Computational RNA Nanodesign

计算RNA纳米设计

• 批准号: 8349306
• 负责人: Bruce Shapiro
• 金额: $ 86.09万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8349306
• 关键词: Academia; Automation; B-DNA; Biochemical; Biocompatible Materials; Biological Assay; Caliber; Cereals; Chemicals; Chemistry; China; Collaborations; Complex; Computer Simulation; Computing Methodologies; DNA; Data; Databases; Detection; Development; Dicer Enzyme; Dimensions; Discipline; Disease; Drug Industry; Electron Microscopy; Endotoxins; Engineering; Environment; France; Functional RNA; Gel; Genetic; Genetic Transcription; Goals; Government; HIV; Human; Hybrids; In Vitro; International; Knowledge; Label; Major Groove; Malignant Neoplasms; Methodology; Methods; Minor Groove; Modeling; Modification; Molecular; Molecular Conformation; Motion; Nanostructures; Nanotechnology; Normal Range; Nucleotides; Oligonucleotides; Pathway interactions; Polymers; Principal Component Analysis; Process; Production; Property; Protein Binding; Protocols documentation; RNA; RNA Conformation; RNA I; RNA Interference; RNA chemical synthesis; Receptor Cell; Recombinants; Reporting; Research Personnel; Resistance; Ribonucleases; Route; Series; Shapes; Small Interfering RNA; South Korea; Specific qualifier value; Structure; Sweden; System; Technology; Testing; Therapeutic; Time; United States; Variant; Vertebral column; Vision; analog; aptamer; base; catalyst; chemical synthesis; cryogenics; design; flexibility; human DICER1 protein; interest; light scattering; meetings; molecular dynamics; nano; nanobiology; nanobiotechnology; nanodevice; nanomedicine; nanoparticle; nanoscale; nanosecond; particle; pre-clinical; programs; scaffold; self assembly; sensor; simulation; single molecule; stem; sugar; symposium; synthetic biology

