Process for detecting or quantifying nucleic acids in a library

• US 20090042733A1
• Filed: 07/29/2004
• Published: 02/12/2009
• Est. Priority Date: 06/30/2001
• Status: Active Grant

• Current Assignee: Enzo Life Sciences Incorporated (Enzo Biochem Incorporated)
• Original Assignee: Enzo Life Sciences Incorporated (Enzo Biochem Incorporated)
• Inventors: Stavrianopoulos, Jannis G., Donegan, James J., Rabbani, Elazar, Coleman, Jack
• Granted Patent: US 9,163,280 B2
• Time in Patent Office: Days
• US Class Current: 506/9
• 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 2219/00599 Solution-phase processes
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12N 15/1006 by means of a solid support carrier, e.g. particles, polymers
• CPC Class Codes: C12N 15/1058 Directional evolution of libraries, e.g. evolution of libraries is achieved by mutagenesis and screening or selection of mixed population of organisms
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid
• 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 2565/537 : characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: C40B 40/00 : Libraries per se, e.g. arrays, mixtures
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: G01N 33/68 : involving proteins, peptides or amino acids involving lipoproteins G01N33/92

Abstract

This invention provides novel compositions and processes for analyte detection, quantification and amplification. Nucleic acid arrays and libraries of analytes are usefully incorporated into such compositions and processes. Universal detection elements, signaling entities and the like are employed to detect and if necessary or desirable, to quantify analytes. Amplification of target analytes are also provided by the compositions and processes of this invention.

Claims

1. (canceled)

2-557. -557. (canceled)

558. A process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of:

a) providing;

(i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of said nucleic acids of interest;

(ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and

(iii) polymerizing means for synthesizing nucleic acid copies of said nucleic acid analytes, said polymerizing means comprising a first set of primers, a second set of primers and a third set of primers wherein said third set comprises at least one production center; and

b) contacting said library of nucleic acid analytes with said first set of primers to form a first set of bound primers;

c) extending said first set of bound primers by means of template sequences provided by said nucleic acid analytes to form first copies of said analytes;

d) contacting said extended first copies with said second set of primers to form a second set of bound primers;

e) extending said second set of bound primers by means of template sequences provided by said extended first copies to form second copies of said nucleic acid analytes;

f) contacting said second copies with said third set of primers to form more than one third bound entity to form a third set of bound primers;

g) extending said third set of bound primers by means of template sequences provided by said extended second set of primers to form a hybrid comprising a second copy, a third copy and at least one production center;

h) synthesizing from said production center in said second set of primers in said complexes one or more nucleic acid copies under isothermal or isostatic conditions;

i) hybridizing said nucleic acid copies formed in step i) to said array of nucleic acids provided in step a) (i); and

j) detecting or quantifying any of said hybridized copies obtained in step i).

559. The process of claim 558, wherein said nucleic acid array comprises members selected from the group consisting of DNA, RNA and analogs thereof.

560. The process of claim 559, wherein said analogs comprise PNA.

561. The process of claims 559 or 560, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

562. The process of claim 558, wherein said nucleic acid array is fixed or immobilized to a solid support.

563. The process of claim 562, wherein said solid support is porous or non-porous.

564. The process of claim 563, wherein said porous solid support is selected from the group consisting of polyacrylamide and agarose.

565. The process of claim 563, wherein said non-porous solid support comprises glass or plastic.

566. The process of claim 562, wherein said solid support is transparent, translucent, opaque or reflective.

567. The process of claim 562, wherein said nucleic acids are directly or indirectly fixed or immobilized to said solid support.

568. The process of claim 562, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

569. The process of claim 558, wherein said library of nucleic acid analytes is derived from a biological source selected from the group consisting of organs, tissues and cells.

570. The process of claim 558, wherein said library of nucleic acids analytes are derived from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.

571. The process of claim 558, wherein said first set of primers comprise one or more sequences which are complementary to inherent universal detection targets (UDTs).

572. The process of claim 558, wherein said inherent UDTs are selected from the group consisting of 3′

poly A segments, consensus sequences, and a combination of both.

573. The process of claim 572, wherein said consensus sequences is selected from the group consisting of signal sequences for poly A addition, splicing elements, multicopy repeats, and a combination of any of the foregoing.

