Patents by Inventor Tyson Shepherd
Tyson Shepherd 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: 11961008Abstract: Methods for controlled segregation of blocks of information encoded in the sequence of a biopolymer, such as nucleic acids and polypeptides, with rapid retrieval based on multiply addressing nanostructured data have been developed. In some embodiments, sequence controlled polymer memory objects include data-encoded biopolymers of any length or form encapsulated by natural or synthetic polymers and including one or more address tags. The sequence address labels are used to associate or select memory objects for sequencing read-out, enabling organization and access of distinct memory objects or subsets of memory objects using Boolean logic. In some embodiments, a memory object is a single-stranded nucleic acid scaffold strand encoding bit stream information that is folded into a nucleic acid nanostructure of arbitrary geometry, including one or more sequence address labels. Methods for controlled degradation of biopolymer-encoded blocks of information in the memory objects are also developed.Type: GrantFiled: October 28, 2022Date of Patent: April 16, 2024Assignee: MASSACHUSETTS INSTITUTE OF TECHNOLOGYInventors: Mark Bathe, Sakul Ratanalert, Remi Veneziano, James Banal, Tyson Shepherd
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Publication number: 20240076654Abstract: Methods for the automated template-free synthesis of user-defined sequence controlled biopolymers using microfluidic devices are described. The methods facilitate simultaneous synthesis of up to thousands of uniquely addressed biopolymers from the controlled movement and combination of regents as fluid droplets using microfluidic and EWOD-based systems. In some forms, biopolymers including nucleic acids, peptides, carbohydrates, and lipids are synthesized from step-wise assembly of building blocks based on a user-defined sequence of droplet movements. In some forms, the methods synthesize uniquely addressed nucleic acids of up to 1,000 nucleotides in length. Methods for adding, removing and changing barcodes on biopolymers are also provided. Biopolymers synthesized according to the methods, and libraries and databases thereof are also described. Modified biopolymers, including chemically modified nucleotides and biopolymers conjugated to other molecules are described.Type: ApplicationFiled: November 9, 2023Publication date: March 7, 2024Inventors: James Banal, Joseph Don Berleant, Tyson Shepherd, Mark Bathe
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Patent number: 11851651Abstract: Methods for the automated template-free synthesis of user-defined sequence controlled biopolymers using microfluidic devices are described. The methods facilitate simultaneous synthesis of up to thousands of uniquely addressed biopolymers from the controlled movement and combination of regents as fluid droplets using microfluidic and EWOD-based systems. In some forms, biopolymers including nucleic acids, peptides, carbohydrates, and lipids are synthesized from step-wise assembly of building blocks based on a user-defined sequence of droplet movements. In some forms, the methods synthesize uniquely addressed nucleic acids of up to 1,000 nucleotides in length. Methods for adding, removing and changing barcodes on biopolymers are also provided. Biopolymers synthesized according to the methods, and libraries and databases thereof are also described. Modified biopolymers, including chemically modified nucleotides and biopolymers conjugated to other molecules are described.Type: GrantFiled: June 19, 2018Date of Patent: December 26, 2023Assignee: MASSACHUSETTS INSTITUTE OF TECHNOLOGYInventors: James Banal, Joseph Don Berleant, Tyson Shepherd, Mark Bathe
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Publication number: 20230302423Abstract: Methods for designing scaffolded RNA nanostructures of desired shape are described. In some forms, the methods design nucleic acid “staple” sequences that hybridize to a user-defined RNA scaffold and fold it into the desired shape based on A-form helical nucleic acid geometry. In some forms, the methods implement asymmetry in nucleotide positions across two helices of an edge to account for A-form nucleic acid geometry. In preferred forms, crossover asymmetry is implemented in the staples. In other forms, crossover asymmetry is implemented in the RNA scaffold. In other forms, the methods do not introduce crossover asymmetry. Scaffolded RNA nanostructures produced according to the methods including messenger RNAs, replicating RNAs, functional RNAs and other RNA species within the scaffold, staples, or both scaffold and staples are provided. Modified nanostructures including chemically modified nucleotides are also described.Type: ApplicationFiled: March 28, 2023Publication date: September 28, 2023Inventors: Mark Bathe, Tyson Shepherd, Molly Frances Parsons
