Nucleic acid detecting or quantifying processes

• US 9,428,797 B2
• Filed: 07/29/2004
• Issued: 08/30/2016
• 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.
• Assistant Examiner(s): Tung, Joyce
• Application Number:
  US10/902,682
• Publication Number:
  US 20060014156A1
• Time in Patent Office: 4,415 Days
• Field of Search: 536/23.1, 536/23.4, 536/22.1, 435/6, 435/91.2, 435/4
• 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 non-nucleic analytes of interest, said process comprising the steps of:

1) providing;

a) a sample comprising analytes, said analytes of the sample comprising or suspected of comprising one or more of a first non-nucleic acid analyte of interest and a second non-nucleic acid analyte of interest, wherein

said non-nucleic acid analytes comprise oligopeptides, polypeptides, oligosaccharides, polysaccharides, lipids, ligands, or combinations thereof;

b) an array on a solid surface, said array comprising a plurality of discrete areas;

wherein

at least two of said discrete areas comprise a first discrete area and a second discrete area, said first discrete area and said second discrete area comprising a chimeric composition consisting of a nucleic acid portion covalently bound to a non-nucleic acid portion;

said nucleic acid portion of the chimeric composition located at said first discrete area has a different sequence from that of said nucleic acid portion of the chimeric composition located at said second discrete area;

said covalently bound non-nucleic acid portion of the chimeric composition of said first discrete area has a binding affinity for the first non-nucleic acid analyte of interest,

said covalently bound non-nucleic acid portion of the chimeric composition of said second discrete area has a binding affinity for the second non-nucleic acid analyte,

said first non-nucleic acid analyte is different from said second non-nucleic acid analyte, and

when the non-nucleic acid portion is a peptide or protein, the nucleic acid portion does not comprise a sequence which is either identical or complementary to a sequence that codes for said peptide or protein; and

c) signal generating means;

2) labeling said non-nucleic acid analytes of the sample with said signal generating means;

3) contacting said array with said labeled non-nucleic acid analytes under conditions permissive of binding said labeled non-nucleic acid analytes to said non-nucleic acid portion; and

4) detecting or quantifying the presence of said first and second non-nucleic acid analytes of interest by measuring said signal generating means respectively bound to said first and second discrete areas of said array.

2. The process of claim 1, wherein said solid surface is porous.

3. The process of claim 2, wherein said porous solid surface comprises polyacrylamide or agarose.

4. The process of claim 1, wherein said solid surface is non-porous.

5. The process of claim 4, wherein said non-porous solid surface comprises glass or plastic.

6. The process of claim 2, wherein said solid surface is transparent, translucent, opaque or reflective.

7. The process of claim 1, wherein said nucleic acid portion comprises DNA, RNA, a DNA analog, an RNA analog, or combinations thereof.

8. The process of claim 7, wherein said nucleic acid portion comprises PNA.

9. The process of claim 7 or 8, wherein said nucleic portion is modified on any of the sugar, phosphate or base moieties.

10. The process of claim 1, wherein said nucleic acid portions are directly or indirectly fixed or immobilized to said solid surface.

11. The process of claim 1, wherein said non-nucleic acid portions comprise peptides, proteins, ligands, enzyme substrates, hormones, receptors, drugs, or a combination of any of the foregoing.

12. The process of claim 1, wherein said signal generating means comprises a direct signal generating means.

13. The process of claim 12, wherein said direct signal generating means comprises 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.

14. The process of claim 1, wherein said signal generating means comprise an indirect signal generating means.

15. The process of claim 14, wherein said indirect signal generating means comprises an antibody, an antigen, a hapten, a receptor, a hormone, a ligand, an enzyme, or a combination of any of the foregoing.

16. The process of claim 15, wherein said indirect signal generating means comprises an enzyme that catalyzes a reaction comprising a fluorogenic reaction, a chromogenic reaction or a chemiluminescent reaction.

17. The process of claim 1, wherein said non-nucleic acid analytes comprise ligands comprising non-peptide antigens, hormones, enzymes, substrates, vitamins, drugs, non-peptide signal molecules, or combinations thereof.

18. The process of claim 1, wherein said non-nucleic acid analytes of the sample comprise polypeptides and one or both of the first and second non-nucleic acid analytes of interest are polypeptides.

19. The process of claim 18, wherein said solid surface is non-porous.

20. The process of claim 1, wherein said non-nucleic acid analytes of the sample comprise oligopeptides and one or both of the first and second non-nucleic acid analytes of interest are oligopeptides.

21. The process of claim 1, wherein said non-nucleic acid analytes of the sample comprise polysaccharides and one or both of the first and second non-nucleic acid analytes of interest are polysaccharides.

22. The process of claim 1, wherein said non-nucleic acid analytes of the sample comprise lipids and one or both of the first and second non-nucleic acid analytes of interest are lipids.

23. The process of claim 1, wherein said non-nucleic acid analytes of the sample comprise ligands and one or both of the first and second non-nucleic acid analytes of interest are ligands.