Processes for detecting or quantifying nucleic acids in a library

• US 9,611,508 B2
• Filed: 03/21/2016
• Issued: 04/04/2017
• Est. Priority Date: 06/30/2001
• Status: Expired due to Term

• Current Assignee: Enzo Life Sciences Incorporated (Enzo Biochem Incorporated)
• Original Assignee: Enzo Life Sciences Incorporated (Enzo Biochem Incorporated)
• Inventors: Rabbani, Elazar, Stavrianopoulos, Jannis G., Donegan, James J., Coleman, Jack
• Primary Examiner(s): HORLICK, KENNETH R
• Application Number:
  US15/075,495
• Publication Number:
  US 20160194693A1
• Time in Patent Office: 379 Days
• Field of Search: 435 611, 435 911
• 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. 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 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) a first set of primers; and

(iv) polymerizing means for synthesizing nucleic acid copies of said nucleic acid analytes using said first set of primers;

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

d) separating said first nucleic acid copies from the said analytes;

e) repeating steps b), c) and d) until a desirable amount of first nucleic acid copies have been synthesized;

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

g) detecting or quantifying any of said hybridized first nucleic acid copies obtained in step f).

2. The process of claim 1, wherein said nucleic acid array is selected from the group consisting of DNA, RNA and analogs thereof.

3. The process of claim 2, wherein said analogs comprise PNA.

4. The process of claim 2, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

5. The process of claim 3, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

6. The process of claim 1, wherein said array of nucleic acids are fixed or immobilized to a solid support.

7. The process of claim 6, wherein said solid support is non-porous.

8. The process of claim 6, wherein said solid support is a porous solid support selected from the group consisting of polyacrylamide and agarose.

9. The process of claim 7, wherein said non-porous solid support comprises glass or plastic.

10. The process of claim 6, wherein said solid support is transparent, translucent, opaque or reflective.

11. The process of claim 6, wherein said nucleic acids are directly or indirectly fixed or immobilized to said solid support.

12. The process of claim 11, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

13. The process of claim 1, wherein said library of nucleic acid analytes is derived from a biological source selected from the group consisting of organs, tissues and cells.

14. The process of claim 1, wherein said nucleic acid analytes are selected from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.

15. The process of claim 1, wherein said nucleic acid analytes comprise an inherent UDT selected from the group consisting of poly T segments, secondary structures, consensus sequences, and a combination of any of the foregoing.

16. The process of claim 15, wherein said consensus sequences are selected from the group consisting of signal sequences for poly A addition, splicing elements, multicopy repeats, and a combination of any of the foregoing.

17. The process of claim 1, further comprising the step of adding one or more non-inhererent UDTs to said nucleic acid analytes or said first copies by an enzymatic means selected from the group consisting of poly A polymerase, terminal transferase, T4 DNA ligase, T4 RNA ligase and a combination of any of the foregoing.

18. The process of claim 1, wherein the first set of primers comprise one or more UDTs.

19. The process of claim 1, wherein said polymerizing means comprises an enzyme 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.

20. The process of claim 19, wherein an additional amount of enzyme is added after step d) or after repeating step d).

21. The process of claim 1, wherein said hybridized nucleic acid copies further comprise one or more signaling entities attached or incorporated thereto.

22. The process of claim 1, wherein the first set of primers comprise a UDE.

23. The process of claim 22, wherein the UDE comprises a direct signaling moiety 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.

24. The process of claim 22, wherein said UDE is capable of generating a signal indirectly.

25. The process of claims 24, wherein the indirect signal generation is mediated by an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme or a combination of any of the foregoing.

26. The process of claim 25, wherein the indirect signal generation is mediated by an enzyme that catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.