Composition comprising library of double stranded nucleic acids

• US 9,487,821 B2
• Filed: 07/29/2004
• Issued: 11/08/2016
• 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: Rabbani, Elazar, Stavrianopoulos, Jannis G., Donegan, James J., Coleman, Jack
• Primary Examiner(s): Horlick, Kenneth
• Application Number:
  US10/902,586
• Publication Number:
  US 20060040272A1
• Time in Patent Office: 4,485 Days
• Field of Search: 435/6, 435/91.2, 435/91.52, 436/6, 436/6.12
• 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 library of linear double-stranded nucleic acids, wherein said linear double-stranded nucleic acids consist of

at least one inherent universal detection target (UDT) proximate to one end of said double strand,

at least one non-inherent production center comprising a bacteriophage RNA promoter proximate to the other end of said double strand, and

between the at least one inherent UDT and the at least one non-inherent production center, nucleic acid sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample,

wherein said inherent UDT allows detection of the presence of sequences of interest, said sequences of interest being located between said inherent UDT proximate to one end and said bacteriophage promoter proximate to the other end of said double strand in a linear double-stranded nucleic acid of the library,

wherein said at least one inherent UDT is selected from the group consisting of (i) a 3′

poly A segment, (ii) a consensus sequence, and (iii) a combination of a 3′

poly A segment and a consensus sequence,

wherein said consensus sequence is selected from the group consisting of a signal sequence for poly A addition, a splicing element, a multicopy repeat, and any combination thereof, and

wherein said double-stranded nucleic acids do not comprise a non-inherent homopolymeric sequence.

2. The library of claim 1, wherein said sample comprises a biological source comprising an organ, a tissue, a cell, or any combination thereof.

3. The library of claim 1, wherein said library of nucleic acids is derived from genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA, or combinations thereof.

4. The library of claim 1, wherein said bacteriophage RNA promoter comprises a T3, T7 or SP6 promoter, or a combination thereof.

5. A library of double-stranded nucleic acids, wherein said double-stranded nucleic acids consist of

at least one inherent universal detection target (UDT) proximate to one end of said double strand,

at least one non-inherent production center comprising a bacteriophage RNA promoter proximate to the other end of said double strand, and

between the at least one inherent UDT and the at least one non-inherent production center, nucleic acid sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample, and

wherein said double-stranded nucleic acids do not comprise a non-inherent homopolymeric sequence.

6. The library of claim 5, wherein said sample comprises a biological source comprising an organ, a tissue, a cell, or a combination thereof.

7. The library of claim 5, wherein said library is derived from genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA, or any combination thereof.

8. The library of claim 5, wherein the at least one inherent UDT comprises a 3′

poly A segment, a consensus sequence, or both.

9. The library of claim 5, wherein the at least one inherent UDT comprises a consensus sequence, wherein said consensus sequence comprises a signal sequence for poly A addition, a splicing element, a multicopy repeat, or any combination thereof.

10. The library of claim 5, wherein said bacteriophage RNA promoter is a T3, T7 or SP6 promoter, or any combination thereof.