Ligase/polymerase mediated genetic bit analysis of single nucleotide polymorphisms and its use in genetic analysis

• US 5,679,524 A
• Filed: 08/09/1996
• Issued: 10/21/1997
• Est. Priority Date: 02/07/1994
• Status: Expired due to Term

• Current Assignee: Beckman Coulter Incorporated (Danaher Corporation)
• Original Assignee: Molecular Tool, Inc. (Laboratory Corporation Of America Holdings)
• Inventors: Nikiforov, Theo, Karn, Jonathan, Goelet, Philip
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/694,835
• Time in Patent Office: 438 Days
• Field of Search: 435/5, 435/6, 435/91.1, 435/91.2, 435/810, 436/501, 536/24.1, 536/24.3-33, 935/77, 935/78
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/6862 Ligase chain reaction [LCR]
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2561/125 Ligase Detection Reaction [LDR]
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C12Q 2565/537 characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: Y10S 435/81 Packaged device or kit

Abstract

A method is provided for determining the identity of a nucleotide at a preselected site in a nucleic acid molecule. The method involves the incorporation of a nucleoside triphosphate that is complementary to the nucleotide present at the preselected site onto the terminus of a primer molecule, and their subsequent ligation to a second oligonucleotide. The reaction is monitored by detecting a specific label attached to the reaction'"'"'s solid phase or by detection in solution.

Claims

1. A method for determining the identity of nucleotide present at a preselected single nucleotide long site in a single-stranded target nucleic acid molecule, said method employing a set of oligonucleotides consisting of two oligonucleotides hybridizable to said target, and comprising the steps:

A) immobilizing a first oligonucleotide of said set of oligonucleotides, said first oligonucleotide being a primer oligonucleotide or a linker oligonucleotide, to a solid support;

said first oligonucleotide having a nucleotide sequence complementary to, that of a first region of said target molecule, and being capable of hybridizing to said first region of said target molecule such that a terminus of said hybridized first oligonucleotide is immediately adjacent to said preselected site;

B) incubating said immobilized first oligonucleotide in the presence of said target molecule, and in the further presence of a labeled or unlabeled second oligonucleotide of said set of oligonucleotides, said second oligonucleotide being a primer oligonucleotide when said first oligonucleotide is a linker oligonucleotide or a linker oligonucleotide when said first oligonucleotide is a primer oligonucleotide;

said second oligonucleotide having a sequence complementary to that of a second region of said target molecule, and being capable of hybridizing to said second region of said target molecule, wherein said first and second regions are separated from one another by said preselected site;

said incubation being under conditions sufficient to permit said first and second oligonucleotides to hybridize to said target molecule to thereby form a hybridized product in which said first and second oligonucleotides are separated from one another by a space of a single nucleotide, said space being opposite to said preselected site;

C) further incubating said hybridized product, in the presence of a polymerase, a ligase, and a nucleoside triphosphate mixture containing a nucleoside triphosphate species that is complementary to the nucleotide of said preselected site and is detectably labeled if said second oligonucleotide is unlabeled, said mixture composed of one deoxynucleoside triphosphate species and three dideoxynucleoside triphosphate species, such that regardless of the identity of the nucleotide of said preselected site, a template-dependent, polymerase-mediated extension reaction will occur, causing a nucleoside triphosphate species of said nucleoside triphosphate mixture, complementary to that of the nucleotide of the preselected site, to become incorporated onto the 3'"'"' terminus of whichever of said first or said second oligonucleotide is the primer oligonucleotide;

said incubation being under conditions sufficient to permit said template-dependent, polymerase mediated, incorporation to occur, and to thereby fill the space between said hybridized oligonucleotides and cause said oligonucleotides to abut;

D) permitting said ligase to ligate together abutting first and second hybridized oligonucleotides;

E) further incubating said immobilized first oligonucleotide under conditions sufficient to separate any non-covalently bonded target or second oligonucleotide therefrom; and

F) determining whether said immobilized first oligonucleotide of step E has become labeled, wherein the presence of an immobilized labeled oligonucleotide indicates that the identity of said nucleotide of said preselected site is complementary to the deoxynucleoside triphosphate of said deoxynucleoside triphosphate mixture.

