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公开(公告)号：WO2019094928A1
公开(公告)日：2019-05-16
申请号：PCT/US2018/060727
申请日：2018-11-13
发明人： SHEPHERD, Tyson , DU, Rebecca , BATHE, Mark
摘要： 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.
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2.发明申请
公开(公告)号：WO2018236889A3
公开(公告)日：2018-12-27
申请号：PCT/US2018/038311
申请日：2018-06-19
摘要： 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, carbohydratess, 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.
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公开(公告)号：WO2017189914A1
公开(公告)日：2017-11-02
申请号：PCT/US2017/029948
申请日：2017-04-27
摘要： 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.
摘要翻译： 已经开发了用基于多重寻址纳米结构化数据的快速检索来控制分离在生物聚合物序列中编码的信息块如核酸和多肽的方法。 在一些实施方案中，序列控制的聚合物记忆对象包括由天然或合成聚合物包封并且包括一个或多个地址标签的任何长度或形式的数据编码的生物聚合物。 序列地址标签用于关联或选择用于排序读出的内存对象，使用布尔逻辑可以组织和访问不同的内存对象或内存对象的子集。 在一些实施方案中，记忆对象是编码比特流信息的单链核酸支架链，其被折叠成任意几何形状的核酸纳米结构，包括一个或多个序列地址标记。 还开发了记忆对象中受控降解生物聚合物编码信息块的方法。
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4.发明申请
公开(公告)号：WO2016054613A1
公开(公告)日：2016-04-07
申请号：PCT/US2015/053894
申请日：2015-10-03
发明人： BATHE, Mark , PAN, Keyao , KIM, Do-Nyun
摘要： Techniques for controlling nucleic acid structures include determining, for each junction type, values for parameters indicating ground-state geometry and both translational and rotational stiffness coefficients. Topological design data indicates a number of bases in each helix connected to corresponding junctions. Initial positions of each base are determined by connecting helices to junctions using the ground-state geometry and arbitrary coordinates not confined to lattice coordinates. Misalignment vectors each indicate a difference in coordinates and orientations between initial positions of a pair of bases that are not adjacent in the initial positions but are adjacent or coincident in the design data. Forces and moments at the junctions to reduce misalignment magnitudes are determined based on the translational and rotational stiffness coefficients at each junction. Position and orientation in 3D coordinates of each base are determined by reducing or eliminating the misalignment magnitudes and balancing forces and moments across the nanostructure.
摘要翻译： 用于控制核酸结构的技术包括为每个结型确定指示基态几何以及平移和旋转刚度系数的参数的值。 拓扑设计数据表示每个螺旋中连接到相应连接点的基数。 每个基座的初始位置通过使用基态几何和不限于格子坐标的任意坐标将螺旋连接到结点来确定。 未对准矢量各自表示在初始位置中不相邻但在设计数据中相邻或重合的一对基座的初始位置之间的坐标和取向上的差异。 基于每个连接处的平移和旋转刚度系数确定在接合点处的力和力矩以减小不对准幅度。 通过减少或消除跨越纳米结构的不对准量级和平衡力和力矩来确定每个基座的3D坐标中的位置和取向。
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公开(公告)号：WO2023077119A1
公开(公告)日：2023-05-04
申请号：PCT/US2022/078972
申请日：2022-10-31
IPC分类号： C12Q1/6818 , G01N33/542
摘要： Disclosed are nucleic acid-chromophores and nucleic acid assembly containing the nucleic acid-chromophores. The nucleic acid-chromophore contains a nucleic acid strand and two or more adjacent chromophores. The two or more adjacent chromophores can be covalently incorporated in the backbone of the nucleic acid strand. One or more photophysical properties of the adjacent chromophores can be altered by a change in the nucleic acid assembly. In some forms, the nucleic acid assembly can contain a nucleic acid scaffold. In these forms, the change in the nucleic acid assembly can be a change in the length of a nucleic acid hybrid in the nucleic acid scaffold that is opposite the adjacent chromophores. Typically, the nucleic acid hybrid does not contain any chromophore. The nucleic acid-chromophores can serve as molecular fluorophores with emission properties that are highly sensitive to local geometry and the chemical environment.
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公开(公告)号：WO2020051507A1
公开(公告)日：2020-03-12
申请号：PCT/US2019/050029
申请日：2019-09-06
发明人： ZHANG, Feng , SHEPHERD, Tyson , VENEZIANO, Remi , BATHE, Mark , SLAYMAKER, Ian , ZETSCHE, Bernd
摘要： 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.
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公开(公告)号：WO2019094928A9
公开(公告)日：2019-05-16
申请号：PCT/US2018/060727
申请日：2018-11-13
发明人： SHEPHERD, Tyson , DU, Rebecca , BATHE, Mark
摘要： 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.
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公开(公告)号：WO2022261318A1
公开(公告)日：2022-12-15
申请号：PCT/US2022/032831
申请日：2022-06-09
发明人： BANAL, James L. , BERLEANT, Joseph , LEISERSON, Charles E. , SCHARDL, Tao Benjamin , BATHE, Mark
IPC分类号： C12Q1/6806
摘要： Disclosed are compositions and methods relating to sequence-controlled storage objected. The disclosed sequence-controlled storage objects can include (a) one or more different sequence-controlled polymers, and (b) a plurality of different feature tags. The sequence-controlled storage object can include (a) one or more different sequence-controlled polymers, and (b) a plurality of different digit tags. Also disclosed are methods of storing desired sequence-controlled polymers as a sequence-controlled storage object, comprising assembling a sequence-controlled storage object from (i) one or more different sequence-controlled polymers, (ii) a plurality of different feature tags, and (iii) optionally one or more encapsulating agents. Also disclosed are methods of automating the assembly of a sequence-controlled storage object comprising using a device with flow.
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9.发明申请
公开(公告)号：WO2020154595A1
公开(公告)日：2020-07-30
申请号：PCT/US2020/014957
申请日：2020-01-24
发明人： BATHE, Mark , VENEZIANO, Remi , WAMHOFF, Eike-Christian , MOYER, Tyson , READ, Benjamin Joseph , IVRINE, Darrell
摘要： Compositions containing a nucleic acid nanostructure having a desired geometric shape and antigens bound to its surface are provided. The nanostructures can be, for example, in the form of a 6-helix bundle or icosahedron. The nanostructure design allows for control of the relative position and/or stoichiometry of the antigen bound to its surface. The antigens displayed on the nanostructure surface are arranged with the preferred number, spacing, and 3D organization to elicit a robust immune response. The displayed antigen can be an HIV immunogen such as eOD-GT6, eOD-GT8, or variants thereof. The compositions may thus be useful as immunogens, vaccines, immunostimulators, adjuvants, and the like. Methods of inducing immune responses, inducing protective immunity, inducing the production of neutralizing antibodies or inhibitory antibodies, inducing tolerance, and treating cancer, infectious or autoimmune diseases are also provided.
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10.发明申请
公开(公告)号：WO2018236889A2
公开(公告)日：2018-12-27
申请号：PCT/US2018/038311
申请日：2018-06-19
摘要： 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, carbohydratess, 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.
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