Processes for detecting or quantifying analytes of interest

• US 20050202456A1
• Filed: 07/29/2004
• Published: 09/15/2005
• 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: Stavrianopoulos, Jannis G., Donegan, James J., Rabbani, Elazar, Coleman, Jack
• Granted Patent: US 9,279,147 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)

2-888. -888. (canceled)

889. 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 nucleic acids fixed or immobilized to said discrete areas,

b) chimeric compositions comprising;

i) a nucleic acid portion; and

ii) a non-nucleic acid portion;

said nucleic acid portion comprising at least one sequence, wherein said non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when said non-nucleic acid portion is a peptide or protein, said nucleic acid portion does not comprises sequences which are either identical or complementary to sequences that code for said peptide or protein;

c) a sample containing or suspected of containing said analytes of interest; and

d) signal generating means;

2) contacting said array with said chimeric compositions to hybridize the nucleic acid portions of said chimeric compositions to complementary nucleic acids fixed or immobilized to said array;

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

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

5) detecting or quantifying the presence of said analytes.

890. The process of claim 889, wherein said solid surfaces are porous or non-porous.

891. The process of claim 890, wherein said porous solid surfaces are selected from the group consisting of polyacrylamide and agarose.

892. The process of claim 890, wherein said non-porous solid surfaces comprises glass or plastic.

893. The process of claim 889, wherein said solid surfaces are transparent, translucent, opaque or reflective.

894. The process of claim 889, wherein said fixed or immobilized nucleic acid is selected from the group consisting of DNA, RNA and analogs thereof.

895. The process of claim 894, wherein said analogs comprise PNA.

896. The process of claims 894 or 895, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

897. The process of claim 889, wherein said nucleic acid portion is selected from the group consisting of DNA, RNA and analogs thereof.

898. The process of claim 897, wherein said analogs comprise PNA.

899. The process of claims 897 or 898, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

900. The process of claim 889, 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.

901. The process of claim 889, wherein said signal generating means comprise direct signal generating means and indirect signal generating means.

902. The process of claim 901, 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.

903. The process of claim 901, 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.

904. The process of claim 903, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

905. 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 nucleic acids fixed or immobilized to said discrete areas,

b) chimeric compositions comprising;

i) a nucleic acid portion; and

ii) a non-nucleic acid portion;

said nucleic acid portion comprising at least one sequence, wherein said non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when said non-nucleic acid portion is a peptide or protein, said nucleic acid portion does not comprises sequences which are either identical or complementary to sequences that code for said peptide or protein;

c) a sample containing or suspected of containing said analytes of interest; and

d) signal generating means;

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

3) contacting said array with said chimeric compositions to hybridize the nucleic acid portions of said chimeric compositions to complementary nucleic acids fixed or immobilized to said array;

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

5) detecting or quantifying the presence of said analytes.

906. The process of claim 905, wherein said solid surfaces are porous or non-porous.

907. The process of claim 906, wherein said porous solid surfaces are selected from the group consisting of polyacrylamide and agarose.

908. The process of claim 906, wherein said non-porous solid surfaces comprises glass or plastic.

909. The process of claim 905, wherein said solid surfaces are transparent, translucent, opaque or reflective.

910. The process of claim 905, wherein said fixed or immobilized nucleic acid is selected from the group consisting of DNA, RNA and analogs thereof.

911. The process of claim 910, wherein said analogs comprise PNA.

912. The process of claims 910 or 911, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

913. The process of claim 905, wherein said nucleic acid portion is selected from the group consisting of DNA, RNA and analogs thereof.

914. The process of claim 913, wherein said analogs comprise PNA.

915. The process of claims 913 or 914, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

916. The process of claim 905, 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.

917. The process of claim 905, wherein said signal generating means comprise direct signal generating means and indirect signal generating means.

