# US 9,434,984 B2 · Composition comprising an array which further comprises chimeric compositions

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- Number: US 9,434,984 B2
- Document ID: US9434984B2
- Status: Granted
- Kind: B2
- Application number: 10/902,597
- Filed: 2004-07-29
- Published: 2006-02-16
- Granted: 2016-09-06
- Earliest claimed: 2001-06-30
- Assignees: Enzo Life Sciences, Inc.
- Applicants: Elazar Rabbani; Jannis G. Stavrianopoulos; James J. Donegan; Jack Coleman
- Inventors: Elazar Rabbani; Jannis G. Stavrianopoulos; James J. Donegan; Jack Coleman
- Web page: https://patentgrep.com/patent/US9434984B2

## CPC

- C40B 40/06: Libraries containing nucleotides or polynucleotides, or derivatives thereof
- 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)}
- 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
- C12N 15/1006: {by means of a solid support carrier, e.g. particles, polymers}
- 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}
- C12Q 1/68: involving nucleic acids
- C12Q 1/6809: Methods for determination or identification of nucleic acids involving differential detection
- C12Q 1/6825: Nucleic acid detection involving sensors
- C12Q 1/6837: using probe arrays or probe chips (C12Q1/6874 takes precedence)
- C40B 40/10: Libraries containing peptides or polypeptides, or derivatives thereof
- G01N 33/68: involving proteins, peptides or amino acids {(involving lipoproteins G01N33/92)}
- B01J 2219/00599: Solution-phase processes
- B01J 2219/0061: The surface being organic
- B01J 2219/00612: the surface being inorganic
- B01J 2219/00648: by the use of solid beads
- B01J 2219/00722: Nucleotides
- B01J 2219/00725: Peptides
- C07B 2200/11: Compounds covalently bound to a solid support
- C40B 40/00: Libraries per se, e.g. arrays, mixtures
- C40B: COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES (in silico combinatorial libraries of nucleic acids, proteins or peptides G16B35/00; in silico combinatorial chemistry G16C20/60)
- B01J: CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
- C07H: SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS (derivatives of aldonic or saccharic acids C07C, C07D; aldonic acids, saccharic acids C07C59/105, C07C59/285; cyanohydrins C07C255/16; glycals C07D; compounds of unknown constitution C07G; polysaccharides, derivatives thereof C08B; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification C12N15/00; sugar industry C13)
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- C07B: GENERAL METHODS OF ORGANIC CHEMISTRY; APPARATUS THEREFOR (preparation of carboxylic acid esters by telomerisation C07C67/47; telomerisation C08F)

## 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

### Claim 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.

### Claim 2 (depends on 1)

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

### Claim 3 (depends on 1)

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

### Claim 4 (depends on 3)

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

### Claim 5 (depends on 1)

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

### Claim 6 (depends on 5)

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

### Claim 7 (depends on 1)

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

### Claim 8 (depends on 1)

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

### Claim 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.

### Claim 10 (depends on 9)

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

### Claim 11 (depends on 10)

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

### Claim 12 (depends on 9)

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

### Claim 13 (depends on 12)

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

### Claim 14 (depends on 9)

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

### Claim 15 (depends on 9)

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

### Claim 16 (depends on 8)

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.

### Claim 17 (depends on 9)

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.

### Claim 18 (depends on 1)

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.

### Claim 19 (depends on 1)

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

### Claim 20 (depends on 9)

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

### Claim 21 (depends on 1)

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.