Composition comprising library of double stranded nucleic acids

• US 20060040272A1
• Filed: 07/29/2004
• Published: 02/23/2006
• 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 9,487,821 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

1-400. -400. (canceled)

401. A composition of matter comprising a library of double-stranded nucleic acids substantially incapable of in vivo replication and free of non-inherent homopolymeric sequences, said nucleic acids comprising sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample, wherein said double-stranded nucleic acids comprise at least one inherent universal detection target (UDT) proximate to one end of said double strand and at least one non-inherent production center proximate to the other end of said double strand.

402. The composition of claim 401, wherein said sample comprises a biological source selected from the group consisting of organs, tissues and cells.

403. The composition of claim 401, wherein said library of nucleic acids are derived from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.

404. The composition of claim 401, wherein said inherent UDT is selected from the group consisting of 3′

polyA segments, consensus sequences, or both.

405. The composition of claim 404, wherein said consensus sequences is selected from the group consisting of signal sequences for poly A addition, splicing elements, multicopy repeats, and a combination of any of the foregoing.

406. The composition of claim 401, wherein said production center is selected from the group consisting of primer binding sites, RNA promoters, or a combination of both.

407. The composition of claim 406, wherein said RNA promoters comprise phage promoters.

408. The composition of claim 407, wherein said phage promoters are selected from the group consisting of T3, T7 and SP6.

409. A composition of matter comprising a library of double-stranded nucleic acids substantially incapable of in vivo replication, said nucleic acids comprising sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample, wherein said double-stranded nucleic acids comprise at least four (4) non-inherent nucleotides proximate to one end of said double strand and a non-inherent production center proximate to the other end of said double strand.

410. The composition of claim 409, wherein said sample comprises a biological source selected from the group consisting of organs, tissues and cells.

411. The composition of claim 409, wherein said library of nucleic acids are derived from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.

412. The composition of claim 409, further comprising one or more inherent UDTs selected from the group consisting of 3′

polyA segments, consensus sequences, or both.

413. The composition of claim 412, wherein said consensus sequences is selected from the group consisting of signal sequences for polyA addition, splicing elements, multicopy repeats, and a combination of any of the foregoing.

414. The composition of claim 409, wherein said at least four (4) non-inherent nucleotides are homopolymeric.

415. The composition of claim 409, wherein said non-inherent production center is selected from the group consisting of primer binding sites, RNA promoters, or a combination of both.

416. The composition of claim 415, wherein said RNA promoters comprise phage promoters.

417. The composition of claim 416, wherein said phage promoters are selected from the group consisting of T3, T7 and SP6.

418. A composition of matter comprising a library of double-stranded nucleic acids fixed to a solid support, said nucleic acids comprising sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample and said nucleic acids further comprising at least one first sequence segment of non-inherent nucleotides proximate to one end of said double strand and at least one second sequence segment proximate to the other end of said double strand, said second sequence segment comprising at least one production center.

419. The composition of claim 418, wherein said solid support comprises beads.

420. The composition of claim 419, wherein said beads are magnetic.

421. The composition of claim 418, wherein said sample comprises a biological source selected from the group consisting of organs, tissues and cells.

422. The composition of claim 418, wherein said library of nucleic acids are derived from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.

423. The composition of claim 418, further comprising one or more inherent UDTs selected from the group consisting of 3′

poly A segments, consensus sequences, or both.

424. The composition of claim 423, wherein said consensus sequences is selected from the group consisting of signal sequences for poly A addition, splicing elements, multicopy repeats, and a combination of any of the foregoing.

425. The composition of claim 418, wherein said non-inherent production center is selected from the group consisting of primer binding sites, RNA promoters, or a combination of both.

426. The composition of claim 425, wherein said RNA promoters comprise phage promoters.

427. The composition of claim 426, wherein said phage promoters are selected from the group consisting of T3, T7 and SP6.

428. A composition of matter comprising a library of double-stranded nucleic acids attached to a solid support, said nucleic acids comprising sequences complementary or identical in part or whole to inherent sequences of a library obtained from a sample, wherein said double-stranded nucleic acids comprise at least one inherent universal detection target (UDT) proximate to one end of said double strand and at least one non-inherent production center proximate to the other end of said double strand.

429. The composition of claim 428, wherein said solid support comprises beads.

430. The composition of claim 429, wherein said beads are magnetic.

431. The composition of claim 428, wherein said sample comprises a biological source selected from the group consisting of organs, tissues and cells.

432. The composition of claim 428, wherein said library of nucleic acids are derived from the group consisting of genomic DNA, episomal DNA, unspliced RNA, mRNA, rRNA, snRNA and a combination of any of the foregoing.

433. The composition of claim 428, wherein said inherent UDT is selected from the group consisting of 3′

polyA segments, consensus sequences, or both.

434. The composition of claim 433, wherein said consensus sequences is selected from the group consisting of signal sequences for polyA addition, splicing elements, multicopy repeats, and a combination of any of the foregoing.

435. The composition of claim 428, wherein said production center is selected from the group consisting of primer binding sites, RNA promoters, or a combination of both.

436. The composition of claim 435, wherein said RNA promoters comprise phage promoters.

437. The composition of claim 436, wherein said phage promoters are selected from the group consisting of T3, T7 and SP6.

438-952. -952. (canceled)