Patents by Inventor Jon Karpilow
Jon Karpilow has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 9353368Abstract: The present disclosure provides a non-naturally occurring miRNA having a stem-loop structure comprising a scaffold derived from a first endogenous miRNA (e.g., miR-196a-2 or miR-204), a mature strand derived from a second endogenous miRNA, and a star strand sequence that is at least partially complementary to the mature strand sequence. The present disclosure also provides a non-naturally occurring miRNA having a stem-loop structure comprising a scaffold derived from an endogenous miRNA (e.g., miR-196a-2 or miR-204), a mature strand designed t be at least partially complementary to a target RNA, and a star strand sequence that is at least partially complementary to the mature strand sequence. The methods and compositions of the disclosure may be used to mediate gene silencing via the RNAi pathway.Type: GrantFiled: May 22, 2008Date of Patent: May 31, 2016Assignee: GE Healthcare Dharmacon, Inc.Inventors: Melissa Kelley, Amanda Birmingham, Jon Karpilow, Anastasia Khvorova, Kevin Sullivan
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Patent number: 9334495Abstract: Compositions and methods for inhibiting the actions of non-coding RNAs such as miRNAs and piRNAs are provided. The compositions comprise single or double stranded oligonucleotides conjugated with Minor Groove Binders (“MGBs”). The oligonucleotides can vary in length, can contain nucleotides having one or more modifications, and have regions that are substantially complementary to one or more mature miRNAs or piRNAs.Type: GrantFiled: November 23, 2010Date of Patent: May 10, 2016Assignee: ELITECHGROUP B.V.Inventors: Anastasia Khvorova, Annaleen Vermeulen, Rob Kaiser, Jon Karpilow, Nicolaas M. J. Vermeulen, Walt Mahoney
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Patent number: 9284552Abstract: The present disclosure provides a method of modifying cells in order to enhance lentiviral titers, cell lines that are modified and modifying reagents. By mediating individual genes and combination thereof, lentiviral titers may be increased.Type: GrantFiled: April 2, 2013Date of Patent: March 15, 2016Assignee: GE Healthcare Dharmacon, Inc.Inventors: Katie Jansen Spayd, Jon Karpilow, John K. Wakefield
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Patent number: 9284554Abstract: The present disclosure provides a non-naturally occurring miRNA having a stem-loop structure comprising a scaffold derived from a first endogenous miRNA (e.g., miR-196a-2 or miR-204), a mature strand derived from a second endogenous miRNA, and a star strand sequence that is at least partially complementary to the mature strand sequence. The present disclosure also provides a non-naturally occurring miRNA having a stem-loop structure comprising a scaffold derived from an endogenous miRNA (e.g., miR-196a-2 or miR-204), a mature strand designed to be at least partially complementary to a target RNA, and a star strand sequence that is at least partially complementary to the mature strand sequence. The methods and compositions of the disclosure may be used to mediate gene silencing via the RNAi pathway.Type: GrantFiled: July 30, 2014Date of Patent: March 15, 2016Assignee: GE Healthcare Dharmacon, Inc.Inventors: Melissa Kelley, Amanda Birmingham, Jon Karpilow, Anastasia Khvorova, Kevin Sullivan
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Patent number: 8980855Abstract: Compositions and methods for inhibiting the actions of non-coding RNAs such as miRNAs and piRNAs are provided. The compositions comprise single or double stranded oligonucleotides conjugated with Minor Groove Binders (“MGBs”). The oligonucleotides can vary in length, can contain nucleotides having one or more modifications, and have regions that are substantially complementary to one or more mature miRNAs or piRNAs.Type: GrantFiled: June 7, 2012Date of Patent: March 17, 2015Assignees: Elitech Holding B.V., GE Healthcare Dharmacon, Inc.Inventors: Anastasia Khvorova, Annaleen Vermeulen, Rob Kaiser, Jon Karpilow, Nicolaas M. J. Vermeulen, Walt Mahoney
