Process for detecting or quantifying nucleic acids in a library

• US 9,163,280 B2
• Filed: 07/29/2004
• Issued: 10/20/2015
• 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: Rabbani, Elazar, Stavrianopoulos, Jannis G., Donegan, James J., Coleman, Jack
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Tung, Joyce
• Application Number:
  US10/902,564
• Publication Number:
  US 20090042733A1
• Time in Patent Office: 4,100 Days
• Field of Search: 435/6, 435/91.2, 435/91.52, 435/6.12, 536/23.1, 536/23.4, 536/22.1
• US Class Current: 1/1
• 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) a first array of fixed or immobilized nucleic acids 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) a second array comprising a first set of primers, wherein said first set of primers are complementary, in part or in whole, to sequences of said nucleic acids of interest, and b) a second set of primers, wherein said first set of primers are fixed or immobilized to the second array, 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 RNA promoter; and

(iv) means for synthesizing labeled RNA copies from said RNA promoter;

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

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

c′

) separating or removing said template sequences from said first copies;

d) contacting said first copies on the second array 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 first copies to form more than one complex comprising first copies and second copies formed by extension of said second set of primers;

f) synthesizing labeled RNA copies from the RNA promoter in said second copies;

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

h) detecting or quantifying any of said copies hybridized to said first array in step g).

2. The process of claim 1, wherein said second array comprises a set of beads.

3. The process of claim 2, wherein said beads are magnetic.

4. The process of claim 1, wherein said first nucleic acid array comprises members selected from the group consisting of DNA, RNA and analogs thereof.

5. The process of claim 4, wherein said analogs comprise PNA.

6. The process of claim 4 or 5, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

7. The process of claim 1, wherein said first nucleic acid array is fixed or immobilized to a solid support.

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

9. The process of claim 8, wherein said first array is a porous solid support comprising a material selected from the group consisting of polyacrylamide and agarose.

10. The process of claim 8, wherein said first array is a non-porous solid support comprising glass or plastic.

11. The process of claim 7, wherein said solid support is transparent, translucent, opaque or reflective.

12. The process of claim 7, wherein said nucleic acids are directly or indirectly fixed or immobilized to said solid support.

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

14. 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, cells and any combination thereof.

15. The process of claim 1, 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.

16. The process of claim 1, wherein said first set of primers comprise one or more sequences which are complementary to an inherent universal detection target (UDT), wherein the inherent UDT is selected from the group consisting of a signal sequence for poly A addition, a splicing element, a multicopy repeat, and a combination of any of the foregoing.

17. The process of claim 1, wherein said RNA polymerase promoter is a phage promoter.

18. The process of claim 17, wherein said phage promoter is selected from the group consisting of a T3 promoter, a T7 promoter and an SP6 promoter.

19. The process of claim 1, wherein said label generates a signal directly.

20. The process of claim 19, 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.

21. The process of claim 1, wherein said label generates a signal indirectly.

22. The process of claim 21, wherein said indirect signal is generated from an entity 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.

23. The process of claim 22, wherein said indirect signal is generated from an enzyme that catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

24. The process of claim 1, wherein said polymerizing means of step a)(iii) 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.

25. The process of claim 1, further comprising the step of repeating step b) after step c′

.

26. The process of claim 1, further comprising the step of using unlabeled nucleotides in step (f), isolating unlabeled RNA copies made in step (f), contacting said unlabeled RNA copies with said first set of primers on another second array and carrying out steps (e) through (h).

27. The process of claim 1, wherein step g) is carried out repeatedly.