. The group of beads of claim 14, wherein each type of capture oligonucleotide has a sequence configured to hybridize to a nucleic acid molecule having a complementary nucleotide sequence when incubated for 15 minutes at 60°

C. in a solution comprising 0.5 M Na₂HPO₄ having a pH of 7.2, 1% BSA, 1 mM EDTA, and 7% SDS.

22. The group of beads of claim 21, wherein each type of capture oligonucleotide has a sequence configured to remain hybridized to its complementary nucleic acid molecule following washing at 60°

C. in a low stringency wash buffer comprising 300 mM sodium chloride, 30 mM sodium citrate, and 0.1% SDS, and washing at 60°

C. in a high stringency wash buffer comprising 30 mM sodium chloride, 3 mM sodium citrate, and 0.1% SDS.

23. The group of beads of claim 21, wherein each type of capture oligonucleotide has a sequence configured to remain hybridized to its complementary nucleic acid molecule following washing at 65°

C. in a low stringency wash buffer comprising 300 mM sodium chloride, 30 mM sodium citrate, and 0.1% SDS, and washing at 65°

C. in a high stringency wash buffer comprising 30 mM sodium chloride, 3 mM sodium citrate, and 0.1% SDS.

24. The group of beads of claim 21, wherein each type of capture oligonucleotide has a sequence configured to remain hybridized to its complementary nucleic acid molecule following washing at 70°

C. in a low stringency wash buffer comprising 300 mM sodium chloride, 30 mM sodium citrate, and 0.1% SDS, and washing at 70°

C. in a high stringency wash buffer comprising 30 mM sodium chloride, 3 mM sodium citrate, and 0.1% SDS.

25. The group of beads of claim 14, wherein each type of capture oligonucleotide has a sequence configured to hybridize to a nucleic acid molecule having a complementary nucleotide sequence when incubated for 15 minutes at 65°

C. in a solution comprising 0.5 M Na₂HPO₄ having a pH of 7.2, 1% BSA, 1 mM EDTA, and 7% SDS.

26. The group of beads of claim 14, wherein each type of capture oligonucleotide has a sequence configured to hybridize to a nucleic acid molecule having a complementary nucleotide sequence when incubated for 15 minutes at 70°

C. in a solution comprising 0.5 M Na₂HPO₄ having a pH of 7.2, 1% BSA, 1 mM EDTA, and 7% SDS.