Title:
METHODS OF PREDICTING PAIRABILITY AND SECONDARY STRUCTURES OF RNA MOLECULES
Document Type and Number:
WIPO Patent Application WO/2010/109463
Kind Code:
A3
Abstract:
Provided are methods of predicting a pairability of nucleotides of a plurality of RNA polynucleotides by (a) simultaneously determining a paired state or an unpaired state of nucleotides of the plurality of RNA polynucleotides; and (b) corresponding the paired state or the unpaired state of the nucleotides to a database of nucleic acid sequences, the database comprises nucleic acid sequences representing the plurality of RNA polynucleotides, thereby determining the pairability of nucleotides of the plurality of RNA polynucleotides. Also provided are methods of determining a secondary structure of a plurality of RNA molecules; methods of determining if a molecule is capable of modulating a secondary structure of at least one RNA polynucleotide of a plurality of RNA polynucleotides; and methods of screening for a marker associated with a pathology.
Inventors:
SEGAL ERAN (IL)
KERTESZ MICHAEL (IL)
CHANG HOWARD Y (US)
RINN JOHN (US)
ADLER ADAM (US)
WAN YUE (US)
KERTESZ MICHAEL (IL)
CHANG HOWARD Y (US)
RINN JOHN (US)
ADLER ADAM (US)
WAN YUE (US)
Application Number:
PCT/IL2010/000246
Publication Date:
November 25, 2010
Filing Date:
March 24, 2010
Export Citation:
Assignee:
YEDA RES & DEV (IL)
UNIV LELAND STANFORD JUNIOR (US)
SEGAL ERAN (IL)
KERTESZ MICHAEL (IL)
CHANG HOWARD Y (US)
RINN JOHN (US)
ADLER ADAM (US)
WAN YUE (US)
UNIV LELAND STANFORD JUNIOR (US)
SEGAL ERAN (IL)
KERTESZ MICHAEL (IL)
CHANG HOWARD Y (US)
RINN JOHN (US)
ADLER ADAM (US)
WAN YUE (US)
International Classes:
C12Q1/68
Domestic Patent References:
| WO2007145940A2 | 2007-12-21 | |||
| WO1999058947A2 | 1999-11-18 |
Other References:
MITRA SOMDEB ET AL: "High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis", NUCLEIC ACIDS RESEARCH, vol. 36, no. 11, June 2008 (2008-06-01), XP002586894, ISSN: 0305-1048
FRIEDLAENDER MARC R ET AL: "Discovering microRNAs from deep sequencing data using miRDeep", NATURE BIOTECHNOLOGY, vol. 26, no. 4, April 2008 (2008-04-01), pages 407 - 415, XP002586895, ISSN: 1087-0156
TUPLIN A ET AL: "Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods", JOURNAL OF GENERAL VIROLOGY, vol. 85, no. Part 10, October 2004 (2004-10-01), pages 3037 - 3047, XP002586896, ISSN: 0022-1317
HOFACKER I L ET AL: "Prediction of locally stable RNA secondary structures for genome-wide surveys.", BIOINFORMATICS (OXFORD), vol. 20, no. 2, 22 January 2004 (2004-01-22), pages 186 - 190, XP002586897, ISSN: 1367-4803
FRIEDLAENDER MARC R ET AL: "Discovering microRNAs from deep sequencing data using miRDeep", NATURE BIOTECHNOLOGY, vol. 26, no. 4, April 2008 (2008-04-01), pages 407 - 415, XP002586895, ISSN: 1087-0156
TUPLIN A ET AL: "Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods", JOURNAL OF GENERAL VIROLOGY, vol. 85, no. Part 10, October 2004 (2004-10-01), pages 3037 - 3047, XP002586896, ISSN: 0022-1317
HOFACKER I L ET AL: "Prediction of locally stable RNA secondary structures for genome-wide surveys.", BIOINFORMATICS (OXFORD), vol. 20, no. 2, 22 January 2004 (2004-01-22), pages 186 - 190, XP002586897, ISSN: 1367-4803
Attorney, Agent or Firm:
G.E. EHRLICH (1995) LTD. et al. (Ramat Gan, IL)
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