2. The method of claim 1, wherein said first and second oligonucleotides and said target molecule are DNA molecules.

3. The method of claim 1, wherein said first and second oligonucleotides and said target molecule are RNA molecules.

4. The method of claim 3, wherein said polymerase is reverse transcriptase and said ligase is RNA ligase.

5. The method of claim 2, wherein in step A, said first oligonucleotide is a linker oligonucleotide, and wherein the 3'"'"'-terminus of said first oligonucleotide is immobilized to said solid support, and wherein in step C, said conditions permit the incorporation of said nucleoside triphosphate onto the 3'"'"'-terminus of said second hybridized oligonucleotide, said second oligonucleotide being a primer oligonucleotide.

6. The method of claim 2, wherein step C, said nucleoside triphosphate mixture contains at least one detectably labeled deoxynucleoside triphosphate.

7. The method of claim 6, wherein said detectable label is an enzyme label, a fluorescent label, a radioisotopic label, or a chemiluminescent label.

8. The method of claim 6, wherein in step F, the identity of said nucleotide of said preselected site is determined by detecting the immobilized label of said nucleotide.

9. The method of claim 2, wherein said second oligonucleotide is a primer oligonucleotide, and wherein in step B, said second oligonucleotide is detectably labeled and all of the nucleoside triphosphates are unlabeled.

10. The method of claim 9, wherein said detectable label is an enzyme label, a fluorescent label, a radioisotopic label, or a chemiluminescent label.

11. The method of claim 9, wherein in step F, the identity of said nucleotide of said preselected site is deduced from the mixture of deoxynucleotide and dideoxynucleotide triphosphates used in step C.

12. The method of claim 1, wherein said first oligonucleotide is a primer oligonucleotide, and wherein in step A, the 5'"'"'-terminus of said first oligonucleotide is immobilized to said solid support, and wherein in step C, said conditions permit the incorporation of said nucleoside triphosphate onto the 3'"'"'-terminus of said immobilized oligonucleotide.

13. The method of claim 12, wherein said second oligonucleotide is a linker oligonucleotide, and wherein said second oligonucleotide is detectably labeled at its 3'"'"'-end.

14. The method of claim 13, wherein in step F, the identity of said nucleotide of said preselected site is deduced from the mixture of deoxynucleotide and dideoxynucleotide triphosphates used in step C.

15. The method of claim 1, wherein said target molecule contains a polymorphism, and said preselected site contains the variable nucleotide of said polymorphism.

16. The method of claim 15, wherein said target molecule is obtained from an animal selected from the group consisting of a horse, a sheep, a bovine, a canine, a feline, and a human.

17. The method of claim 15, wherein said target molecule is amplified in vitro from nucleic acid of an animal.

18. The method of claim 17, wherein said animal is selected from the group consisting of a horse, a sheep, a bovine, a canine, a feline, and a human.

19. The method of claim 15, wherein said target molecule is obtained from a plant.

20. The method of claim 15, wherein said target molecule is amplified in vitro from nucleic acid of a plant.

21. The method of claim 15, wherein said target molecule is obtained from a virus, a bacterium, a yeast or a fungi.

22. The method of claim 15, wherein said target molecule is amplified in vitro from nucleic acid of a virus, a bacterium, a yeast or a fungi.

23. A method for determining the identity of a nucleotide present at a preselected single nucleotide long site in a single-stranded target nucleic acid molecule, said method employing a set of oligonucleotides consisting of two oligonucleotides hybridizable to said target, and comprising the steps:

A) incubating said target molecule in the presence of a first oligonucleotide of said set of oligonucleotides, said first oligonucleotide being a primer oligonucleotide or a linker oligonucleotide, wherein said first oligonucleotide contains a bound ligand selected from the group consisting of biotin and fluorescein;

said first oligonucleotide having a nucleotide sequence complementary to that of a first region of said target molecule, and being capable of hybridizing to said first region of said target molecule such that a terminus of said hybridized first oligonucleotide is immediately adjacent to said preselected site;

B) further incubating said provided first oligonucleotide and said target molecule in the presence of a labeled or unlabeled second oligonucleotide of said set of oligonucleotides, said second oligonucleotide being a primer oligonucleotide when said first oligonucleotide is a linker oligonucleotide or a linker oligonucleotide when said first oligonucleotide is a primer oligonucleotide;

said second oligonucleotide having a sequence complementary to that of a second region of said target molecule, and being capable of hybridizing to said second region of said target molecule, wherein said first and second regions are separated from one another by said preselected site;

said incubation being under conditions sufficient to permit said first and second oligonucleotides to hybridize to said target molecule to thereby form a hybridized product in which said first and second oligonucleotides are separated from one another by a space of a single nucleotide, said space being opposite to said preselected site;