574. The process of claim 558, wherein said second set of primers are random primers.

575. The process of claim 558, further comprising the step c′

) of adding a primer binding site after step c).

576. The process of claim 575, wherein said second set of primers are complementary to said primer binding site.

577. The process of claim 575, wherein said primer binding site is added by means of T4 DNA ligase or terminal transferase.

578. The process of claim 558, wherein said production center is selected from the group consisting of primer binding sites, RNA promoters, or a combination of both.

579. The process of claim 578, wherein said RNA promoters comprise phage promoters.

580. The process of claim 579, wherein said phage promoters are selected from the group consisting of T3, T7 and SP6.

581. The process of claim 558, wherein said hybridized nucleic acid copies further comprise one or more signaling entities attached or incorporated thereto.

582. The process of claim 581, wherein said signaling entities generate a signal directly or indirectly.

583. The process of claim 582, wherein said direct signal generation is selected from the group consisting of a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound and a combination of any of the foregoing.

584. The process of claim 582, wherein said indirect signal generation is selected from the group consisting of an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme and a combination of any of the foregoing.

585. The process of claim 584, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

586. The process of claim 558, wherein said polymerizing means are selected from the group consisting of E. coli DNA Pol I, Klenow fragment of E. coli DNA Pol I, Bst DNA polymerase, Bca DNA polymerase, Taq DNA polymerase, Tth DNA Polymerase, T4 DNA polymerase, ALV reverse transcriptase, MuLV reverse transcriptase, RSV reverse transcriptase, HIV-1 reverse transcriptase, HIV-2 reverse transcriptase, Sensiscript and Omniscript.

587. The process of claim 558, further comprising the step of separating the first copies obtained from step c) from their templates and repeating step b).

588. The process of claim 558, further comprising the step of separating the extended second set of primers obtained from step f) from their templates and repeating step e).

589. The process of claim 558, wherein step g) is carried out repeatedly.

590. The process of claim 558, further comprising the step f′

) of separating said extended second set of primers obtained in step e).

591. The process of claim 558, further comprising the step of separating the first copies obtained from step c) from their templates and repeating step b).

592. The process of claim 558, further comprising the step of separating the extended second set of primers obtained from step f) from their templates and repeating step e).

593. The process of claim 558, wherein step g) is carried out repeatedly.

594. The process of claim 558, wherein said means for synthesizing nucleic acid copies under isothermal or isostatic conditions is carried out by one or more members selected from the group consisting of RNA transcription, strand displacement amplification and secondary structure amplification.

595. The process of claim 594, wherein said second set of primers comprise at least one production center which differs in nucleotide sequence from said production center in the third set of primers.

596. A process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of:

a) providing;

(i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of said nucleic acids of interest;

(ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified; and

(iii) polymerizing means for synthesizing nucleic acid copies of said nucleic acid analytes, said polymerizing means comprising a first set of primers and a second set of primers, wherein said first set of primers are fixed or immobilized to a solid support, and wherein said second set of primers comprises at least two segments, the first segment at the 3′

end comprising random sequences, and the second segment comprising at least one production center;

(iv) means for synthesizing nucleic acid copies under isothermal or isostatic conditions;

b) contacting said library of nucleic acid analytes with said first set of primers to form more than one first bound entity;

c) extending said bound first set of primers by means of template sequences provided by said nucleic acid analytes to form first copies of said analytes;

d) contacting said extended first copies with said second set of primers to form more than one second bound entity;

e) extending said bound second set of primers by means of template sequences provided by said extended first copies to form more than one complex comprising extended first copies and extended second set of primers;

f) synthesizing from a production center in said second set of primers in said complexes one or more nucleic acid copies under isothermal or isostatic conditions;

g) hybridizing said nucleic acid copies formed in step f) to said array of nucleic acids provided in step a) (i); and

h) detecting or quantifying any of said hybridized copies obtained in step g).

597. The process of claim 596, wherein said solid support comprises beads.

598. The process of claim 597, wherein said beads are magnetic.

599. The process of claim 596, wherein said nucleic acid array comprises members selected from the group consisting of DNA, RNA and analogs thereof.

