Abstract: Provided herein are methods for determining potency of RNAi agents. Such methods include, but are not limited to, cell-based and cell-free assays that measure binding of an RNAi agent with Ago2 or that measure Ago2 activity in the presence of such RNAi agents. Also provided are assays that determine potency of RNAi agents by assessing their ability to compete with other RNAi agents, including control RNAi agents, for binding and/or activation of Ago2.
Type:
Grant
Filed:
December 5, 2011
Date of Patent:
December 25, 2012
Assignee:
Isis Pharmaceuticals, Inc.
Inventors:
Walter F. Lima, Timothy Vickers, Stanley T. Crooke
Abstract: Compositions comprising first and second oligomers are provided wherein at least a portion of the first oligomer is capable of hybridizing with at least a portion of the second oligomer, at least a portion of the first oligomer is complementary to and capable of hybridizing to a selected target nucleic acid, and at least one of the first or second oligomers includes a modified sugar and/or backbone modification. In some embodiments the modification is a 2? substituent group on a sugar moiety that is not H or OH. Oligomer/protein compositions are also provided comprising an oligomer complementary to and capable of hybridizing to a selected target nucleic acid and at least one protein comprising at least a portion of an RNA-induced silencing complex (RISC), wherein at least one nucleotide of the oligomer has a modified sugar and/or backbone modification.
Type:
Grant
Filed:
November 4, 2003
Date of Patent:
April 5, 2011
Assignee:
Isis Pharmaceuticals, Inc.
Inventors:
Brenda F. Baker, Anne B. Eldrup, Muthiah Manoharan, Balkrishen Bhat, Richard Griffey, Eric E. Swayze, Stanley T. Crooke, Thazha P. Prakash
Abstract: The present invention provides methods of identifying oligomeric compounds, such as siRNA and double-stranded RNA compounds, having bioactivity in vivo, and kits.
Type:
Grant
Filed:
September 7, 2005
Date of Patent:
February 8, 2011
Assignee:
Isis Pharmaceuticals, Inc.
Inventors:
C. Frank Bennett, Robert McKay, Brett P. Monia, Brenda F. Baker, Namir Sioufi
Abstract: Compositions and methods are provided for the nucleic acid mimic determination of nucleic acids. The compositions and methods may be used in the diagnosis and treatment of diseases amenable through modulation of nucleic acids which encode proteins that are implicated in disease states. In accordance with preferred embodiments, mimics are comprised of non-naturally occurring backbones to which are appended modified heterocyclic bases. Such bases preferably have sterically bulky substituents 1, 2, or 3 atoms removed from the sites of attachment to the backbone.
Type:
Grant
Filed:
March 8, 1996
Date of Patent:
November 2, 2010
Inventors:
Leif Christensen, Henrik Frydenlund Hansen, Peter E. Nielsen
Abstract: Compositions comprising first and second oligomers are provided wherein at least a portion of the first oligomer is capable of hybridizing with at least a portion of the second oligomer, at least a portion of the first oligomer is complementary to and capable of hybridizing to a selected target nucleic acid, and at least one of the first or second oligomers includes a modified sugar and/or backbone modification. In some embodiments the modification is a 2?-F substituent group on a sugar moiety. Oligomer/protein compositions are also provided comprising an oligomer complementary to and capable of hybridizing to a selected target nucleic acid and at least one protein comprising at least a portion of an RNA-induced silencing complex (RISC), wherein at least one nucleoside of the oligomer has a modified sugar and/or backbone modification.
Type:
Grant
Filed:
November 4, 2003
Date of Patent:
October 12, 2010
Assignee:
Isis Pharmaceuticals, Inc.
Inventors:
Thazha P. Prakash, Brenda F. Baker, Anne B. Eldrup, Muthiah Manoharan, Balkrishen Bhat, Richard Griffey, Eric E. Swayze, Stanley T. Crooke
Abstract: The present invention provides double stranded compositions that have a region that is complementary to a target nucleic acid. One of the targeting strand or the second strand comprises linked ribofuranosyl nucleosides and the other strand comprises linked modified nucleosides that have 3?-endo conformational geometry. The strands can be linked together or separate and may contain additional groups. The present invention also provides methods of using the compositions for modulating gene expression.
Type:
Grant
Filed:
June 3, 2004
Date of Patent:
September 7, 2010
Assignee:
Isis Pharmaceuticals, Inc.
Inventors:
Bryan A. Kraynack, Brenda F. Baker, Balkrishen Bhat, Eric E. Swayze, Richard H. Griffey
Abstract: A process of manufacturing oligonucleotides includes a 5?-deblocking step in which the 5-blocking group is removed with dichloroacetic acid that is essentially free of chloral. The process is useful for making oligonucleotides that are substantially free of chloral adducts.
Type:
Grant
Filed:
January 29, 2007
Date of Patent:
July 20, 2010
Assignee:
Isis Pharmaceuticals, Inc.
Inventors:
Achim Krotz, Daniel C. Capaldi, Hans-Joachim Josef Gaus, Brett Turney
Abstract: Methods for the formation of sulfurized oligonucleotides are provided. The methods allow for the formation of phosphorothioate linkages in the oligonucleotides or derivatives, without the need for complex solvent mixtures and repeated washing or solvent changes. Oligonucleotides having from about 8, and up to about 50, nucleotides can be sulfurized according to the methods of the invention with higher yields than have been previously reported.
