Title:
NUCLEIC ACID ACCESSIBLE HYBRIDIZATION SITES
Document Type and Number:
WIPO Patent Application WO2001098537
Kind Code:
A3
Abstract:
The present invention relates to methods and compositions for analyzing nucleic acids, and in particular, methods and compositions for detection and characterization of nucleic acid sequences and sequence changes. The present invention also provides methods and compositions for identifying oligonucleotides with desired hybridization properties to nucleic acid targets containing secondary structure.
Inventors:
LYAMICHEV VICTOR (US)
ALLAWI HATIM (US)
DONG FANG (US)
NERI BRUCE P (US)
VENER I TATIANA (US)
ALLAWI HATIM (US)
DONG FANG (US)
NERI BRUCE P (US)
VENER I TATIANA (US)
Application Number:
PCT/US2001/019401
Publication Date:
October 16, 2003
Filing Date:
June 15, 2001
Export Citation:
Assignee:
THIRD WAVE TECH INC (US)
LYAMICHEV VICTOR (US)
ALLAWI HATIM (US)
DONG FANG (US)
NERI BRUCE P (US)
VENER I TATIANA (US)
LYAMICHEV VICTOR (US)
ALLAWI HATIM (US)
DONG FANG (US)
NERI BRUCE P (US)
VENER I TATIANA (US)
International Classes:
C07H21/04; C12P19/34; C12Q1/68; C12Q1/6827; C12Q1/70; C12Q1/686; (IPC1-7): C12Q1/68
Domestic Patent References:
| WO1999007890A1 | 1999-02-18 | |||
| WO1999061665A2 | 1999-12-02 |
Other References:
HAN HOGYU ET AL: "Mapping RNA regions in eukaryotic ribosomes that are accessible to methidiumpropyl-EDTA cntdot Fe(II) and EDTA cntdot Fe(II).", BIOCHEMISTRY, vol. 33, no. 33, 1994, pages 9831 - 9844, XP002231229, ISSN: 0006-2960
JEPPESEN C ET AL: "NUCLEOTIDE SEQUENCE DETERMINATION AND SECONDARY STRUCTURE OF XENOPUS U3 SMALL NUCLEAR RNA", NUCLEIC ACIDS RESEARCH, vol. 16, no. 5 PART B, 1988, pages 2127 - 2148, XP001145453, ISSN: 0305-1048
AJUH PAUL M ET AL: "Chemical secondary structure probing of two highly methylated regions in Xenopus laevis 28S ribosomal RNA.", BIOCHIMICA ET BIOPHYSICA ACTA, vol. 1219, no. 1, 1994, pages 89 - 97, XP009005659, ISSN: 0006-3002
SHELNESS G S ET AL: "SECONDARY STRUCTURE ANALYSIS OF APOLIPOPROTEIN II MESSENGER RNA USING ENZYMATIC PROBES AND REVERSE TRANSCRIPTASE EVALUATION OF PRIMER EXTENSION FOR HIGH RESOLUTION STRUCTURE MAPPING OF MESSENGER RNA", JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 260, no. 14, 1985, pages 8637 - 8646, XP002231230, ISSN: 0021-9258
HO SP ET AL: "Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries", NATURE BIOTECHNOLOGY, NATURE PUBLISHING, US, vol. 16, no. 1, January 1998 (1998-01-01), pages 59 - 63, XP002139261, ISSN: 1087-0156
MATVEEVA O ET AL: "A RAPID IN VITRO METHOD FOR OBTAINING RNA ACCESSIBILITY PATTERNS FOR COMPLEMENTARY DNA PROBES: CORRELATION WITH A INTRACELLULAR PATTERN AND KNOWN RNA STRUCTURES", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 25, no. 24, 1997, pages 5010 - 5016, XP002919159, ISSN: 0305-1048
CHEN H-H ET AL: "In vivo, high-resolution analysis of yeast and mammalian RNA-protein interactions, RNA structure, RNA splicing and rybozyme cleavage by use of terminal transferase-dependent PCR", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 28, no. 7, 1 April 2000 (2000-04-01), pages 1656 - 1664, XP002155278, ISSN: 0305-1048
SCHERR M ET AL: "Rapid determination and quantitation of the accessibility to native RNAs by antisense oligodeoxynucleotides in murine cell extracts", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 26, no. 22, 1998, pages 5079 - 5085, XP002155275, ISSN: 0305-1048
ALLAWI HATIM T ET AL: "Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase.", RNA (NEW YORK), vol. 7, no. 2, February 2001 (2001-02-01), pages 314 - 327, XP002231231, ISSN: 1355-8382
JEPPESEN C ET AL: "NUCLEOTIDE SEQUENCE DETERMINATION AND SECONDARY STRUCTURE OF XENOPUS U3 SMALL NUCLEAR RNA", NUCLEIC ACIDS RESEARCH, vol. 16, no. 5 PART B, 1988, pages 2127 - 2148, XP001145453, ISSN: 0305-1048
AJUH PAUL M ET AL: "Chemical secondary structure probing of two highly methylated regions in Xenopus laevis 28S ribosomal RNA.", BIOCHIMICA ET BIOPHYSICA ACTA, vol. 1219, no. 1, 1994, pages 89 - 97, XP009005659, ISSN: 0006-3002
SHELNESS G S ET AL: "SECONDARY STRUCTURE ANALYSIS OF APOLIPOPROTEIN II MESSENGER RNA USING ENZYMATIC PROBES AND REVERSE TRANSCRIPTASE EVALUATION OF PRIMER EXTENSION FOR HIGH RESOLUTION STRUCTURE MAPPING OF MESSENGER RNA", JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 260, no. 14, 1985, pages 8637 - 8646, XP002231230, ISSN: 0021-9258
HO SP ET AL: "Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries", NATURE BIOTECHNOLOGY, NATURE PUBLISHING, US, vol. 16, no. 1, January 1998 (1998-01-01), pages 59 - 63, XP002139261, ISSN: 1087-0156
MATVEEVA O ET AL: "A RAPID IN VITRO METHOD FOR OBTAINING RNA ACCESSIBILITY PATTERNS FOR COMPLEMENTARY DNA PROBES: CORRELATION WITH A INTRACELLULAR PATTERN AND KNOWN RNA STRUCTURES", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 25, no. 24, 1997, pages 5010 - 5016, XP002919159, ISSN: 0305-1048
CHEN H-H ET AL: "In vivo, high-resolution analysis of yeast and mammalian RNA-protein interactions, RNA structure, RNA splicing and rybozyme cleavage by use of terminal transferase-dependent PCR", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 28, no. 7, 1 April 2000 (2000-04-01), pages 1656 - 1664, XP002155278, ISSN: 0305-1048
SCHERR M ET AL: "Rapid determination and quantitation of the accessibility to native RNAs by antisense oligodeoxynucleotides in murine cell extracts", NUCLEIC ACIDS RESEARCH, OXFORD UNIVERSITY PRESS, SURREY, GB, vol. 26, no. 22, 1998, pages 5079 - 5085, XP002155275, ISSN: 0305-1048
ALLAWI HATIM T ET AL: "Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase.", RNA (NEW YORK), vol. 7, no. 2, February 2001 (2001-02-01), pages 314 - 327, XP002231231, ISSN: 1355-8382
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