Composition of matter comprising library of first nucleic acid analyte copies

• US 9,790,621 B2
• Filed: 07/27/2004
• Issued: 10/17/2017
• 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): Riley, Jezia
• Application Number:
  US10/900,455
• Publication Number:
  US 20050009077A1
• Time in Patent Office: 4,830 Days
• Field of Search: 435 6, 435 912, 435395, 435397, 4352883, 4352887, 435 612, 536 231, 536 234, 536 221, 506 16
• 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 composition of matter comprising:

a library of nucleic acid copies of different nucleic acid analytes,

said copies having been copied from different nucleic acid analytes comprising genomic DNA, episomal DNA, mRNA or a combination of any of the forgoing isolated or derived from a eukaryotic cell, and

said copies comprising an inherent universal detection target (UDT) derived from the different nucleic acid analytes that have been copied;

an array comprising different nucleic acids located at different locations of the array,

said nucleic acids being fixed or immobilized to a solid support, and

nucleic acid copies of the library which have complementarity to a nucleic acid of a location of the array being hybridized to the nucleic acid of the array at said location; and

a universal detection element (UDE) bound to said UDT of nucleic acid copies hybridized to nucleic acids of said array,

wherein said UDT comprises a secondary structure,

wherein the binding of the UDE to the UDT is mediated by said secondary structure of the UDT, and

wherein said UDE generates a signal directly or indirectly to detect the presence or quantity of said analyte copies.

2. The composition of claim 1, wherein said nucleic acid array comprises DNA, DNA analogs, RNA, RNA analogs, or a combination thereof.

3. The composition of claim 2, wherein said nucleic acid array comprises analogs comprising PNA.

4. The composition of claim 2, wherein said DNA, RNA or analogs are modified on the sugar moiety.

5. The composition of claim 1, wherein said solid support is porous.

6. The composition of claim 5, wherein said porous solid support comprises polyacrylamide or agarose.

7. The composition of claim 1, wherein said solid support is nonporous.

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

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

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

11. The composition of claim 1, wherein said nucleic acids are indirectly-fixed or immobilized to said solid support.

12. The composition 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 composition of claim 1, wherein said UDE comprises nucleic acids, nucleic acid analogs, polypeptides, polysaccharides, synthetic polymers, or a combination of any of the foregoing.

14. The composition of claim 13, wherein said UDE comprises nucleic acid analogs, wherein the nucleic acid analogs comprise PNA.

15. The composition of claim 1, wherein said UDE comprises direct signal generating means and generates a signal directly.

16. The composition of claim 15, wherein said direct signal generating means comprises a compound selected from the group consisting of 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 composition of claim 1, wherein said UDE generates a signal indirectly by indirect signal generating means.

18. The composition of claim 17, 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.

19. The composition of claim 18, wherein said indirect signal generation comprises an enzyme, wherein the enzyme catalyzes a reaction comprising a fluorogenic reaction, a chromogenic reaction or a chemiluminescent reaction.

20. The composition of claim 2, wherein said DNA, RNA or analogs are modified on the phosphate moiety.

21. The composition of claim 2, wherein said DNA, RNA or analogs are modified on the base moiety.

22. The composition of claim 1, wherein the nucleic acid copies are unlabeled.