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Publication number: 20230086008Abstract: The present disclosure relates to cell populations and systems for detection of compounds in an environment. Specifically the disclosure relates to methods for generating reproducible genome-wide edited populations of microbes that display novel, defined, and reproducible phenotypes when exposed to one or more chemicals. In some applications, such phenotypes are read out by barcode amplicon and compared against population fingerprints. In other applications digital information is stored in such populations of microorganisms. The digital information can be retrieved from the microorganisms with Boolean logic.Type: ApplicationFiled: March 1, 2022Publication date: March 23, 2023Inventor: Tyson Shepherd
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Publication number: 20230073209Abstract: Methods for controlled segregation of blocks of information encoded in the sequence of a biopolymer, such as nucleic acids and polypeptides, with rapid retrieval based on multiply addressing nanostructured data have been developed. In some embodiments, sequence controlled polymer memory objects include data-encoded biopolymers of any length or form encapsulated by natural or synthetic polymers and including one or more address tags. The sequence address labels are used to associate or select memory objects for sequencing read-out, enabling organization and access of distinct memory objects or subsets of memory objects using Boolean logic. In some embodiments, a memory object is a single-stranded nucleic acid scaffold strand encoding bit stream information that is folded into a nucleic acid nanostructure of arbitrary geometry, including one or more sequence address labels. Methods for controlled degradation of biopolymer-encoded blocks of information in the memory objects are also developed.Type: ApplicationFiled: October 28, 2022Publication date: March 9, 2023Inventors: Mark Bathe, Sakul Ratanalert, Remi Veneziano, James Banal, Tyson Shepherd
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Publication number: 20220380825Abstract: The present disclosure is directed to devices, instruments, and methods, including automated methods, for enhanced production and efficient screening of biosynthesized antibiotics. More particularly, the present disclosure provides for accelerated biosynthesis and screening on a single-cell scale.Type: ApplicationFiled: February 28, 2022Publication date: December 1, 2022Inventors: Tyson Shepherd, Steve Federowicz, Dan Held
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Publication number: 20220383976Abstract: Methods for the top-down design of nucleic acid nanostructures of arbitrary geometry based on target shape of spherical or non-spherical topology are described. The methods facilitate 3D molecular programming of lipids, proteins, sugars, and RNAs based on a DNA scaffold of arbitrary 2D or 3D shape. Geometric objects are rendered as node-edge networks of parallel nucleic acid duplexes, and a nucleic acid scaffold routed throughout the network using a spanning tree formula. Nucleic acid nanostructures produced according to top-down design methods are also described. In some embodiments, the nanostructures include single-stranded nucleic acid scaffold, DX crossovers, and staple strands. In other embodiments, the nanostructures include single-stranded nucleic acid scaffold, PX crossovers and no staples. Modified nanostructures include chemically modified nucleotides and conjugated to other molecules are described.Type: ApplicationFiled: August 2, 2022Publication date: December 1, 2022Inventors: Remi Veneziano, Sakul Ratanalert, Tyson Shepherd, Hyungmin Jun, Mark Bathe