918. The process of claim 917, 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.

919. The process of claim 917, 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.

920. The process of claim 919, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

921. 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 nucleic acids fixed or immobilized to said discrete areas,

b) chimeric compositions comprising;

i) a nucleic acid portion; and

ii) a non-nucleic acid portion;

said nucleic acid portion comprising at least one sequence, wherein said non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when said non-nucleic acid portion is a peptide or protein, said nucleic acid portion does not comprises sequences which are either identical or complementary to sequences that code for said peptide or protein;

c) a sample containing or suspected of containing said analytes of interest; and

d) signal generating means;

2) contacting said array with said chimeric compositions to hybridize the nucleic acid portions of said chimeric compositions to complementary nucleic acids fixed or immobilized to said array;

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

4) contacting said array with the labeled analytes to bind said analytes to said non-nucleic acid portion; and

5) detecting or quantifying the presence of said analytes.

922. The process of claim 921, wherein said solid surfaces are porous or non-porous.

923. The process of claim 922, wherein said porous solid surfaces are selected from the group consisting of polyacrylamide and agarose.

924. The process of claim 922, wherein said non-porous solid surfaces comprises glass or plastic.

925. The process of claim 921, wherein said solid surfaces are transparent, translucent, opaque or reflective.

926. The process of claim 921, wherein said fixed or immobilized nucleic acid is selected from the group consisting of DNA, RNA and analogs thereof.

927. The process of claim 926, wherein said analogs comprise PNA.

928. The process of claims 926 or 927, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

929. The process of claim 921, wherein said nucleic acid portion is selected from the group consisting of DNA, RNA and analogs thereof.

930. The process of claim 929, wherein said analogs comprise PNA.

931. The process of claims 929 or 930, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

932. The process of claim 921, 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.

933. The process of claim 921, wherein said signal generating means comprise direct signal generating means and indirect signal generating means.

934. The process of claim 933, 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.

935. The process of claim 933, 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.

936. The process of claim 935, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.

937. 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 nucleic acids fixed or immobilized to said discrete areas,

b) chimeric compositions comprising;

i) a nucleic acid portion; and

ii) a non-nucleic acid portion;

said nucleic acid portion comprising at least one sequence, wherein said non-nucleic acid portion has a binding affinity for analytes of interest, and wherein when said non-nucleic acid portion is a peptide or protein, said nucleic acid portion does not comprises sequences which are either identical or complementary to sequences that code for said peptide or protein;

c) a sample containing or suspected of containing said analytes of interest; and

d) signal generating means;

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

3) contacting said chimeric compositions with the labeled analytes to bind said analytes to said non-nucleic acid portion;

4) contacting said array with said chimeric compositions to hybridize the nucleic acid portions of said chimeric compositions to complementary nucleic acids fixed or immobilized to said array; and

5) detecting or quantifying the presence of said analytes.

938. The process of claim 937, wherein said solid surfaces are porous or non-porous.

939. The process of claim 938, wherein said porous solid surfaces are selected from the group consisting of polyacrylamide and agarose.

940. The process of claim 938, wherein said non-porous solid surfaces comprises glass or plastic.

941. The process of claim 937, wherein said solid surfaces are transparent, translucent, opaque or reflective.

942. The process of claim 937, wherein said fixed or immobilized nucleic acid is selected from the group consisting of DNA, RNA and analogs thereof.

943. The process of claim 942, wherein said analogs comprise PNA.

944. The process of claims 942 or 943, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

945. The process of claim 937, wherein said nucleic acid portion is selected from the group consisting of DNA, RNA and analogs thereof.

946. The process of claim 945, wherein said analogs comprise PNA.

947. The process of claims 945 or 946, wherein said nucleic acids or analogs are modified on any one of the sugar, phosphate or base moieties.

948. The process of claim 937, 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.

949. The process of claim 937, wherein said signal generating means comprise direct signal generating means and indirect signal generating means.

950. The process of claim 949, 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.

951. The process of claim 949, 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.

952. The process of claim 951, wherein said enzyme catalyzes a reaction selected from the group consisting of a fluorogenic reaction, a chromogenic reaction and a chemiluminescent reaction.