Novel compositions and processes for analyte detection, quantification and amplification

• US 20050170370A1
• Filed: 07/29/2004
• Published: 08/04/2005
• 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: Stavrianopqulos, Jannis G., Donegan, James J., Rabbani, Elazar, Coleman, Jack
• Granted Patent: US 9,057,100 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• 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. (canceled)

2-784. -784. (canceled)

785. A composition of matter that comprises

an array of solid surfaces comprising discrete areas;

wherein at least two of said discrete areas each comprises;

a first set of nucleic acid primers; and

a second set of nucleic acid primers;

wherein the nucleotide sequences in said first set of nucleic acid primers are different from the nucleotide sequences in said second set of nucleic acid primers;

wherein the nucleotide sequences of a first set of nucleic acid primers of a first discrete area and the nucleotide sequences of a first set of nucleic acid primers of a second discrete area differ from each other by at least one base; and

wherein the nucleotide sequences of the second set of nucleic acid primers of a first discrete area and the nucleotide sequences of the second set of nucleic acid primers of a second discrete area are substantially the same or identical.

786. The composition of claim 785, wherein said array of solid surfaces has been designed/synthesized such that D1 is less than D2, said D1 being the physical distance on said array between a nucleic acid primer that is part of a first set of an area and the nucleic acid primer is part of a second set of the same area, and D2 being the physical distance in a nucleic acid in a sample between the sequence of a primer binding site in said nucleic acid in a sample for the nucleic acid primer of the first set and the complement of the primer binding site in the said nucleic acid in the sample for the nucleic acid primer in the second set.

787. The composition of claim 785, wherein said nucleic acid primers are selected from the group consisting of DNA, RNA and analogs thereof.

788. The composition of claim 787, wherein said analogs comprise PNA.

789. The composition of claims 787 or 788, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

790. The composition of claim 785, wherein said solid surfaces are porous or non-porous.

791. The composition of claim 789, wherein said porous solid surfaces are selected from the group consisting of polyacrylamide and agarose.

792. The composition of claim 790, wherein said non-porous solid surfaces comprise glass or plastic.

793. The composition of claim 785, wherein said solid surfaces are transparent, translucent, opaque or reflective.

794. The composition of claim 785, wherein nucleic acid primers are directly or indirectly fixed or immobilized to said solid surfaces.

795. The composition of claim 794, wherein said nucleic acid primers are indirectly fixed or immobilized to said solid surfaces by means of a chemical linker or linkage arm.

797. The composition of claim 795, wherein said array of solid surfaces has been designed/synthesized such that D1 is less than D2, said D1 being the physical distance on said array between a nucleic acid primer that is part of a first set of an area and the nucleic acid primer is part of a second set of the same area, and D2 being the physical distance in a nucleic acid in a sample between the sequence of a primer binding site in said nucleic acid in a sample for the nucleic acid primer of the first set and the complement of the primer binding site in the said nucleic acid in the sample for the nucleic acid primer in the second set.

796. A composition of matter that comprises

an array of solid surfaces comprising a plurality of discrete areas;

wherein at least two of said discrete areas each comprises;

a first set of nucleic acid primers; and

a second set of nucleic acid primers;

wherein the nucleotide sequences in said first set of nucleic acid primers are different from the nucleotide sequences in said second set of nucleic acid primers;

wherein the nucleotide sequences of a first set of nucleic acid primers of a first discrete area and the nucleotide sequences of a first set of nucleic acid primers of a second discrete area differ substantially from each other; and

wherein the nucleotide sequences of the second set of nucleic acid primers of a first discrete area and the nucleotide sequences of the second set of nucleic acid primers of a second discrete area are substantially the same or identical.

798. The composition of claim 796, wherein said nucleic acid primers are selected from the group consisting of DNA, RNA and analogs thereof.

799. The composition of claim 798, wherein said analogs comprise PNA.

800. The composition of claims 798 or 799, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

801. The composition of claim 796, wherein said solid surfaces are porous or non-porous.

802. The composition of claim 801, wherein said porous solid surfaces are selected from the group consisting of polyacrylamide and agarose.

803. The composition of claim 796, wherein said non-porous solid surfaces comprise glass or plastic.

804. The composition of claim 796, wherein said solid surfaces are transparent, translucent, opaque or reflective.

805. The composition of claim 796, wherein nucleic acid primers are directly or indirectly fixed or immobilized to said solid surfaces.

806. The composition of claim 805, wherein said nucleic acid primers are indirectly fixed or immobilized to said solid surfacees by means of a chemical linker or linkage arm.

807-952. -952. (canceled)