C) further incubating said hybridized product, in the presence of a polymerase, a ligase, and a nucleoside triphosphate mixture containing a nucleoside triphosphate species that is complementary to the nucleotide of said preselected site and is detectably labeled if said second oligonucleotide is unlabeled, said mixture composed of one deoxynucleoside triphosphate species and three dideoxynucleoside triphosphate species, such that regardless of the identity of the nucleotide of said preselected site, a template-dependent, polymerase-mediated extension reaction will occur, causing a nucleoside triphosphate species of said nucleoside triphosphate mixture, complementary, to that of the nucleotide of the preselected site, to become incorporated onto the 3'"'"' terminus of whichever of said first or said second oligonucleotide is the primer oligonucleotide;

said incubation being under conditions sufficient to permit said template-dependent, polymerase mediated, incorporation to occur, and to thereby fill the space between said hybridized oligonucleotides and cause said oligonucleotides to abut;

D) permitting said ligase to ligate together abutting first and second hybridized oligonucleotides to thereby form a first and second oligonucleotide ligation product;

E) capturing the first and second oligonucleotide ligation product onto a solid phase using the ligand and further incubating said provided first oligonucleotide under conditions sufficient to remove any non-covalently bonded target or second oligonucleotide from said incubation; and

F) determining whether said immobilized first oligonucleotide of step E has become labeled, wherein the presence of an immobilized labeled oligonucleotide indicates that the identity of said nucleotide of said preselected site is complementary to the deoxynucleoside triphosphate of said deoxynucleoside triphosphate mixture.

24. A method for determining the identity of a nucleotide present at a preselected single nucleotide long site in a single-stranded target nucleic acid molecule, said method employing a set of oligonucleotides consisting of two oligonucleotides hybridizable to said target, and comprising the steps:

A) incubating said target molecule in the presence of a first oligonucleotide of said set of oligonucleotides, said first oligonucleotide being a primer oligonucleotide or a linker oligonucleotide, wherein said first oligonucleotide is labeled with a ligand selected from the group consisting of biotin and fluorescein;

said first oligonucleotide having a nucleotide sequence complementary to that of a first region of said target molecule, and being capable of hybridizing to said first region of said target molecule such that a terminus of said hybridized first oligonucleotide is immediately adjacent to said preselected site;

B) further incubating said provided first oligonucleotide and said target molecule in the presence of a second oligonucleotide of said set of oligonucleotides, said second oligonucleotide being a primer oligonucleotide when said first oligonucleotide is a linker oligonucleotide or a linker oligonucleotide when said first oligonucleotide is a primer oligonucleotide;

said second oligonucleotide having a sequence complementary to that of a second region of said target molecule, and being capable of hybridizing to said second region of said target molecule, wherein said first and second regions are separated from one another by said preselected site;

said incubation being under conditions sufficient to permit said first and second oligonucleotides to hybridize to said target molecule to thereby form a hybridized product in which said first and second oligonucleotides are separated from one another by a space of a single nucleotide, said space being opposite to said preselected site;

C) further incubating said hybridized product, in the presence of a polymerase, a ligase, and a nucleoside triphosphate mixture containing a nucleoside triphosphate species that is complementary to the nucleotide of said preselected site and is detectably labeled if said second oligonucleotide is unlabeled, said mixture composed of one deoxynucleoside triphosphate species and three dideoxynucleoside triphosphate species, such that regardless of the identity of the nucleotide of said preselected site, a template-dependent, polymerase-mediated extension reaction will occur, causing a nucleoside triphosphate species of said nucleoside triphosphate mixture, complementary to that of the nucleotide of the preselected site, to become incorporated onto the 3'"'"' terminus of whichever of said first or said second oligonucleotide is the primer oligonucleotide;

said incubation being under conditions sufficient to permit said template-dependent, polymerase mediated, incorporation to occur, and to thereby fill the space between said hybridized oligonucleotides and cause said oligonucleotides to abut;

D) permitting said ligase to ligate together abutting first and second hybridized oligonucleotides to thereby form a first and second oligonucleotide ligation product;

E) further incubating said provided first oligonucleotide under conditions sufficient to separate any non-covalently bonded target or second oligonucleotide therefrom and to retain the ligated oligonucleotides in solution;

F) determining whether said immobilized first oligonucleotide of step E has become labeled, wherein the presence of an immobilized labeled oligonucleotide indicates that the identity of said nucleotide of said preselected site is complementary to the deoxynucleoside triphosphate of said deoxynucleoside triphosphate mixture.