Methods of obtaining active antisense compounds

Freier, Susan M.; Matveeva, Olga; Tsodikov, Alexander; Giddings, Michael C.; Wyatt, Jacqueline R.

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Title: Methods of obtaining active antisense compounds

Abstract

Methods for obtaining antisense oligonucleotides with activity against a desired target are provided. Methods of identifying oligonucleotide sequence motifs which are predictive of antisense oligonucleotide activity are provided, as are motifs identified according to this method. Methods of selecting effective antisense oligonucleotide sequences and effective antisense target sequences are provided, as are sequences selected according to these methods. In other methods of the invention, oligonucleotides are designed to hybridize to target sequences containing one or more activity-enhancing motifs. Antisense oligonucleotides designed according to these methods are also provided.

Inventors:: Freier, Susan M.; Matveeva, Olga; Tsodikov, Alexander; Giddings, Michael C.; Wyatt, Jacqueline R.

Issue Date:: Tue Jun 19 00:00:00 EDT 2012

Research Org.:: Isis Phramaceuticals, Inc., Carlsbad, CA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1531738

Patent Number(s):: 8202982

Application Number:: 12/557,358

Assignee:: Isis Pharmaceuticals, Inc. (Carlsbad, CA)

Patent Classifications (CPCs):: C - CHEMISTRY C07 - ORGANIC CHEMISTRY C07H - SUGARS

C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES

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C - CHEMISTRY C07 - ORGANIC CHEMISTRY C07H - SUGARS
C07H21/00 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids

C - CHEMISTRY C12 - BIOCHEMISTRY C12N - MICROORGANISMS OR ENZYMES
C12N15/113 - Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides

C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
C12Q1/6811 - Selection methods for production or design of target specific oligonucleotides or binding molecules

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DOE Contract Number:: FG03-99ER62732

Resource Type:: Patent

Resource Relation:: Patent File Date: 2009-09-10

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Freier, Susan M., Matveeva, Olga, Tsodikov, Alexander, Giddings, Michael C., and Wyatt, Jacqueline R. Methods of obtaining active antisense compounds.  United States: N. p., 2012. 
        Web.

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                    Freier, Susan M., Matveeva, Olga, Tsodikov, Alexander, Giddings, Michael C., & Wyatt, Jacqueline R. Methods of obtaining active antisense compounds.  United States.

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                    Freier, Susan M., Matveeva, Olga, Tsodikov, Alexander, Giddings, Michael C., and Wyatt, Jacqueline R. Tue .  
        "Methods of obtaining active antisense compounds".  United States.  https://www.osti.gov/servlets/purl/1531738.

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@article{osti_1531738,

  title        = {Methods of obtaining active antisense compounds},

  author       = {Freier, Susan M. and Matveeva, Olga and Tsodikov, Alexander and Giddings, Michael C. and Wyatt, Jacqueline R.},

  abstractNote = {Methods for obtaining antisense oligonucleotides with activity against a desired target are provided. Methods of identifying oligonucleotide sequence motifs which are predictive of antisense oligonucleotide activity are provided, as are motifs identified according to this method. Methods of selecting effective antisense oligonucleotide sequences and effective antisense target sequences are provided, as are sequences selected according to these methods. In other methods of the invention, oligonucleotides are designed to hybridize to target sequences containing one or more activity-enhancing motifs. Antisense oligonucleotides designed according to these methods are also provided.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {Tue Jun 19 00:00:00 EDT 2012},

  month        = {Tue Jun 19 00:00:00 EDT 2012}

}

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Works referenced in this record:

Kinetics of G-Quartet-Mediated Tetramer Formation
journal, January 1996

Wyatt, Jacqueline R.; Davis, Peter W.; Freier, Susan M.
Biochemistry, Vol. 35, Issue 24
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Antisense oligonucleotides to human serine/threonine protein phosphatase genes
patent, September 1999

Honkanen, Richard E.; Dean, Nicholas M.
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Optimized antisense oligonucleotides complementary to DNA methyltransferase sequences
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MacLeod, Robert A.
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Antisense oligonucleotides against human protein kinase C
patent, March 1999

Bennett, C. Frank; Dean, Nicholas M.
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Phosphorothioate oligonucleotides that bind to the V3-loop and uses thereof
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Stein, Cy; Lederman, Seth; Sullivan, Gregory
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RNase L activators and antisense oligonucleotides effective to treat RSV infections
patent, April 2001

Torrence, Paul F.; Silverman, Robert H.; Cirino, Nick M.
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Human VEGF-specific oligonucleotides
patent, August 1997

Robinson, Gregory S.
US Patent Document 5,661,135
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Predicting antisense oligonucleotide inhibitory efficacy: a computational approach using histograms and thermodynamic indices
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Stull, Robert A.; Taylor, Leslie A.; Szoka, Francis C.
Nucleic Acids Research, Vol. 20, Issue 13
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Bias in Nucleotide Composition of Antisense Oligonucleotides
journal, January 1996

Smetsers, Toon F. C. M.; Boezeman, Jan B. M.; Mensink, Ewald J. B. M.
Antisense and Nucleic Acid Drug Development, Vol. 6, Issue 1
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A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability
journal, November 1999

Patzel, V.; Steidl, U.; Kronenwett, R.
Nucleic Acids Research, Vol. 27, Issue 22
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Inhibitors of human immunodeficiency virus
patent, June 1996

