Compositions and processes for analyte detection, quantification and amplification

• US 9,873,956 B2
• Filed: 09/10/2015
• Issued: 01/23/2018
• Est. Priority Date: 06/30/2001
• Status: Expired due to Term

• Current Assignee: Enzo Biochem Incorporated
• Original Assignee: Enzo Biochem Incorporated
• Inventors: Rabbani, Elazar, Stavrianopoulos, Jannis G., Donegan, James J., Coleman, Jack
• Primary Examiner(s): Wilder, Cynthia B
• Application Number:
  US14/849,993
• Publication Number:
  US 20160032372A1
• Time in Patent Office: 866 Days
• Field of Search: 435 61
• 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 complementary to 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,

wherein each of the nucleic acid analytes in the library comprises at least one non-inherent universal detection target (UDT) attached thereto, and

wherein said at least one non-inherent UDT comprises a homopolymeric nucleic acid sequence or a heteropolymeric nucleic acid sequence; and

(iii) universal detection elements (UDEs) which generate a signal directly or indirectly, wherein said UDEs are capable of binding said at least one non-inherent UDT;

b) hybridizing said library (ii) with said array of nucleic acids (i) to form hybrids when said nucleic acids of interest are present;

c) contacting said UDEs with said UDTs of hybrids formed in step b) to form complexes bound to said array in which said UDEs are bound to said UDTs; and

d) detecting or quantifying said more than one nucleic acid of interest by detecting or measuring the amount of signal generated from UDEs of any said complexes bound to said array.

2. The process of claim 1, wherein the fixed or immobilized nucleic acids of said nucleic acid array are 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 or 3, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

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

6. The process of claim 5, wherein said porous solid support is selected from the group consisting of polyacrylamide and agarose.

7. The process of claim 5, 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 or indirectly fixed or immobilized to said solid support.

10. The process of claim 9, 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 library of analytes is derived from a biological source selected from the group consisting of organs, tissues and cells.

12. The process of claim 1, wherein said 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.

13. The process of claim 1, wherein said at least one non-inherent universal detection target (UDT) comprises a homopolymeric nucleic acid sequence.

14. The process of claim of 1, wherein said at least one non-inherent universal detection target (UDT) comprises a heteropolymeric nucleic acid sequence.

15. The process of claim 1, wherein said UDEs comprise nucleic acids, nucleic acid analogs or modified forms thereof.

16. The process of claim 15, wherein said analogs comprise PNA.

17. The process of claim 1, wherein said UDEs generate a signal directly or indirectly.

18. The process of claim 17, 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.

19. The process of claim 17, 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.

20. The process of claim 19, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

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

43. The process of claim 1, wherein the library of nucleic acid analytes contains the nucleic acids of interest sought to be detected or quantified.

22. 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 complementary to 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,

wherein each of the nucleic acid analytes in the library comprises at least one non-inherent universal detection target (UDT) attached thereto, and

wherein said at least one non-inherent UDT comprises a homopolymeric nucleic acid sequence or a heteropolymeric nucleic acid sequence; and

(iii) universal detection elements (UDEs) which generate a signal directly or indirectly, wherein said UDEs are capable of binding said at least one non-inherent UDT;

b) contacting said UDEs with said UDTs in said library of nucleic acid analytes to form one or more complexes in which a UDE is bound to a UDT;

c) hybridizing the one more complexes formed in step b) with said array to form hybrids when said nucleic acids of interest are present in said library;

d) detecting or quantifying said more than one nucleic acids of interest by detecting or measuring the amount of signal generated from UDEs of any said complexes hybridized to said array.

23. The process of claim 22, wherein the fixed or immobilized nucleic acids of said nucleic acid array are selected from the group consisting of DNA, RNA and analogs thereof.

24. The process of claim 23, wherein said analogs comprise PNA.

25. The process of claim 23 or 24, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

26. The process of claim 22, wherein said solid support is porous or non-porous.

27. The process of claim 26, wherein said porous solid support is selected from the group consisting of polyacrylamide and agarose.

28. The process of claim 22, wherein said non-porous solid support comprises glass or plastic.

29. The process of claim 22, wherein said solid support is transparent, translucent, opaque or reflective.

30. The process of claim 22, wherein said nucleic acids are directly or indirectly fixed or immobilized to said solid support.

31. The process of claim 30, wherein said nucleic acids are indirectly fixed or immobilized to said solid support by means of a chemical linker or linkage arm.

32. The process of claim 22, wherein said library of analytes is derived from a biological source selected from the group consisting of organs, tissues and cells.

33. The process of claim 22, wherein said 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.

34. The process of claim 22, wherein said at least one non-inherent universal detection target (UDT) comprises a homopolymeric nucleic said sequence.

35. The process of claim of 22, wherein said at least one non-inherent universal detection target (UDT) comprises a heteropolymeric nucleic acid sequence.

36. The process of claim 22, wherein said UDEs comprise nucleic acids, nucleic acid analogs or modified forms thereof.

37. The process of claim 36, wherein said analogs comprise PNA.

38. The process of claim 22, wherein said UDEs generate a signal directly or indirectly.

39. The process of claim 38, 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.

40. The process of claim 38, 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.

41. The process of claim 40, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

42. The process of claim 22, further comprising one or more washing steps.

44. The process of claim 22, wherein the library of nucleic acid analytes contains the nucleic acids of interest sought to be detected or quantified.