Multi-zone polymerase/ligase chain reaction

• US 5,912,129 A
• Filed: 03/05/1998
• Issued: 06/15/1999
• Est. Priority Date: 03/05/1998
• Status: Expired due to Term

• Current Assignee: Roger Grant Hodkinson, Thuraiayah Vinayagamoorthy
• Original Assignee: Roger Grant Hodkinson, Thuraiayah Vinayagamoorthy
• Inventors: Vinayagamoorthy, Thuraiayah, Hodkinson, Roger Grant
• Primary Examiner(s): MCKELVEY, TERRY ALAN
• Application Number:
  US09/035,091
• Time in Patent Office: 467 Days
• Field of Search: 435/91.2, 435/6
• US Class Current: 435/6.12
• CPC Class Codes: B01J 2219/00313 the reactor vessels being formed by arrays of wells in blocks
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/00495 Means for heating or cooling the reaction vessels
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 7/52 with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples amplification or hybridisation processes per se C12Q1/68; controlling sequential reactions for synthesis B01J19/0046
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 for creating libraries

Abstract

A process of amplifying a nucleic acid sequence by a procedure involving a polymerase chain reaction or a ligase chain reaction. The process involves repeated cycles of steps including a nucleic acid denaturing step and a nucleic acid synthesis step, the synthesis step being carried out under the action of an enzyme (a nucleic acid polymerase or ligase). The denaturing step and the synthesis step are carried out in different denaturing and synthesis reaction zones, respectively, and, during the repeated cycles, the enzyme is maintained in isolation from the denaturing reaction zone, and conditions or reagents required for the denaturing step are maintained in isolation from the synthesis reaction zone to the extent that the reagents and conditions required for denaturing do not impede the synthesis reaction to a substantial extent. The use of separate zones for the steps of the reactions means that an enzyme that is destroyed or degraded by the reagents and conditions required for denaturing (e.g. a thermolabile or alkalolabile polymerase or ligase) may be used in the reaction. Moreover, the use of multiple zones means that inexpensive equipment may be used for the process.

Claims

1. A process of amplifying a nucleic acid sequence by a procedure selected from the group consisting of a polymerase chain reaction and a ligase chain reaction, comprising repeated cycles of steps including:

(a) a nucleic acid denaturing step comprising subjecting double-stranded nucleic acid to conditions, or contacting said double-stranded nucleic acid with a reagent, that causes separation of said double-stranded nucleic acid into single-stranded nucleic acid; and

(b) a nucleic acid synthesis step comprising using an enzyme to form a complementary strand of nucleic acid from said single-stranded nucleic acid by nucleic acid polymerization, thereby forming double-stranded nucleic acid, wherein

said nucleic acids resulting from steps (a) and (b) are immobilized on a solid support,

steps (a) and (b) are carried out in different denaturing and synthesis reaction zones, respectively, with said solid support immersed in a liquid during steps (a) and (b), and

during said repeated cycles, substantially all of the enzyme is maintained in isolation from the denaturing reaction zone, and said conditions or said reagent of step (a) are maintained in isolation from the synthesis reaction zone to the extent that said conditions or said reagent do not impede said synthesis step substantially, said isolation being achieved, at least in part, by separating said solid support having immobilized nucleic acids from substantially all of said liquid present in one of said denaturing and synthesis reaction zones before subjecting said immobilized nucleic acids to a step in another of said zones.

2. The process of claim 1, wherein the procedure is a polymerase chain reaction, and said enzyme is a nucleic acid polymerase enzyme.

3. The process of claim 2, wherein said double-stranded nucleic acid in step (a) is subjected to elevated temperature in said denaturing reaction zone to cause said separation, and wherein said polymerase enzyme is thermolabile.

4. The process of claim 2, wherein said double-stranded nucleic acid in step (a) is subjected to elevated alkalinity in said denaturing reaction zone to cause said separation, and wherein-said polymerase enzyme is alkali-sensitive.

5. The process of claim 1, wherein the procedure is a ligase chain reaction, and said enzyme is a nucleic acid ligase enzyme.

