Ligation assembly and detection of polynucleotides on solid-support

• US 5,942,609 A
• Filed: 11/12/1998
• Issued: 08/24/1999
• Est. Priority Date: 11/12/1998
• Status: Expired due to Term

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: The Porkin-Elmer Corporation
• Inventors: Hunkapiller, Michael W., Hiatt, Andrew C.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US09/191,390
• Time in Patent Office: 285 Days
• Field of Search: 435/6, 435/810, 435/91.2, 436/501, 935/77, 935/78, 536/25.3
• US Class Current: 536/25.3
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 2533/101 Primer extension
• CPC Class Codes: C12Q 2533/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2565/525 characterised by the capture oligonucleotide being double stranded

Abstract

The present invention concerns methods of assembly of a polynucleotide on a solid-support by performing steps of annealing, ligation, and extension. The steps may be repeated in a cyclical manner to assemble immobilized double- or single-stranded polynucleotides with functional gene properties. The immobilized polynucleotides may be amplified by the polymerase chain reaction, and detected and quantitated by an exonuclease assay with a self-quenching, fluorescent probe. The polynucleotide may be cleaved from the solid-support by chemical or enzymatic cleavage.

Claims

1. A method of synthesizing a polynucleotide on a solid-support, the method comprising the steps of:

a. annealing one or more bridging oligonucleotides and two or more assembly oligonucleotides such that a ligatable nick site is formed between adjacent assembly oligonucleotides, wherein one of the assembly oligonucleotides is immobilized to a solid support;

b. ligating the ligatable nick sites thereby forming an immobilized ligation product;

c. annealing a primer to the immobilized ligation product; and

d. extending the primer to create an immobilized, double-stranded polynucleotide.

2. The method claim 1 wherein steps a. and b. are repeated a plurality of cycles.

3. The method claim 1 wherein steps a. and b. are repeated from 1 to 100 cycles.

4. The method of claim 1 wherein the solid support is comprised of small particles, beads, membranes, frits, non-porous surfaces, addressable arrays, vectors, plasmids, or polynucleotide-immobilizing media.

5. The method of claim 1 to synthesize a polynucleotide of length between 50 and 5000 nucleotide base pairs.

6. The method of claim 1 wherein the assembly oligonucleotides are 20-200 nucleotides in length and the bridging oligonucleotides are 6-40 nucleotides in length.

7. The method of claim 1 wherein step d. of extending the primer annealed to the immobilized ligation product comprises nucleotide 5'"'"' triphosphates selected from the group consisting of;

ATP, dATP, CTP, dCTP, GTP, dGTP, UTP, TTP, dUTP, 5-methyl-CTP, 5-methyl-dCTP, ITP, dITP, 2-amino-ATP, 2-amino-dATP, 5-Br-UTP, 5-Br-dUTP, 5-F-UTP, 5-F-dUTP, 5-propynyl dCTP, 5-propynyl-dUTP and;

the corresponding α

-thiotriphosphates, 2'"'"'-O-methyl-ribonucleotide triphosphates, 2'"'"'-fluoro-NTP, 2'"'"'-amino-NTP analogs, and fluorescent labelled-NTP.

8. The method of claim 7 wherein said fluorescent labels are attached at the N-9 or C-8 positions of the purine or deazapurine, and the C-5 position of the pyrimidine and are selected from the group consisting of FAM, TET, HEX or JOE.

9. The method of claim 1 wherein said assembly and bridging oligonucleotides are comprised of;

A, dA, C, dC, G, dG, U, T, dU, 5-methyl-C, 5-methyl-dC, I, dI, 2-amino-A, 2-amino-dA, 5-Br-U, 5-Br-dU, 5-F-U, 5-F-dU, 5-propynyl dC, 5-propynyl-dU and;

the corresponding phosphorothioate, N-3-phosphoramidate, 2'"'"'-O-methyl-ribonucleotides, 2'"'"'-fluoro-ribonucleotides, and 2'"'"'-amino-ribonucleotides analogs.

10. The method of claim 1 further comprising the step of periodic washing under non-denaturing conditions after steps a. and b.

11. The method of claim 1 further comprising the steps of washing the support under denaturing conditions after each ligation step b.

12. The method of claim 11 wherein the denaturants are selected from the group consisting of sodium hydroxide, ammonium hydroxide, formamide, urea, sodium chloride and sodium acetate.

13. The method of claim 1 wherein the polynucleotide is cleaved from the support by chemical cleavage.

14. The method of claim 1 wherein the polynucleotide is cleaved from the support by enzymatic cleavage.

15. The method of claim 1 further comprising the step of annealing a self-quenching, fluorescence probe complementary to said immobilized polynucleotide.

16. The method of claim 15 wherein said self-quenching, fluorescence probe is comprised of nucleotides near the 5'"'"' terminus substantially complementary to the nucleotides near the 3'"'"' terminus whereby the unannealed probe exists in a quenched state.

17. The method of claim 15 wherein annealing of the self-quenching, fluorescence probe to the immobilized double-stranded polynucleotide is measured by fluorescence detection.

18. The method of claim 1 wherein step d. of extending the primer annealed to the immobilized ligation product is a polymerase chain reaction comprised of;

a thermal-stable nucleic acid polymerase having 5'"'"'→

3'"'"' nuclease activity, said primer complementary to the immobilized ligation product, a second primer complementary to the complement of the immobilized ligation product, 5'"'"' nucleotide triphosphates; and

a self-quenching fluorescence probe,

said probe existing in at least one single-stranded conformation when unannealed to polynucleotide wherein a quencher quenches the fluorescence of a reporter and at least one conformation when annealed to said immobilized ligation product, wherein the fluorescence of the reporter is unquenched; and

the steps of

annealing said primers to said immobilized ligation product;

amplifying the immobilized ligation product by PCR, whereby target polynucleotide amplification products are produced.

19. The method of claim 18 wherein said nucleic acid polymerase digests said self-quenching, fluorescence probe during amplification to separate said reporter from said quencher.

20. The method of claim 18 wherein the target polynucleotide amplification products are measured by fluorescence detection.

21. The method of claim 18 wherein the target polynucleotide amplification products are measured and quantitated by end-point analysis.

22. The method of claim 18 wherein the target polynucleotide amplification products are measured and quantitated by real-time analysis.