600. The process of claim 599, wherein said analogs comprise PNA.

601. The process of claims 599 or 600, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

602. The process of claim 596, wherein said nucleic acid array is fixed or immobilized to a solid support.

603. The process of claim 602, wherein said solid support is porous or non-porous.

604. The process of claim 603, wherein said porous solid support is selected from the group consisting of polyacrylamide and agarose.

605. The process of claim 603, wherein said non-porous solid support comprises glass or plastic.

606. The process of claim 602, wherein said solid support is transparent, translucent, opaque or reflective.

607. The process of claim 602, wherein said nucleic acids are directly or indirectly fixed or immobilized to said solid support.

608. The process of claim 607, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

609. The process of claim 596, wherein said library of nucleic acid analytes is derived from a biological source selected from the group consisting of organs, tissues and cells.

610. The process of claim 596, wherein said library of nucleic acids analytes are derived from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.

611. The process of claim 596, wherein said first set of primers comprise one or more sequences which are complementary to inherent universal detection targets (UDTs).

612. The process of claim 596, wherein said inherent UDTs are selected from the group consisting of 3′

poly A segments, consensus sequences, and a combination of both.

613. The process of claim 612, wherein said consensus sequences is selected from the group consisting of signal sequences for poly A addition, splicing elements, multicopy repeats, and a combination of any of the foregoing.

614. The process of claim 596, wherein said production center is selected from the group consisting of primer binding sites, RNA promoters, or a combination of both.

615. The process of claim 614, wherein said RNA promoters comprise phage promoters.

616. The process of claim 615, wherein said phage promoters are selected from the group consisting of T3, T7 and SP6.

617. The process of claim 596, wherein said hybridized nucleic acid copies further comprise one or more signaling entities attached or incorporated thereto.

618. The process of claim 617, wherein said signaling entities generate a signal directly or indirectly.

619. The process of claim 618, wherein said direct signal generation is selected from the group consisting of a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound and a combination of any of the foregoing.

620. The process of claim 618, wherein said indirect signal generation is selected from the group consisting of an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme and a combination of any of the foregoing.

621. The process of claim 620, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

622. The process of claim 596, wherein said polymerizing means are selected from the group consisting of E. coli DNA Pol I, Klenow fragment of E. coli DNA Pol I, Bst DNA polymerase, Bca DNA polymerase, Taq DNA polymerase, Tth DNA Polymerase, T4 DNA polymerase, ALV reverse transcriptase, MuLV reverse transcriptase, RSV reverse transcriptase, HIV-1 reverse transcriptase, HIV-2 reverse transcriptase, Sensiscript and Omniscript.

623. The process of claim 596, further comprising the step of separating the first copies obtained from step c) from their templates and repeating step b).

624. The process of claim 596, further comprising the step of separating the extended second set of primers obtained from step f) from their templates and repeating step e).

625. The process of claim 596, wherein step g) is carried out repeatedly.

626. The process of claim 596, wherein said means for synthesizing nucleic acid copies under isothermal or isostatic conditions is carried out by one or more members selected from the group consisting of RNA transcription, strand displacement amplification and secondary structure amplification.

627. A process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of:

a) providing;

(i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of said nucleic acids of interest;

(ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified;

(iii) polymerizing means for synthesizing nucleic acid copies of said nucleic acid analytes, said polymerizing means comprising a first set of primers and a second set of primers, wherein said first set of primers are fixed or immobilized to a solid support, and wherein said first set of primers comprise at least one production center; and

(iv) means for synthesizing nucleic acid copies under isothermal or isostatic conditions;

b) contacting said library of nucleic acid analytes with said first set of primers to form more than one first bound entity;

c) extending said bound first set of primers by means of template sequences provided by said nucleic acid analytes to form first copies of said analytes;

d) extending said first copies by means of at least four (4) or more non-inherent homopolymeric nucleotides;

e) contacting said extended first copies with said second set of primers to form more than one second bound entity;

f) extending said bound second set of primers by means of template sequences provided by said extended first copies to form more than one complex comprising extended first copies and extended second set of primers;

f) synthesizing from a production center in said second set of primers in said complexes one or more nucleic acid copies under isothermal or isostatic conditions;

h) hybridizing said nucleic acid copies formed in step g) to said array of nucleic acids provided in step a) (i); and

i) detecting or quantifying any of said hybridized copies obtained in step h).