Type:
Grant
Filed:
April 21, 2008
Date of Patent:
May 25, 2010
Assignee:
Isis Pharmaceuticals, Inc.
Inventors:
Douglas L. Cole, Vasulinga Ravikumar, Zacharia S. Cheruvallath
Abstract: The invention concerns compositions comprising a nucleic acid mimic. The compositions may be used in the diagnosis and treatment of diseases amenable through modulation of nucleic acids which encode proteins that are implicated in disease states. In accordance with preferred embodiments, mimics are comprised of non-naturally occurring backbones to which are appended modified heterocyclic bases. Such bases preferably have sterically bulky substituents 1, 2, or 3 atoms removed from the sites of attachment to the backbone.
Type:
Grant
Filed:
March 7, 1997
Date of Patent:
August 4, 2009
Inventors:
Leif Christensen, Henrik Frydenlund Hansen, Peter E. Nielsen
Abstract: Compounds having structure (1) wherein R1 is —H a protecting group, a linker or a binding partner; and R2 and R34 are as defined in the specification. The invention also provides intermediates and methods make the structure (1) compounds, as well as methods to use the compounds as labels in diagnostic assays and to enhance binding to complementary bases.
Abstract: The present invention provides polynucleotides encoding human RNase III and polypeptides encoded thereby. Methods of using said polynucleotides and polypeptides are also provided.
Abstract: The present invention relates to oligonucleotide synthesis. In particular, the present invention provides methods for characterizing samples useful for making oligonucleotides.
Type:
Grant
Filed:
August 22, 2005
Date of Patent:
September 23, 2008
Assignee:
Isis Pharmaceuticals, Inc.
Inventors:
Daniel C. Capaldi, Hans-Joachim Josef Gaus, Claus Andre Frank Rentel, Philip Dmitri Olsen, Christine C. Kurata, Quanlai Song
Abstract: A novel class of compounds, known as peptide nucleic acids, bind complementary ssDNA and RNA strands more strongly than a corresponding DNA. The peptide nucleic acids generally comprise ligands such as naturally occurring DNA bases attached to a peptide backbone through a suitable linker.
Type:
Grant
Filed:
May 23, 2002
Date of Patent:
May 27, 2008
Inventors:
Ole Buchardt, Michael Egholm, Peter Eigil Nielsen, Rolf Henrik Berg
Abstract: The present invention provides solid support media for use in oligomer synthesis, methods of producing the media, and methods of using the media. In some embodiments, the processes of the invention comprise (a) providing an organic phase comprising an olefin monomer, a cross-linker, a functionalizing reagent and an initiator; and (b) contacting the organic phase with an aqueous phase under conditions of time and temperature effective to form the polymeric bead.
Abstract: For use in controlling biologic functions in an organism, a stabilized oligonucleotide, preferably in a phosphotriester form, having a base sequence substantially complementary to a portion of messenger ribonucleic acid coding for a biological component, such as a protein, of the organism. The oligonucleotide has about fourteen bases or more, such as twenty-three bases, and can be a deoxyribo-nucleotide. The oligonucleotide sequence can be derived from the organism's ribonucleic or deoxyribonucleic acid that codes for a vital protein, and can be synthesized in bulk either chemically or by insertion into a plasmid.
Abstract: Linked nucleosides having at least one functionalized nucleoside that bears a substituent such as a steroid molecule, a reporter molecule, a non-aromatic lipophilic molecule, a reporter enzyme, a peptide, a protein, a water soluble vitamin, a lipid soluble vitamin, an RNA cleaving complex, a metal chelator, a porphyrin, an alkylator, a pyrene, a hybrid photonuclease/intercalator, or an aryl azide photo-crosslinking agent exhibit increased cellular uptake and other properties. The substituent can be attached at the 2?-position of the functionalized nucleoside via a linking group. If at least a portion of the remaining liked nucleosides are 2?-deoxy-2?-fluoro, 2?-O-methoxy, 2?-O-ethoxy, 2?-O-propoxy, 2?-O-aminoalkoxy or 2?-O-allyloxy nucleosides, the substituent can be attached via a linking group at any of the 3? or the 5? positions of the nucleoside or on the heterocyclic base of the nucleoside or on the inter-nucleotide linkage linking the nucleoside to an adjacent nucleoside.
Type:
Grant
Filed:
October 31, 2002
Date of Patent:
June 26, 2007
Assignee:
Isis Pharmaceuticals, Inc.
Inventors:
Muthiah Manoharan, Phillip Dan Cook, Clarence Frank Bennett
Abstract: Synthetic processes are provided wherein oligomeric compounds are prepared having phosphodiester, phosphorothioate, phosphorodithioate, or other covalent linkages. The oligomers have substantially reduced exocyclic adducts deriving from acrylonitrile or related contaminants.
Type:
Grant
Filed:
December 28, 2004
Date of Patent:
June 5, 2007
Assignee:
Isis Pharmaceuticals, Inc.
Inventors:
Vasulinga T. Ravikumar, Muthiah Manoharan, Daniel C. Capaldi, Achim Krotz, Douglas L. Cole, Andrei Guzaev