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Publication number: 20140343130Abstract: The present disclosure provides non-naturally occurring miR-196a-2 miRNAs and non-naturally occurring miR-204 miRNAs. The non-naturally occurring miRNAs of the disclosure have mature strand sequences distinct from their endogenous counterparts. The disclosure also provides methods of selecting mature strand sequences that function optimally in non-naturally occurring miR-196a-2 miRNAs. The methods and compositions of the disclosure may be used to mediate gene silencing via the RNAi pathway.Type: ApplicationFiled: August 7, 2014Publication date: November 20, 2014Inventors: Melissa Kelley, Amanda Birmingham, Jon Karpilow, Anastasia Khvorova, Kevin Sullivan
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Publication number: 20140336242Abstract: The present disclosure provides a non-naturally occurring miRNA having a stem-loop structure comprising a scaffold derived from a first endogenous miRNA (e.g., miR-196a-2 or miR-204), a mature strand derived from a second endogenous miRNA, and a star strand sequence that is at least partially complementary to the mature strand sequence. The present disclosure also provides a non-naturally occurring miRNA having a stem-loop structure comprising a scaffold derived from an endogenous miRNA (e.g., miR-196a-2 or miR-204), a mature strand designed to be at least partially complementary to a target RNA, and a star strand sequence that is at least partially complementary to the mature strand sequence. The methods and compositions of the disclosure may be used to mediate gene silencing via the RNAi pathway.Type: ApplicationFiled: July 30, 2014Publication date: November 13, 2014Inventors: Melissa Kelley, Amanda Birmingham, Jon Karpilow, Anastasia Khvorova, Kevin Sullivan
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Patent number: 8841267Abstract: The present disclosure provides non-naturally occurring miR-196a-2 miRNAs and non-naturally occurring miR-204 miRNAs. The non-naturally occurring miRNAs of the disclosure have mature strand sequences distinct from their endogenous counterparts. The disclosure also provides methods of selecting mature strand sequences that function optimally in non-naturally occurring miR-196a-2 miRNAs. The methods and compositions of the disclosure may be used to mediate gene silencing via the RNAi pathway.Type: GrantFiled: May 22, 2008Date of Patent: September 23, 2014Assignee: GE Healthcare Dharmacon, Inc.Inventors: Melissa Kelley, Amanda Birmingham, Jon Karpilow, Anastasia Khvorova, Kevin Sullivan
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Publication number: 20140066595Abstract: Cell-free extracts, methods for producing these extracts, methods for using these extracts, compositions that facilitate production of these extracts and kits that contain these extracts are provided. By increasing or decreasing certain gene products through, for example, the use of siRNA or mimics, one can develop mammalian cell-free extracts that have desired levels of efficiency.Type: ApplicationFiled: August 26, 2013Publication date: March 6, 2014Applicant: THERMO FISHER SCIENTIFIC BIOSCIENCES INC.Inventors: Emily Anderson, Peter Bell, Penny Jensen, Jon Karpilow, Anja Smith, Krishna Vattem, Brian Webb, Devin Leake, Alex Medford, Elena Maksimova, Craig Smith
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Publication number: 20130217121Abstract: The present disclosure provides a method of modifying cells in order to enhance lentiviral titers, cell lines that are modified and modifying reagents. By mediating individual genes and combination thereof, lentiviral titers may be increased.Type: ApplicationFiled: April 2, 2013Publication date: August 22, 2013Applicant: DHARMACON, INC.Inventors: Katie Jansen Spayd, Jon Karpilow, John K. Wakefield
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Publication number: 20120245219Abstract: Compositions and methods for inhibiting the actions of non-coding RNAs such as miRNAs and piRNAs are provided. The compositions comprise single or double stranded oligonucleotides conjugated with Minor Groove Binders (“MGBs”). The oligonucleotides can vary in length, can contain nucleotides having one or more modifications, and have regions that are substantially complementary to one or more mature miRNAs or piRNAs.Type: ApplicationFiled: June 7, 2012Publication date: September 27, 2012Applicants: DHARMACON, INC., ELITECH HOLDING B.V.Inventors: Anastasia Khvorova, Annaleen Vermeulen, Rob Kaiser, Jon Karpilow, Nicolaas M.J. Vermeulen, Walt Mahoney
