Patents by Inventor Sunil S. Chandran
Sunil S. Chandran 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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Publication number: 20140038294Abstract: Systems and methods are provided for defining a nucleic acid construct for integration at locus L of an organism. Nucleic acid requests are received, each such request specifying a genetic change to L. The request are expanded into component polynucleotides which are then arranged into {AR1, . . . , ARm} different arrangements, each ARi in {AR1, . . . , ARm} defining a different arrangement of the component polynucleotides. A score Si for each ARi in {AR1, . . . , ARm} is determined based on whether source constructs encoding a portion of ARi are physically present. An ARf in {AR1, . . . , ARm} is selected based on the score for ARf. Primer pairs are calculated to amplify the portions of ARf not represented in the source constructs. The portions of ARf amplified by the primer pairs and the portions of ARf in the source constructs, ordered by ARf, define the nucleic acid construct.Type: ApplicationFiled: October 11, 2012Publication date: February 6, 2014Applicant: Amyris Biotechnologies, Inc.Inventors: Darren M. Platt, Michael W. Bissell, Sunil S. Chandran, Brian L. Hawthorne, Erik Jedediah Dean, Christopher Dolan
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Patent number: 8546136Abstract: The present invention provides compositions and methods for rapid assembly of one or more assembled polynucleotides from a plurality of component polynucleotides. The methods of the invention utilize circular nucleic acid vectors that comprise a DNA segment D flanked by an annealable linker sequence, annealable linker sequence pairs LA and LB, or annealable linker sequence/primer binding segment pairs LA and PB or PA and LB. Restriction endonuclease digestion of a plurality of vectors containing the DNA segments to be assembled generates a plurality of DNA fragments comprising the elements PA-D-LB, LA-D-LB, and LA-D-PB or D-LB, LA-D-LB, and LA-D. The sequences of annealable linker sequences LA and LB provide complementary termini to the DNA fragments, which are utilized in host cell mediated homologous recombination or together with promer binding segments PA and PB in a polymerase cycling assembly reaction for the ordered assembly of the various DNA segments into one or more assembled polynucleotides.Type: GrantFiled: March 26, 2012Date of Patent: October 1, 2013Assignee: Amyris, Inc.Inventors: Zach Serber, Raymond Lowe, Jeffrey A. Ubersax, Sunil S. Chandran
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Patent number: 8332160Abstract: Systems and methods are provided for defining a nucleic acid construct for integration at locus L of an organism. Nucleic acid requests are received, each such request specifying a genetic change to L. The request are expanded into component polynucleotides which are then arranged into {AR1, . . . , ARm} different arrangements, each ARi in {AR1, . . . , ARm} defining a different arrangement of the component polynucleotides. A score Si for each ARi in {AR1, . . . , ARm} is determined based on whether source constructs encoding a portion ofARi are physically present. An ARf in {AR1, . . . , ARm} is selected based on the score for ARf. Primer pairs are calculated to amplify the portions of ARf not represented in the source constructs. The portions of ARf amplified by the primer pairs and the portions of ARf in the source constructs, ordered by ARf, define the nucleic acid construct.Type: GrantFiled: April 9, 2012Date of Patent: December 11, 2012Assignee: Amyris Biotechnologies, Inc.Inventors: Darren M. Platt, Michael W. Bissell, Sunil S. Chandran, Brian L. Hawthorne, Erik Jedediah Dean, Christopher Dolan
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Publication number: 20120245056Abstract: The present invention provides compositions and methods for rapid assembly of one or more assembled polynucleotides from a plurality of component polynucleotides. The methods of the invention utilize circular nucleic acid vectors that comprise a DNA segment D flanked by an annealable linker sequence, annealable linker sequence pairs LA and LB, or annealable linker sequence/primer binding segment pairs LA and PB or PA and LB. Restriction endonuclease digestion of a plurality of vectors containing the DNA segments to be assembled generates a plurality of DNA fragments comprising the elements PA-D-LB, LA-D-LB, and LA-D-PB or D-LB, LA-D-LB, and LA-D. The sequences of annealable linker sequences LA and LB provide complementary termini to the DNA fragments, which are utilized in host cell mediated homologous recombination or together with promer binding segments PA and PB in a polymerase cycling assembly reaction for the ordered assembly of the various DNA segments into one or more assembled polynucleotides.Type: ApplicationFiled: March 26, 2012Publication date: September 27, 2012Applicant: Amyris, Inc.Inventors: Zach Serber, Raymond Lowe, Jeffrey A. Ubersax, Sunil S. Chandran
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Patent number: 8221982Abstract: The present invention provides compositions and methods for rapid assembly of one or more assembled polynucleotides from a plurality of component polynucleotides. The methods of the invention utilize circular nucleic acid vectors that comprise a DNA segment D flanked by an annealable linker sequence, annealable linker sequence pairs LA and LB, or annealable linker sequence/primer binding segment pairs LA and PB or PA and LB. Restriction endonuclease digestion of a plurality of vectors containing the DNA segments to be assembled generates a plurality of DNA fragments comprising the elements PA-D-LB, LA-D-LB, and LA-D-PB or D-LB, LA-D-LB, and LA-D. The sequences of annealable linker sequences LA and LB provide complementary termini to the DNA fragments, which are utilized in host cell mediated homologous recombination or together with promer binding segments PA and PB in a polymerase cycling assembly reaction for the ordered assembly of the various DNA segments into one or more assembled polynucleotides.Type: GrantFiled: November 19, 2009Date of Patent: July 17, 2012Assignee: Amyris, Inc.Inventors: Zach Serber, Raymond Lowe, Jeffrey A. Ubersax, Sunil S. Chandran
