Compositions and processes for analyte detection, quantification and amplification

• US 9,309,563 B2
• Filed: 07/27/2004
• Issued: 04/12/2016
• 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:
  US10/900,453
• Publication Number:
  US 20060099601A1
• Time in Patent Office: 4,277 Days
• Field of Search: 435/6, 435/91.2, 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 multiple different nucleic acid species of interest in a library, the process comprising the steps of:

a) providing;

(i) an array of fixed or immobilized nucleic acids complementary to said nucleic acid species of interest;

(ii) a library of nucleic acid analytes isolated or derived from a biological source, which library of nucleic acid analytes may contain the nucleic acid species of interest sought to be detected or quantified, wherein each of said nucleic acid species of interest comprises at least one inherent universal detection target (UDT); and

(iii) labeled universal detection elements (UDE) which generate a signal directly or indirectly;

b) hybridizing said library (ii) with said array of nucleic acids (i) to form hybrids if said nucleic acid species of interest are present, thereby binding said nucleic acid species of interest comprising said inherent UDTs to said array;

c) contacting said inherent UDTs on said nucleic acid species of interest bound to said array with said labeled UDEs to form a complex between said labeled UDEs and said inherent UDTs, wherein said complex is bound to said array, and wherein the sequence of said labeled UDE consists of a sequence that binds to a 3′

polyA segment, or a consensus sequence when said inherent UDT is a nucleic acid; and

d) detecting or quantifying said multiple different nucleic acid species of interest by detecting or measuring the amount of signal generated from labeled UDEs complexed to inherent UDTs on each nucleic acid species of interest bound to said array.

2. The process of claim 1, wherein said nucleic acid array comprises DNA, RNA, DNA analogs, RNA analogs, or a combination of the foregoing.

3. The process of claim 2, wherein said nucleic acid array comprises PNA.

4. The process of claim 1, wherein said solid support is porous.

5. The process of claim 4, wherein said porous solid support comprises polyacrylamide or agarose.

6. The process of claim 1, wherein said solid support is non-porous.

7. The process of claim 6, wherein said non-porous solid support comprises glass or plastic.

8. The process of claim 1, wherein said solid support is transparent, translucent, opaque or reflective.

9. The process of claim 1, wherein said nucleic acids are directly fixed or immobilized to said solid support.

10. The process of claim 1, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

11. The process of claim 1, wherein said biological source comprises organs, tissues or cells.

12. The process of claim 1, wherein said analytes comprise genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA, or a combination of any of the foregoing.

13. The process of claim 1, wherein said inherent UDT comprises a 3′

polyA segment, a 5′

cap, a secondary structure, or a consensus sequence, or a combination of any of the foregoing.

14. The process of claim 13, wherein said inherent UDT is a consensus sequence that comprises a signal sequence for polyA addition, a splicing element, a multicopy repeat, or a combination of any of the foregoing.

15. The process of claim 1, Wherein said UDE comprises a nucleic acid, a nucleic acid analog, a polypeptide, a polysaccharide, a synthetic polymer, or a combination of any of the foregoing.

16. The process of claim 1, wherein said signal generated from said labeled UDE is a direct signal from an agent comprising 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, or a combination of any of the foregoing.

17. The process of claim 1, wherein said signal generated from said labeled UDE is an indirect signal from an agent comprising an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme, or a combination of any of the foregoing.

18. The process of claim 17, wherein said indirect signal is from an agent comprising an enzyme that catalyzes a reaction comprising a fluorogenic reaction, a chromogenic reaction or a chemiluminescent reaction.

19. The process of claim 1, comprising one or more washing steps.

20. A process for detecting or quantifying multiple different nucleic acid species of interest in a library, the process comprising the steps of:

a) providing;

(i) an array of fixed or immobilized nucleic acids complementary to said nucleic acid species of interest;

(ii) a library of nucleic acid analytes isolated or derived from a biological source, which library of nucleic acid analytes may contain the nucleic acid species of interest sought to be detected or quantified, wherein each of said nucleic acid species of interest comprises at least one inherent universal detection target (UDT); and

(iii) labeled universal detection elements (UDE) which generate a signal directly or indirectly;

b) contacting said inherent UDTs on said nucleic acid species of interest with said labeled UDEs in said library of nucleic acid analytes to form one or more complexes, wherein the sequence of said labeled UDE consists of a sequence that binds to a 3′

polyA segment, or a consensus sequence when said inherent UDT is a nucleic acid;

c) hybridizing said library of nucleic acid analytes with said array of nucleic acids (i) to form hybrids if said nucleic acid species of interest are present, wherein said one or more formed complexes are bound to said array; and

d) detecting or quantifying said multiple different nucleic acid species of interest by detecting or measuring the amount of signal generated from labeled UDEs complexed to inherent UDTs on each nucleic acid species of interest bound to said array.

21. The process of claim 20, wherein said nucleic acid array comprises DNA, RNA, DNA analogs, RNA analogs, or a combination of the foregoing.

22. The process of claim 21, wherein said nucleic acid array comprises PNA.

23. The process of claim 20, wherein said solid support is porous.

24. The process of claim 23, wherein said porous solid support comprises polyacrylamide or agarose.

25. The process of claim 20, wherein said solid support is or non-porous.

26. The process of claim 25, Wherein said non-porous solid support comprises glass or plastic.

27. The process of claim 20, wherein said solid support is transparent, translucent, opaque or reflective.

28. The process of claim 20, wherein said nucleic acids are directly fixed or immobilized to said solid support.

29. The process of claim 20, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

30. The process of claim 20, wherein said biological source comprises organs, tissues or cells.

31. The process of claim 20, wherein said analytes comprise genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA, or a combination of any of the foregoing.

32. The process of claim 20, wherein said inherent UDT comprises a 3′

polyA segment, a 5′

cap, a secondary structure, a consensus sequence, or a combination of any of the foregoing.

33. The process of claim 32, wherein said inherent UDT is a consensus sequence that comprises a signal sequence for polyA addition, a splicing element, a multicopy repeat, or a combination of any of the foregoing.

34. The process of claim 20, wherein said UDE comprises a nucleic acid, a nucleic acid analog, a polypeptide, a polysaccharide, a synthetic polymer or a combination of any of the foregoing.

35. The process of claim 20, wherein said signal generated from said labeled UDE is a direct signal from an agent comprising 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, or a combination of any of the foregoing.

36. The process of claim 20, wherein said signal generated from said labeled UDE is an indirect signal from an agent comprising an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme, or a combination of any of the foregoing.

37. The process of claim 36, wherein said indirect signal is from an agent comprising an enzyme that catalyzes a reaction comprising a fluorogenic reaction, a chromogenic reaction or a chemiluminescent reaction.

38. The process of claim 20, comprising one or more washing steps.