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Publication number: 20120083035Abstract: The present disclosure provides a method of modifying cells in order to enhance lentiviral titers, cell lines that are modified and modifying reagents. By mediating individual genes and combination thereof, lentiviral titers may be increased.Type: ApplicationFiled: August 31, 2011Publication date: April 5, 2012Applicant: DHARMACON, INC.Inventors: Katie Jansen Spayd, Jon Karpilow, John K. Wakefield
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Publication number: 20110172289Abstract: Compositions and methods for inhibiting the actions of non-coding RNAs such as miRNAs and piRNAs are provided. The compositions comprise single or double stranded oligonucleotides conjugated with Minor Groove Binders (“MGBs”). The oligonucleotides can vary in length, can contain nucleotides having one or more modifications, and have regions that are substantially complementary to one or more mature miRNAs or piRNAs.Type: ApplicationFiled: November 23, 2010Publication date: July 14, 2011Inventors: Anastasia Khvorova, Annaleen Vermeulen, Rob Kaiser, Jon Karpilow, Nicolaas M.J. Vermeulen, Walt Mahoney
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Publication number: 20100292310Abstract: The present disclosure provides a non-naturally occurring miRNA having a stem-loop structure comprising a scaffold derived from a first endogenous miRNA (e.g., miR-196a-2 or miR-204), a mature strand derived from a second endogenous miRNA, and a star strand sequence that is at least partially complementary to the mature strand sequence. The present disclosure also provides a non-naturally occurring miRNA having a stem-loop structure comprising a scaffold derived from an endogenous miRNA (e.g., miR-196a-2 or miR-204), a mature strand designed t be at least partially complementary to a target RNA, and a star strand sequence that is at least partially complementary to the mature strand sequence. The methods and compositions of the disclosure may be used to mediate gene silencing via the RNAi pathway.Type: ApplicationFiled: May 22, 2008Publication date: November 18, 2010Applicant: Dharmacon, Inc.Inventors: Melissa Kelley, Amanda Birmingham, Jon Karpilow, Anastasia Khvorova, Kevin Sullivan
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Publication number: 20100256222Abstract: The present disclosure provides non-naturally occurring miR-196a-2 miRNAs and non-naturally occurring miR-204 miRNAs. The non-naturally occurring miRNAs of the disclosure have mature strand sequences distinct from their endogenous counterparts. The disclosure also provides methods of selecting mature strand sequences that function optimally in non-naturally occurring miR-196a-2 miRNAs. The methods and compositions of the disclosure may be used to mediate gene silencing via the RNAi pathway.Type: ApplicationFiled: May 22, 2008Publication date: October 7, 2010Applicant: DHARMACON, INC.Inventors: Melissa Kelley, Amanda Birmingham, Jon Karpilow, Anastasia Khvorova, Kevin Sullivan
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Publication number: 20100184209Abstract: The present invention provides compositions and methods for inhibiting gene silencing by the RNAi pathway. The RNAi inhibitors of the invention have a reverse complement (RC) region to the target molecule of interest (e.g., miRNA) in association with at least one flanking region coupled to either at the 3? or 5? end of the RC region. The flanking regions can be single-stranded or can have one or more regions of double stranded nucleic acid with or without a hairpin loop. The RNAi inhibitors described herein can inhibit endogenous targets, including but not limited to microRNAs, or piRNAs, or can be used to inhibit the effects of exogenously introduced molecules, such as synthetic siRNAs, siRNAs expressed from vector constructs (e.g., viral expression systems), or siRNAs generated by enzymatic methods. Inhibition is specific, potent, prolonged, and can be performed on a single target or multiple targets simultaneously.Type: ApplicationFiled: February 16, 2007Publication date: July 22, 2010Applicant: Dharmacon, Inc.Inventors: Annaleen Vermeulen, Barbara Robertson, Scott Baskerville, Christina Yamada, Devin Leake, Yuriy Fedorov, Jon Karpilow, Anastasia Khvorova