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Patent number: 11514331Abstract: Methods for controlled segregation of blocks of information encoded in the sequence of a biopolymer, such as nucleic acids and polypeptides, with rapid retrieval based on multiply addressing nanostructured data have been developed. In some embodiments, sequence controlled polymer memory objects include data-encoded biopolymers of any length or form encapsulated by natural or synthetic polymers and including one or more address tags. The sequence address labels are used to associate or select memory objects for sequencing read-out, enabling organization and access of distinct memory objects or subsets of memory objects using Boolean logic. In some embodiments, a memory object is a single-stranded nucleic acid scaffold strand encoding bit stream information that is folded into a nucleic acid nanostructure of arbitrary geometry, including one or more sequence address labels. Methods for controlled degradation of biopolymer-encoded blocks of information in the memory objects are also developed.Type: GrantFiled: April 27, 2017Date of Patent: November 29, 2022Assignee: MASSACHUSETTS INSTITUTE OF TECHNOLOGYInventors: Mark Bathe, Sakul Ratanalert, Remi Veneziano, James Banal, Tyson Shepherd
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Patent number: 11410746Abstract: Methods for the top-down design of nucleic acid nanostructures of arbitrary geometry based on target shape of spherical or non-spherical topology are described. The methods facilitate 3D molecular programming of lipids, proteins, sugars, and RNAs based on a DNA scaffold of arbitrary 2D or 3D shape. Geometric objects are rendered as node-edge networks of parallel nucleic acid duplexes, and a nucleic acid scaffold routed throughout the network using a spanning tree formula. Nucleic acid nanostructures produced according to top-down design methods are also described. In some embodiments, the nanostructures include single-stranded nucleic acid scaffold, DX crossovers, and staple strands. In other embodiments, the nanostructures include single-stranded nucleic acid scaffold, PX crossovers and no staples. Modified nanostructures include chemically modified nucleotides and conjugated to other molecules are described.Type: GrantFiled: April 27, 2017Date of Patent: August 9, 2022Assignee: MASSACHUSETTS INSTITUTE OF TECHNOLOGYInventors: Remi Veneziano, Sakul Ratanalert, Tyson Shepherd, Hyungmin Jun, Mark Bathe
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Publication number: 20220033829Abstract: The present disclosure relates to compositions, methods, modules and automated integrated instrumentation for using sets of short, curated peptide barcodes to track nucleic acid-guided edits and the translated proteins that result from the edits as well as to create in vitro pathways.Type: ApplicationFiled: July 28, 2021Publication date: February 3, 2022Inventors: Tyson Shepherd, Andrew Garst, Daniel Held, Eric Abbate
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Publication number: 20210317479Abstract: Disclosed are compositions and methods involving nucleic acid assemblies that enclose and/or protect cargo. Disclosed are compositions that include a nucleic acid assembly comprising one or more nucleic acid molecules and cargo comprising two or more cargo molecules. The nucleic acid assembly can have physiochemical properties that: (i) enhance targeting of the composition to one or more types of cells, tissues, organs, or microenvironments relative to other types of cells, tissues, organs, or microenvironments in vivo; (ii) enhance stability and/or half-life of the composition in vivo; and/or (iii) reduce immunogenicity of the composition. The nucleic acid assembly and/or cargo can have features that enhance intracellular trafficking of nucleic acid assembly and/or its cargo. The cargo can be enclosed and/or protected by the nucleic acid assembly. Some or all of the cargo molecules in the composition can be present in a defined stoichiometric ratio.Type: ApplicationFiled: September 6, 2019Publication date: October 14, 2021Inventors: Feng Zhang, Tyson Shepherd, Rémi Veneziano, Mark Bathe, Ian Slaymaker, Bernd Zetsche
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Patent number: 10940171Abstract: Methods and compositions for bacterial production of pure single-stranded DNA (ssDNA) composed of custom sequence and size have been developed. The methods enable scalability and bio-orthogonality in applications of scaffolded DNA origami, offering one-step purification of large quantities of pure ssDNA amendable for immediate folding of DNA nanoparticles. The methods produce pure ssDNA directly from bacteria. In some embodiments the E. coli helper strain M13cp combined with a phagemid carrying only an f1-origin allows for, without the need for additional purification from contaminating dsDNA. This system is useful for generalized circular ssDNA synthesis, and here is applied to the assembly of DNA nanoparticles folded both in vitro and direct from phage.Type: GrantFiled: November 13, 2018Date of Patent: March 9, 2021Assignee: MASSACHUSETTS INSTITUTE OF TECHNOLOGYInventors: Tyson Shepherd, Rebecca Du, Mark Bathe