6. The process of claim 5, wherein said double-stranded nucleic acid in step (a) is subjected to elevated temperature in said denaturing reaction zone to cause said separation, and wherein said ligase enzyme is thermolabile.

7. The process of claim 5, wherein said double-stranded nucleic acid in step (a) is subjected to elevated alkalinity in said denaturing reaction zone to cause said separation, and wherein said ligase enzyme is alkali-sensitive.

8. The process of claim 1, wherein said solid support is held immobile.

9. The process of claim 1, wherein said solid support is susceptible to magnetic attraction, and wherein said solid support is moved between said zones by attracting said support to a magnet and moving said magnet to cause said support to move between said zones.

10. The process of claim 1, further comprising an additional step selected from the group consisting of neutralizing said single-stranded nucleic acid and annealing at least one primer to said single-stranded nucleic acid, wherein said additional step is carried out between steps (a) and (b) in at least one additional reaction zone.

11. A process of amplifying a nucleic acid sequence, comprising repeated cycles of steps including:

(a) denaturing double-stranded nucleic acid to form single-stranded nucleic acid;

(b) annealing the single-stranded nucleic acid with at least one complimentary primer that binds adjacent to a target sequence in the single-stranded nucleic acid; and

(c) using the target sequence as a template extending from said at least one complementary primer to form a complementary sequence of nucleic acid by nucleic acid polymerization utilizing a nucleic acid polymerization enzyme, thereby synthesizing double-stranded nucleic acid, wherein

said nucleic acids resulting from steps (a)-(c) are immobilized on a solid support,

steps (a) and (c) are carried out in different denaturing and synthesis reaction zones, respectively, with said solid support immersed in a liquid during steps (a)-(c), and

during said repeated cycles, substantially all of the enzyme is maintained in isolation from the denaturing reaction zone, and conditions or reagent used in step (a) for said denaturing are maintained in isolation from the synthesis reaction zone to the extent that said conditions or reagent do not impede said polymerization substantially, said isolation being achieved, at least in part, by separating said solid support having immobilized nucleic acids from substantially all of said liquid present in one of said denaturing and synthesis reaction zones before subjecting said immobilized nucleic acids to a step in another of said zones.

12. A process of amplifying a nucleic acid sequence, comprising repeated cycles of steps including:

(a) denaturing double-stranded nucleic acid to form single-stranded nucleic acid;

(b) annealing the single-stranded nucleic acid with at least one complimentary primer that binds adjacent to a target sequence in the single-stranded nucleic acid; and

(c) using the target sequence as a template extending from said at least one complementary primer to form a complementary sequence of nucleic acid by nucleic acid polymerization utilizing a nucleic acid polymerization enzyme, thereby synthesizing double-stranded nucleic acid, wherein

said nucleic acids resulting from steps (a)-(c) are immobilized on a solid support,

steps (a), (b), and (c) are carried out in different denaturing, annealing, and synthesis reaction zones, respectively,

said solid support is passed repeatedly through said reaction zones in an order and with residence times in each zone for effecting a polymerase chain reaction, with said solid support immersed in a liquid during steps (a)-(c), and

during said repeated cycles, substantially all of the enzyme is maintained in isolation from the denaturing reaction zone, and conditions or reagent used in step (a) for said denaturing are maintained in isolation from the synthesis reaction zone to the extent that said conditions or reagent do not impede said polymerization substantially, said isolation being achieved, at least in part, by separating said solid support having immobilized nucleic acids from substantially all of said liquid present in one of said denaturing and synthesis reaction zones before subjecting said immobilized nucleic acids to a step in another of said denaturing and synthesis reaction zones.