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Publication number: 20080009012Abstract: The present disclosure provides methods, libraries and computer program products for determining whether a phenotype induced by a candidate siRNA for a target gene in an RNAi experiment is target specific or a false positive. Through the use of a control siRNA that has one or two seed sequences of six or seven bases in combination with a neutral scaffolding sequence, a distinction can be made between false positive and true positive analyses of functionality.Type: ApplicationFiled: July 6, 2007Publication date: January 10, 2008Applicant: DHARMACON, INC.Inventors: Amanda Birmingham, Emily Anderson, Angela Reynolds, Devin Leake, Scott Baskerville, Yuriy Fedorov, Jon Karpilow, William Marshall, Anastasia Khvorova
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Publication number: 20070218495Abstract: The present invention provides methods, libraries and computer program products for selecting siRNA that reduce off-target effects and methods for gene silencing using these siRNAs. By comparing nucleotide sequences at positions 2-7 or 2-8 of the sense and/or antisense regions of candidate siRNAs to the 3? UTR region of mRNAs, one can select siRNAs that have reduced off-target effects.Type: ApplicationFiled: March 15, 2007Publication date: September 20, 2007Applicant: Dharmacon, Inc.Inventors: Amanda Birmingham, Emily Anderson, Angela Reynolds, Devin Leake, Scott Baskerville, Yuriy Fedorov, Jon Karpilow, William Marshall, Anastasia Khvorova
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Publication number: 20060223777Abstract: The present invention provides improved hairpin and fractured hairpin constructs for use in gene silencing through the RNA interference pathway. An exemplary short hairpin polynucleotide for use in gene silencing can include a polynucleotide having from about 42 nucleotides to about 106 nucleotides configured for being processed by Dicer. The polynucleotide can include a first region having from about 19 to about 35 nucleotides, a loop region coupled to the first region, the loop region having from about 4 to about 30 nucleotides, and a second region having from about 19 to about 35 nucleotides and having at least about 80% complementarity to the first region. Optionally, one of the first region or second region can have an overhang having less than about 6 nucleotides. Also, the short hairpin can be formed of a plurality of polynucleotides that cooperate to form a hairpin structure.Type: ApplicationFiled: March 28, 2006Publication date: October 5, 2006Inventors: Annaleen Vermeulen, Angela Reynolds, Jon Karpilow, Devin Leake, Xiaoqin Cheng, Stephanie Hartsel, Anastasia Khvorova
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Publication number: 20050203043Abstract: Toxic nucleic acid sequences and methods for identifying, using, and screening libraries for them, including in silico screening, are provided. Compositions of the invention comprise unimolecular and double stranded polynucleotides comprising at least one toxicity region. Toxic sequences of the invention include A/G UUU A/G/U, G/C AAA G/C, and/or GCCA, NUUU, wherein N is any nucleotide, or complements thereof. The invention also provides a method of inducing a toxic response in a cell, comprising introducing into the cell a unimolecular or double stranded polynucleotide comprising at least one toxicity region comprising a sequence selected from the group consisting of A/G UUU A/G/U, G/C AAA G/C, GAAT, and GCCA, NUUU, wherein N is any nucleotide, or a complement of any of the foregoing, wherein said unimolecular or double stranded polynucleotide is at least 5 base pairs long and is comprises a sense and antisense region that are at least substantially complementary.Type: ApplicationFiled: January 21, 2005Publication date: September 15, 2005Applicant: DHARMACON, INC.Inventors: Yuriy Fedorov, Jon Karpilow, Anastasia Khvorova