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Publication number: 20200327421Abstract: Methods for controlled segregation of blocks of information encoded in the sequence of a biopolymer, such as nucleic acids and polypeptides, with rapid retrieval based on multiply addressing nanostructured data have been developed. In some embodiments, sequence controlled polymer memory objects include data-encoded biopolymers of any length or form encapsulated by natural or synthetic polymers and including one or more address tags. The sequence address labels are used to associate or select memory objects for sequencing read-out, enabling organization and access of distinct memory objects or subsets of memory objects using Boolean logic. In some embodiments, a memory object is a single-stranded nucleic acid scaffold strand encoding bit stream information that is folded into a nucleic acid nanostructure of arbitrary geometry, including one or more sequence address labels. Methods for controlled degradation of biopolymer-encoded blocks of information in the memory objects are also developed.Type: ApplicationFiled: April 27, 2017Publication date: October 15, 2020Inventors: Mark Bathe, Sakul Ratanalert, Remi Veneziano, James Banal, Tyson Shepherd
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Publication number: 20190156911Abstract: Methods for the top-down design of nucleic acid nanostructures of arbitrary geometry based on target shape of spherical or non-spherical topology are described. The methods facilitate 3D molecular programming of lipids, proteins, sugars, and RNAs based on a DNA scaffold of arbitrary 2D or 3D shape. Geometric objects are rendered as node-edge networks of parallel nucleic acid duplexes, and a nucleic acid scaffold routed throughout the network using a spanning tree formula. Nucleic acid nanostructures produced according to top-down design methods are also described. In some embodiments, the nanostructures include single-stranded nucleic acid scaffold, DX crossovers, and staple strands. In other embodiments, the nanostructures include single-stranded nucleic acid scaffold, PX crossovers and no staples. Modified nanostructures include chemically modified nucleotides and conjugated to other molecules are described.Type: ApplicationFiled: April 27, 2017Publication date: May 23, 2019Inventors: Remi Veneziano, Sakul Ratanalert, Tyson Shepherd, Hyungmin Jun, Mark Bathe
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Publication number: 20190142882Abstract: Methods and compositions for bacterial production of pure single-stranded DNA (ssDNA) composed of custom sequence and size have been developed. The methods enable scalability and bio-orthogonality in applications of scaffolded DNA origami, offering one-step purification of large quantities of pure ssDNA amendable for immediate folding of DNA nanoparticles. The methods produce pure ssDNA directly from bacteria. In some embodiments the E. coli helper strain M13cp combined with a phagemid carrying only an f1 -origin allows for, without the need for additional purification from contaminating dsDNA. This system is useful for generalized circular ssDNA synthesis, and here is applied to the assembly of DNA nanoparticles folded both in vitro and direct from phage.Type: ApplicationFiled: November 13, 2018Publication date: May 16, 2019Inventors: Tyson Shepherd, Rebecca Du, Mark Bathe
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Publication number: 20180362969Abstract: Methods for the automated template-free synthesis of user-defined sequence controlled biopolymers using microfluidic devices are described. The methods facilitate simultaneous synthesis of up to thousands of uniquely addressed biopolymers from the controlled movement and combination of regents as fluid droplets using microfluidic and EWOD-based systems. In some forms, biopolymers including nucleic acids, peptides, carbohydrates, and lipids are synthesized from step-wise assembly of building blocks based on a user-defined sequence of droplet movements. In some forms, the methods synthesize uniquely addressed nucleic acids of up to 1,000 nucleotides in length. Methods for adding, removing and changing barcodes on biopolymers are also provided. Biopolymers synthesized according to the methods, and libraries and databases thereof are also described. Modified biopolymers, including chemically modified nucleotides and biopolymers conjugated to other molecules are described.Type: ApplicationFiled: June 19, 2018Publication date: December 20, 2018Inventors: James Banal, Joseph Don Berleant, Tyson Shepherd, Mark Bathe