Nucleic acid detecting or quantifying processes

• US 20060014156A1
• Filed: 07/29/2004
• Published: 01/19/2006
• 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: Stavrianopoulos, Jannis G., Donegan, James J., Rabbani, Elazar, Coleman, Jack
• Granted Patent: US 9,428,797 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)

2-860. -860. (canceled)

861. A process for detecting or quantifying analytes of interest, said process comprising the steps of:

1) providing;

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

wherein at least two of said discrete areas comprise a chimeric composition comprising a nucleic acid portion; and

a non-nucleic acid portion;

wherein said nucleic acid portion of a first discrete area has the same sequence as the nucleic acid portion of a second discrete area; and

wherein said non-nucleic acid portion has a binding affinity for analytes of interest;

b) a sample containing or suspected of containing one or more of said analytes of interest; and

c) signal generating means;

2) contacting said array a) with the sample b) under conditions permissive of binding said analytes to said non-nucleic acid portion;

3) contacting said bound analytes with said signal generating means; and

4) detecting or quantifying the presence of said analytes.

862. The process of claim 861, wherein said solid surfaces are porous or non-porous.

863. The process of claim 862, wherein said porous solid surfaces are selected from the group consisting of polyacrylamide and agarose.

864. The process of claim 862, wherein said non-porous solid surfaces comprise glass or plastic.

865. The process of claim 861, wherein said solid surfaces are transparent, translucent, opaque or reflective.

866. The process of claim 861, wherein said nucleic acid portion is selected from the group consisting of DNA, RNA and analogs thereof.

867. The process of claim 866, wherein said analogs comprise PNA.

868. The process of claims 866 or 867, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

869. The process of claim 861, wherein said nucleic acid portions are directly or indirectly fixed or immobilized to said solid surfaces.

870. The process of claim 861, wherein said non-nucleic acid portions are selected from the group consisting of peptides, proteins, ligands, enzyme substrates, hormones, receptors, drugs and a combination of any of the foregoing.

871. The process of claim 861, wherein said signal generating means comprise direct signal generating means and indirect signal generating means.

872. The process of claim 871, 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.

873. The process of claim 871, 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.

874. The process of claim 873, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

875. A process for detecting or quantifying analytes of interest, said process comprising the steps of:

1) providing;

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

wherein at least two of said discrete areas comprise a chimeric composition comprising a nucleic acid portion; and

a non-nucleic acid portion;

wherein said nucleic acid portion of a first discrete area has the same sequence as the nucleic acid portion of a second discrete area; and

wherein said non-nucleic acid portion has a binding affinity for analytes of interest;

b) a sample containing or suspected of containing one or more of said analytes of interest; and

c) signal generating means;

2) labeling said analytes of interest with said signal generating means;

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

4) detecting or quantifying the presence of said analytes.

876. The process of claim 875, wherein said solid surfaces are porous or non-porous.

877. The process of claim 876, wherein said porous solid surfaces are selected from the group consisting of polyacrylamide and agarose.

878. The process of claim 876, wherein said non-porous solid surfaces comprise glass or plastic.

879. The process of claim 876, wherein said solid surfaces are transparent, translucent, opaque or reflective.

880. The process of claim 875, wherein said nucleic acid portion is selected from the group consisting of DNA, RNA and analogs thereof.

881. The process of claim 880, wherein said analogs comprise PNA.

882. The process of claims 880 or 881, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

883. The process of claim 875, wherein said nucleic acid portions are directly or indirectly fixed or immobilized to said solid surfaces.

884. The process of claim 875, wherein said non-nucleic acid portions are selected from the group consisting of peptides, proteins, ligands, enzyme substrates, hormones, receptors, drugs and a combination of any of the foregoing.

885. The process of claim 875, wherein said signal generating means comprise direct signal generating means and indirect signal generating means.

886. The process of claim 885, 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.

887. The process of claim 885, 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.

888. The process of claim 887, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

889-952. -952. (canceled)