13. A process of amplifying a DNA by a polymerase chain reaction utilizing a polymerase enzyme, comprising the steps of:

(a) creating a plurality of reaction zones containing liquid media, including a denaturing zone having conditions or reagents for separating double-stranded nucleic acid into single-stranded nucleic acid, and a synthesis zone containing said polymerase enzyme and having conditions and reagents for polymerization of nucleic acid;

(b) binding said DNA to a solid transport medium having a surface that binds nucleic acids;

(c) introducing said transport medium resulting from step (b) into said liquid medium in said denaturing zone, thereby resulting in denaturation of said DNA bound to the transport medium;

(d) separating said transport medium from substantially all of said liquid medium in said denaturing zone;

(e) transferring said transport medium resulting from step (d) to said synthesis zone, thereby resulting in polymerization of said DNA bound to the transport medium;

(f) separating said transport medium resulting from step (e) from substantially all of said liquid medium in said synthesis zone;

(g) transferring said transport medium resulting from step (f) to said denaturing zone, thereby resulting in denaturation of said DNA bound to the transport medium;

(h) repeating steps (d)-(g) a plurality of times to amplify said DNA; and

(i) separating said amplified DNA from said liquid media and said transport medium.

14. The process of claim 13, wherein said plurality of reaction zones includes an annealing zone containing oligonucleotide primers, and wherein said transport medium is transferred into said annealing zone after step (d) and prior to step (e).

15. The process of claim 13, wherein said plurality of reaction zones includes a washing zone for washing or neutralizing denaturing reagent from said transport medium, and wherein said transport medium is transferred into said washing zone after step (d) and prior to step (e).

16. A process of amplifying a DNA by a polymerase chain reaction utilizing a polymerase enzyme, comprising the steps of:

(a) fixing a solid medium within a container, said solid medium having a surface that binds nucleic acid;

(b) binding said DNA to said solid medium fixed within said container;

(c) introducing into said container a first liquid medium and subjecting said DNA to conditions or reagents for denaturing double-stranded DNA, thereby creating single-stranded DNA;

(d) removing said first liquid medium from said container resulting from step (c) and removing said conditions or reagents for denaturing double-stranded DNA;

(e) introducing a second liquid medium containing said polymerase enzyme into said container resulting from step (d) and subjecting said single-stranded DNA to polymerization, thereby creating double-stranded DNA using said single-stranded DNA as a template for new strands of complementary base sequences;

(f) removing said second liquid medium from said container resulting from step (e);

(g) repeating steps (c)-(f) a plurality of times to amplify said DNA; and

(h) removing said amplified DNA from said solid medium.

17. The process of claim 16, further comprising introducing an additional liquid medium into said container, and then removing said additional liquid medium, prior to step (e), said additional liquid medium containing primers which anneal to said single-stranded DNA.

18. The process of claim 16, wherein said first liquid medium contains a reagent for denaturing said double-stranded DNA, and wherein said process further comprises introducing an additional liquid medium into said container, and then removing said additional liquid medium, prior to step (e), said additional liquid medium being a solution for washing or neutralizing quantities of said denaturing reagents remaining in said container after step (d).

19. A process of amplifying and testing for a nucleic acid test sequence in a sample by single primer polymerase chain reaction, comprising the steps of:

(a) contacting said sample with an immobilized nucleic acid primer for said test sequence attached to a solid support, and a labeled nucleic acid primer for a sequence complementary to said test sequence, wherein the test sequence in said sample is immobilized by hybridizing to the immobilized nucleic acid primer;

(b) amplifying said test sequence resulting from step (a), thereby creating labeled copies of said test sequence, by cycling said test sequence resulting from step (a) between a plurality of reaction zones while immersed in a liquid, said zones comprising;

(i) a denaturing zone having conditions that cause denaturing of double-stranded nucleic acid, or containing a reagent that causes said denaturing;

(ii) a synthesis zone containing a nucleic acid polymerase enzyme and having conditions that cause primer extension by nucleic acid polymerization; and

(c) testing for said labeled copies of said test sequence,

wherein during said cycling, substantially all of said enzyme is maintained in isolation from the denaturing zone, and said conditions or said reagent of the denaturing zone are maintained in isolation from the synthesis zone to the extent that said conditions or said reagent do not impede said primer extension in said synthesis zone substantially, said isolation being achieved, at least in part, by separating said solid support from substantially all of said liquid present in one of said denaturing and synthesis zones before cycling said solid support to another of said zones.