Composition comprising an array which further comprises chimeric compositions

• US 9,434,984 B2
• Filed: 07/29/2004
• Issued: 09/06/2016
• 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:
  US10/902,597
• Publication Number:
  US 20060035238A1
• Time in Patent Office: 4,422 Days
• Field of Search: 435/6, 435/91.2, 435/4, 435/6.12, 536/24.3, 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 composition of matter that comprises an array of solid surfaces comprising a plurality of discrete areas,

wherein the plurality of discrete areas comprises a first discrete area and a second discrete area, said first discrete area and said second discrete area each comprising:

a chimeric composition consisting of;

(i) a nucleic acid portion covalently attached to

(ii) a peptide portion, wherein

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

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

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

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

said nucleic acid portion of the chimeric composition consists essentially of DNA, a DNA analog, PNA, or combinations thereof,

wherein said covalently attached peptide portion of the chimeric composition of said first discrete area is different from said covalently attached peptide portion of the chimeric composition of said second discrete area.

2. The composition of claim 1, wherein said nucleic acid portion is modified on a sugar, phosphate or base moiety.

3. The composition of claim 1, wherein said solid surfaces are porous.

4. The composition of claim 3, wherein said porous solid surfaces comprises polyacrylamide or agarose.

5. The composition of claim 1, wherein said solid surfaces are nonporous.

6. The composition of claim 5, wherein said non-porous solid surfaces comprise glass or plastic.

7. The composition of claim 1, wherein said solid surfaces are transparent, translucent, opaque or reflective.

8. The composition of claim 1, wherein said nucleic acid portions are directly or indirectly fixed or immobilized to said solid surfaces.

16. The composition of claim 8, wherein said nucleic acid portions are directly or indirectly fixed or immobilized to said solid surfaces through hybridization to complementary nucleic acid sequences.

18. The composition of claim 1, wherein said peptide portion is not encoded by (a) sequences in said nucleic acid portion or (b) sequences complementary thereto.

19. The composition of claim 1, wherein the nucleic acid portion of each chimeric composition is directly bound to the surface of the array.

21. The composition of claim 1, wherein the nucleic acid portion of each chimeric composition is hybridized to a complementary nucleic acid that is immobilized on the solid surface.

9. A composition of matter that comprises an array of solid surfaces comprising a plurality of discrete areas,

wherein the plurality of discrete areas comprises a first discrete area and a second discrete area, said first discrete area and said second discrete area each comprising:

a chimeric composition consisting of;

(i) a nucleic acid portion covalently attached to

(ii) a peptide portion, wherein

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

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

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

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

said nucleic acid portion does not comprise sequences which are either identical or complementary to sequences that code for said peptide, and

said nucleic acid portion of the chimeric composition comprises DNA, DNA analogs, PNA, or combinations thereof,

wherein the nucleic acid portion of the chimeric composition of the first discrete area is hybridized to complementary sequences of nucleic acids fixed or immobilized to the first discrete area,

wherein the nucleic acid portion of the chimeric composition of the second discrete area is hybridized to complementary sequences of nucleic acids fixed or immobilized to the second discrete area, and

wherein said covalently attached peptide portion of the chimeric composition of said first discrete area is different from said covalently attached peptide portion of the chimeric composition of said second discrete area.

10. The composition of claim 9, wherein said solid surfaces are porous.

11. The composition of claim 10, wherein said porous solid surfaces comprise polyacrylamide or agarose.

12. The composition of claim 9, wherein said solid surfaces are non-porous.

13. The composition of claim 12, wherein said non-porous solid surfaces comprises glass or plastic.

14. The composition of claim 9, wherein said solid surfaces are transparent, translucent, opaque or reflective.

15. The composition of claim 9, wherein said nucleic acid portion is modified on a sugar, phosphate or base moiety.

17. The composition of claim 9, wherein said nucleic acid portions are directly or indirectly fixed or immobilized to said solid surfaces through hybridization to complementary nucleic acid sequences.

20. The composition of claim 9, wherein the nucleic acid portion of each chimeric composition is directly bound to the surface of the array.