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Patent number: 8110360Abstract: The present invention provides compositions and methods for rapid assembly of one or more assembled polynucleotides from a plurality of component polynucleotides. The methods of the invention utilize circular nucleic acid vectors that comprise a DNA segment D flanked by an annealable linker sequence, annealable linker sequence pairs LA and LB, or annealable linker sequence/primer binding segment pairs LA and PB or PA and LB. Restriction endonuclease digestion of a plurality of vectors containing the DNA segments to be assembled generates a plurality of DNA fragments comprising the elements PA-D-LB, LA-D-LB, and LA-D-PB or D-LB, LA-D-LB, and LA-D. The sequences of annealable linker sequences LA and LB provide complementary termini to the DNA fragments, which are utilized in host cell mediated homologous recombination or together with primer binding segments PA and PB in a polymerase cycling assembly reaction for the ordered assembly of the various DNA segments into one or more assembled polynucleotides.Type: GrantFiled: January 8, 2010Date of Patent: February 7, 2012Assignee: Amyris, Inc.Inventors: Zach Serber, Raymond Lowe, Jeffrey A. Ubersax, Sunil S. Chandran
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Patent number: 8034928Abstract: Latent fluorescent compounds, comprising a fluorescent molecule with one or more blocking groups attached and optionally one or more urea-containing groups are provided. The urea-containing group can be used to further attach one or more molecules of interest, such as proteins, peptides or nucleic acids. The blocking group(s) is released from the latent fluorescent compound by reaction with a trigger, forming the fluorescent molecule which can be detected. Also provided herein are methods of using latent fluorescent compounds to detect triggers.Type: GrantFiled: April 21, 2009Date of Patent: October 11, 2011Assignees: Wisconsin Alumni Research Foundation, The Penn State Research FoundationInventors: Ronald T. Raines, Sunil S. Chandran, Timothy E. Glass, Luke D. Lavis
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Publication number: 20100136633Abstract: The present invention provides compositions and methods for rapid assembly of one or more assembled polynucleotides from a plurality of component polynucleotides. The methods of the invention utilize circular nucleic acid vectors that comprise a DNA segment D flanked by an annealable linker sequence, annealable linker sequence pairs LA and LB, or annealable linker sequence/primer binding segment pairs LA and PB or PA and LB. Restriction endonuclease digestion of a plurality of vectors containing the DNA segments to be assembled generates a plurality of DNA fragments comprising the elements PA-D-LB, LA-D-LB, and LA-D-PB or D-LB, LA-D-LB, and LA-D. The sequences of annealable linker sequences LA and LB provide complementary termini to the DNA fragments, which are utilized in host cell mediated homologous recombination or together with promer binding segments PA and PB in a polymerase cycling assembly reaction for the ordered assembly of the various DNA segments into one or more assembled polynucleotides.Type: ApplicationFiled: November 19, 2009Publication date: June 3, 2010Inventors: Zach Serber, Raymond Lowe, Jeffrey A. Ubersax, Sunil S. Chandran
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Publication number: 20100124768Abstract: The present invention provides compositions and methods for rapid assembly of one or more assembled polynucleotides from a plurality of component polynucleotides. The methods of the invention utilize circular nucleic acid vectors that comprise a DNA segment D flanked by an annealable linker sequence, annealable linker sequence pairs LA and LB, or annealable linker sequence/primer binding segment pairs LA and PB or PA and LB. Restriction endonuclease digestion of a plurality of vectors containing the DNA segments to be assembled generates a plurality of DNA fragments comprising the elements PA-D-LB, LA-D-LB, and LA-D-PB or D-LB, LA-D-LB, and LA-D. The sequences of annealable linker sequences LA and LB provide complementary termini to the DNA fragments, which are utilized in host cell mediated homologous recombination or together with primer binding segments PA and PB in a polymerase cycling assembly reaction for the ordered assembly of the various DNA segments into one or more assembled polynucleotides.Type: ApplicationFiled: January 8, 2010Publication date: May 20, 2010Inventors: Zach Serber, Raymond Lowe, Jeffrey A. Ubersax, Sunil S. Chandran
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Publication number: 20090299061Abstract: Latent fluorescent compounds, comprising a fluorescent molecule with one or more blocking groups attached and optionally one or more urea-containing groups are provided. The urea-containing group can be used to further attach one or more molecules of interest, such as proteins, peptides or nucleic acids. The blocking group(s) is released from the latent fluorescent compound by reaction with a trigger, forming the fluorescent molecule which can be detected. Also provided herein are methods of using latent fluorescent compounds to detect triggers.Type: ApplicationFiled: April 21, 2009Publication date: December 3, 2009Inventors: Ronald T. RAINES, Sunil S. Chandran, Timothy E. Glass, Luke D. Lavis
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Patent number: 7534902Abstract: Latent fluorescent compounds, comprising a fluorescent molecule with one or more blocking groups attached and optionally one or more urea-containing groups are provided. The urea-containing group can be used to further attach one or more molecules of interest, such as proteins, peptides or nucleic acids. The blocking group(s) is released from the latent fluorescent compound by reaction with a trigger, forming the fluorescent molecule which can be detected. Also provided herein are methods of using latent fluorescent compounds to detect triggers.Type: GrantFiled: November 15, 2004Date of Patent: May 19, 2009Assignees: Wisconsin Alumni Research Foundation, The Penn State Research FoundationInventors: Ronald T. Raines, Sunil S. Chandran, Timothy E. Glass, Luke D. Lavis