628. The process of claim 627, wherein said solid support comprises beads.

629. The process of claim 628, wherein said beads are magnetic.

630. The process of claim 627, wherein said nucleic acid array comprises members selected from the group consisting of DNA, RNA and analogs thereof.

631. The process of claim 630, wherein said analogs comprise PNA.

632. The process of claims 630 or 631, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

633. The process of claim 627, wherein said nucleic acid array is fixed or immobilized to a solid support.

634. The process of claim 633, wherein said solid support is porous or non-porous.

635. The process of claim 634, wherein said porous solid support is selected from the group consisting of polyacrylamide and agarose.

636. The process of claim 634, wherein said non-porous solid support comprises glass or plastic.

637. The process of claim 633, wherein said solid support is transparent, translucent, opaque or reflective.

638. The process of claim 633, wherein said nucleic acids are directly or indirectly fixed or immobilized to said solid support.

639. The process of claim 638, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

640. The process of claim 627, wherein said library of nucleic acid analytes is derived from a biological source selected from the group consisting of organs, tissues and cells.

641. The process of claim 627, wherein said library of nucleic acids analytes are derived from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.

642. The process of claim 627, wherein said first set of primers further comprise one or more sequences complementary to inherent universal detection targets (UDTs).

643. The process of claim 627, wherein said inherent UDT is selected from the group consisting of 3′

poly A segments, consensus sequences, and a combination of both.

644. The process of claim 643, wherein said consensus sequences is selected from the group consisting of signal sequences for poly A addition, splicing elements, multicopy repeats, and a combination of any of the foregoing.

645. The process of claim 627, wherein said production center is selected from the group consisting of primer binding sites, RNA promoters, or a combination of both.

646. The process of claim 645, wherein said RNA promoters comprise phage promoters.

647. The process of claim 646, wherein said phage promoters are selected from the group consisting of T3, T7 and SP6.

648. The process of claim 627, wherein said extending step d), the four or more non-inherent homopolymeric nucleotides are added by terminal transferase.

649. The process of claim 627, wherein said hybridized nucleic acid copies further comprise one or more signaling entities attached or incorporated thereto.

650. The process of claim 649, wherein said signaling entities generate a signal directly or indirectly.

651. The process of claim 650, wherein said direct signal generation is selected from the group consisting of a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound and a combination of any of the foregoing.

652. The process of claim 650, wherein said indirect signal generation is selected from the group consisting of an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme and a combination of any of the foregoing.

653. The process of claim 652, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

654. The process of claim 627, wherein said polymerizing means are selected from the group consisting of E. coli DNA Pol I, Klenow fragment of E. coli DNA Pol I, Bst DNA polymerase, Bca DNA polymerase, Taq DNA polymerase, Tth DNA Polymerase, T4 DNA polymerase, ALV reverse transcriptase, MuLV reverse transcriptase, RSV reverse transcriptase, HIV-1 reverse transcriptase, HIV-2 reverse transcriptase, Sensiscript and Omniscript.

655. The process of claim 627, further comprising the step of separating the first copies obtained from step c) from their templates and repeating step b).

656. The process of claim 627, further comprising the step of separating the extended second set of primers obtained from step f) from their templates and repeating step e).

657. The process of claim 627, wherein step g) is carried out repeatedly.

658. The process of claim 627, wherein said means for synthesizing nucleic acid copies under isothermal or isostatic conditions is carried out by one or more members selected from the group consisting of RNA transcription, strand displacement amplification and secondary structure amplification.

659. A process for detecting or quantifying more than one nucleic acid of interest in a library comprising the steps of:

a) providing;

(i) an array of fixed or immobilized nucleic acids identical or complementary in part or whole to sequences of said nucleic acids of interest;

(ii) a library of nucleic acid analytes which may contain the nucleic acids of interest sought to be detected or quantified;

(iii) polymerizing means for synthesizing nucleic acid copies of said nucleic acid analytes, said polymerizing means comprising a first set of primers and a second set of primers, wherein said first set of primers are fixed or immobilized to a solid support, and wherein said first set comprises at least one production center;