Ecker, David J.; Wyatt, Jacqueline; Imbach, Jean-Louis
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Predicting oligonucleotide affinity to nucleic acid targets
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Mathews, David H.; Burkard, Mark E.; Freier, Susan M.
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Oligonucleotides Containing the G-Quartet Sequence Motif
book, January 1999

Wyatt, Jacqueline R.; Stein, C. A.
Applications of Antisense Therapies to Restenosis
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Oligonucleotides having a conserved G4 core sequence
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Hanecak, Ronnie; Anderson, Kevin P.; Bennett, C. Frank
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Antisense oligonucleotide modulation of multidrug resistance-associated protein
patent, September 1998

Baracchini, Jr., Edgardo; Bennett, C. Frank; Dean, Nicholas M.
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Tetranucleotide GGGA Motif in Primary RNA Transcripts: NOVEL TARGET SITE FOR ANTISENSE DESIGN
journal, September 1998

Tu, Guang-chou; Cao, Qing-na; Zhou, Feng
Journal of Biological Chemistry, Vol. 273, Issue 39
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Reduction of expression of the multidrug resistance protein (MRP) in human tumor cells by antisense phosphorothioate oligonucleotides
journal, February 1996

Stewart, Alistair J.; Canitrot, Yvan; Baracchini, Edgardo
Biochemical Pharmacology, Vol. 51, Issue 4
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Combinatorially selected guanosine-quartet structure is a potent inhibitor of human immunodeficiency virus envelope-mediated cell fusion.
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Methods for obtaining antisense oligonucleotides with activity against a desired target are provided. Methods of identifying oligonucleotide sequence motifs which are predictive of antisense oligonucleotide activity are provided, as are motifs identified according to this method. Methods of selecting effective antisense oligonucleotide sequences and effective antisense target sequences are provided, as are sequences selected according to these methods. In other methods of the invention, oligonucleotides are designed to hybridize to target sequences containing one or more activity-enhancing motifs. Antisense oligonucleotides designed according to these methods are also provided.
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Similar Records

Title: Methods of obtaining active antisense compounds

Abstract

Citation Formats

Kinetics of G-Quartet-Mediated Tetramer Formation journal, January 1996

Antisense oligonucleotides to human serine/threonine protein phosphatase genes patent, September 1999

Optimized antisense oligonucleotides complementary to DNA methyltransferase sequences patent, May 2000

Antisense oligonucleotides against human protein kinase C patent, March 1999

Phosphorothioate oligonucleotides that bind to the V3-loop and uses thereof patent, May 1998

RNase L activators and antisense oligonucleotides effective to treat RSV infections patent, April 2001

Human VEGF-specific oligonucleotides patent, August 1997

Predicting antisense oligonucleotide inhibitory efficacy: a computational approach using histograms and thermodynamic indices journal, January 1992

Bias in Nucleotide Composition of Antisense Oligonucleotides journal, January 1996

A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability journal, November 1999

Inhibitors of human immunodeficiency virus patent, June 1996

Predicting oligonucleotide affinity to nucleic acid targets journal, November 1999

Oligonucleotides Containing the G-Quartet Sequence Motif book, January 1999

Oligonucleotides having a conserved G4 core sequence patent, September 1999

Antisense oligonucleotide modulation of multidrug resistance-associated protein patent, September 1998

Tetranucleotide GGGA Motif in Primary RNA Transcripts: NOVEL TARGET SITE FOR ANTISENSE DESIGN journal, September 1998

Reduction of expression of the multidrug resistance protein (MRP) in human tumor cells by antisense phosphorothioate oligonucleotides journal, February 1996

Combinatorially selected guanosine-quartet structure is a potent inhibitor of human immunodeficiency virus envelope-mediated cell fusion. journal, February 1994

Kinetics of G-Quartet-Mediated Tetramer Formation
journal, January 1996

Antisense oligonucleotides to human serine/threonine protein phosphatase genes
patent, September 1999

Optimized antisense oligonucleotides complementary to DNA methyltransferase sequences
patent, May 2000

Antisense oligonucleotides against human protein kinase C
patent, March 1999

Phosphorothioate oligonucleotides that bind to the V3-loop and uses thereof
patent, May 1998

RNase L activators and antisense oligonucleotides effective to treat RSV infections
patent, April 2001

Human VEGF-specific oligonucleotides
patent, August 1997

Predicting antisense oligonucleotide inhibitory efficacy: a computational approach using histograms and thermodynamic indices
journal, January 1992

Bias in Nucleotide Composition of Antisense Oligonucleotides
journal, January 1996

A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability
journal, November 1999

Inhibitors of human immunodeficiency virus
patent, June 1996

Predicting oligonucleotide affinity to nucleic acid targets
journal, November 1999

Oligonucleotides Containing the G-Quartet Sequence Motif
book, January 1999

Oligonucleotides having a conserved G4 core sequence
patent, September 1999

Antisense oligonucleotide modulation of multidrug resistance-associated protein
patent, September 1998

Tetranucleotide GGGA Motif in Primary RNA Transcripts: NOVEL TARGET SITE FOR ANTISENSE DESIGN
journal, September 1998

Reduction of expression of the multidrug resistance protein (MRP) in human tumor cells by antisense phosphorothioate oligonucleotides
journal, February 1996

Combinatorially selected guanosine-quartet structure is a potent inhibitor of human immunodeficiency virus envelope-mediated cell fusion.
journal, February 1994