(iv) a set of oligonucleotides or polynucleotides complementary to at least one segment or sequence of said second set of primers;

and (v) means for ligating said set of oligonucleotides or polynucleotides (iv);

b) contacting said library of nucleic acid analytes with said first set of primers to form more than one first bound entity;

c) extending said bound first set of primers by means of template sequences provided by said nucleic acid analytes to form first copies of said analytes;

d) ligating said set of oligonucleotides or polynucleotides a) (iv) to the 3′

end of said first copies formed in step c) to form more than one ligated product;

e) contacting said ligated product with said second set of primers to form more than one second bound entity;

f) extending said bound second set of primers by means of template sequences provided by said ligated products formed in step d) to form more than one complex comprising said ligated products and said extended second set of primers;

g) synthesizing from a production center in said second set of primers in said complexes one or more nucleic acid copies under isothermal or isostatic conditions;

h) hybridizing said nucleic acid copies formed in step g) to said array of nucleic acids provided in step a) (i); and

i) detecting or quantifying any of said hybridized copies obtained in step h).

660. The process of claim 659, wherein said solid support comprises beads.

661. The process of claim 660, wherein said beads are magnetic.

662. The process of claim 659, wherein said nucleic acid array comprises members selected from the group consisting of DNA, RNA and analogs thereof.

663. The process of claim 662, wherein said analogs comprise PNA.

664. The process of claims 662 or 663, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

665. The process of claim 659, wherein said nucleic acid array is fixed or immobilized to a solid support.

666. The process of claim 665, wherein said solid support is porous or non-porous.

667. The process of claim 666, wherein said porous solid support is selected from the group consisting of polyacrylamide and agarose.

668. The process of claim 666, wherein said non-porous solid support comprises glass or plastic.

669. The process of claim 665, wherein said solid support is transparent, translucent, opaque or reflective.

670. The process of claim 665, wherein said nucleic acids are directly or indirectly fixed or immobilized to said solid support.

671. The process of claim 665, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

672. The process of claim 659, wherein said library of nucleic acid analytes is derived from a biological source selected from the group consisting of organs, tissues and cells.

673. The process of claim 659, wherein said library of nucleic acids analytes are derived from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.

674. The process of claim 659, wherein said first set of primers comprise one or more sequences which are complementary to inherent universal detection targets (UDTs).

675. The process of claim 659, wherein said inherent UDTs are selected from the group consisting of 3′

poly A segments, consensus sequences, and a combination of both.

676. The process of claim 675, wherein said consensus sequences is selected from the group consisting of signal sequences for poly A addition, splicing elements, multicopy repeats, and a combination of any of the foregoing.

677. The process of claim 659, wherein said production center is selected from the group consisting of primer binding sites, RNA promoters, or a combination of both.

678. The process of claim 677, wherein said RNA promoters comprise phage promoters.

679. The process of claim 678, wherein said phage promoters are selected from the group consisting of T3, T7 and SP6.

680. The process of claim 659, wherein said hybridized nucleic acid copies further comprise one or more signaling entities attached or incorporated thereto.

681. The process of claim 680, wherein said signaling entities generate a signal directly or indirectly.

682. The process of claim 681, wherein said direct signal generation is selected from the group consisting of a fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound and a combination of any of the foregoing.

683. The process of claim 682, wherein said indirect signal generation is selected from the group consisting of an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme and a combination of any of the foregoing.

684. The process of claim 683, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

685. The process of claim 659, wherein said polymerizing means are selected from the group consisting of E. coli DNA Pol I, Klenow fragment of E. coli DNA Pol I, Bst DNA polymerase, Bca DNA polymerase, Taq DNA polymerase, Tth DNA Polymerase, T4 DNA polymerase, ALV reverse transcriptase, MuLV reverse transcriptase, RSV reverse transcriptase, HIV-1 reverse transcriptase, HIV-2 reverse transcriptase, Sensiscript and Omniscript.

686. The process of claim 659, wherein said ligating means comprise T4 DNA ligase.

687. The process of claim 659, further comprising the step of separating the first copies obtained from step c) from their templates and repeating step b).

688. The process of claim 659, further comprising the step of separating the extended second set of primers obtained from step f) from their templates and repeating step e).

689. The process of claim 659, wherein step g) is carried out repeatedly.

690. The process of claim 659, wherein said means for synthesizing nucleic acid copies under isothermal or isostatic conditions is carried out by one or more members selected from the group consisting of RNA transcription, strand displacement amplification and secondary structure amplification.

691-952. -952. (canceled)