In Vitro Assembly of Cubic RNA-based Scaffolds Designed in Silico The organization of biological materials into versatile three dimensional assemblies could be used to build multifunctional therapeutic scaffolds for use in nanomedicine. We reported a strategy to computationally design and experimentally verify the formation of three-dimensional cubic nanoscale scaffolds that can self-assemble from RNA (also DNA and RNA/DNA hybrids) with precise control over their shape, size and composition. These cubic nanoscaffolds are only 13 nm in diameter and are composed of short oligonucleotides, making them amenable to chemical synthesis, point modifications and further functionalization. Nanocube assembly was verified by gel assays, dynamic light scattering and cryogenic electron microscopy. Formation of functional RNA nanocubes was also demonstrated by the use of a fluorescent RNA aptamer that was optimally active only upon full RNA assembly. We showed that the RNA nanoscaffolds can self-assemble in isothermal conditions (37 degrees C) during in vitro transcription, opening a route towards the construction of sensors, programmable packaging and cargo delivery systems for biomedical applications. Self-Assembling RNA Nanorings Based on RNA I/II Inverse Kissing Complexes with Associated Diceable siRNAs We experimentally characterized by biochemical and biophysical methods the formation of thermostable and ribonuclease resistant RNA nanorings which were originally designed by us using computational methods. High yields of fully programmable nanorings were produced based on several RNAI/II kissing complex variants selected for their ability to promote polygon self-assembly. This self-assembly strategy relying on the particular geometry of bended kissing complexes has potential for developing multivalent interfering RNA delivery agents. This was verified by assembling the nanoring with 6 siRNAs. These constructs were then shown to be processed by Dicer, an enzyme that is part of the RNAi silencing pathway. Specification of Protocols for the Design and Self-Assembly of siRNA Functionalized RNA Particles for Use in Automated Nanomedicine We specified three assembly protocols to produce two different types of RNA self-assembling functional NPs using processes which are fully automatable. These NPs were engineered based on two nano-scaffold designs (nanoring and nanocube), which serve as carriers of multiple siRNAs. The NPs were functionalized by extension of up to 6 scaffold strands with siRNA duplexes. The assembly protocols yielded functionalized RNA NPs that we showed interacted in vitro with human recombinant Dicer to produce siRNAs. Our design strategies showed that we can provide fast, economical and easily controlled production of endotoxin-free therapeutic RNA NPs suitable for preclinical development. Using RNA Structural Flexibility Data in Nanostructure Modeling In the emerging field of RNA-based nanotechnology there is a need for automation of the structure design process. Our goal is to develop computer methods for aiding in this process. Our RNAJunction data base contains thousands of RNA junctions that can be used as building blocks to construct RNA nanoparticles. Two programs we developed, NanoTiler and RNA2D3D, can combine such building blocks with idealized fragments of A-form helices to produce desired 3D nanostructures. Initially, the building blocks were treated as rigid objects. Experimental data, however, shows that RNA accommodates its shape to the constraints of larger structural contexts. We included the flexibility of our building blocks into the full design process. By using an experimentally proven system, the RNA tectosquare, we showed that considering the flexibility of its kissing loop motifs as well as distortions in its helical regions appears to be necessary to achieve a realistic design. Understanding the Effects of Carbocyclic Sugars Constrained to North and South Conformations on RNA Nanodesign Relatively new types of modified nucleotides, namely carbocyclic sugars that are constrained to north or south conformations, can be used for RNA nanoparticle design to control their structures and stability by rigidifying nucleotides and altering the helical properties of RNA duplexes. Two RNA structures, an RNA dodecamer and an HIV kissing loop complex where several nucleotides were replaced with north or south constrained sugars, were studied by molecular dynamics (MD) simulations. The substituted south constrained nucleotides in the dodecamer widened the major groove and narrowed and deepened the minor groove thus inducing local conformational changes that resemble a B-form DNA helix. In the HIV kissing loop complex, north and south constrained nucleotides were substituted into flanking bases and stems. The modified HIV kissing loop complex showed a lower RMSD value than the normal kissing loop complex. The overall twist angle was also changed and its standard deviation was reduced. In addition, the modified RNA dodecamer and HIV kissing loop complex were characterized by principal component analysis (PCA) and steered molecular dynamics (SMD). PCA results showed that the constrained sugars stabilized the overall motions. The results of the SMD simulations indicated that as the backbone delta angles were increased by elongation, more force was applied to the modified RNA due to the constrained sugar analogues. Coarse Graining of RNA Nanostructures for Molecular Dynamics Simulations The modeling and characterization of RNA-based nanostructures is a difficult task given the size of such structures. At best, all atom molecular dynamics studies of such molecules can obtain trajectories of a few nanoseconds duration, a limited time scale for a comprehensive characterization of such structures. A series of coarse-grained models have been developed for study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for systems of thousands of nucleotides, a time scale of microseconds and thus enable simulations of large RNA polymers in the context of bionanotechnology. We found that the three-beads-per-nucleotide models, described by a set of just a few universal parameters, were able to describe different RNA conformations and were comparable in structural precision to the models where detailed values of the backbone P-C4' dihedrals taken from a reference structure were included. First International Meeting on RNA Nanotechnology A meeting was held in which I was a co-organizer highlighting the recent advances in RNA nanotechnology as presented at the First International Conference of RNA Nanotechnology and Therapeutics, in Cleveland, OH. The conference was the first of its kind to bring together invited speakers in RNA nanotechnology from France, Sweden, South Korea, China, and throughout the United States to discuss RNA nanotechnology and its applications. It provided a platform for researchers from academia, government, and the pharmaceutical industry to share existing knowledge, vision, technology, and challenges in the field and promoted collaborations among researchers interested in advancing this emerging scientific discipline. The meeting covered a range of topics, including biophysical and single-molecule approaches for characterization of RNA nanostructures; structure studies on RNA nanoparticles by chemical or biochemical approaches, computation, prediction, and modeling of RNA nanoparticle structures; methods for the assembly of RNA nanoparticles; chemistry for RNA synthesis, conjugation, and labeling; and application of RNA nanoparticles in therapeutics.

在硅中设计的基于立方RNA的脚手架的体外组装可以使用生物材料组织到多功能三维组件中，可用于构建用于纳米医学中的多功能治疗脚手架。我们报道了一种在计算设计上的策略，并在实验上验证了三维立方纳米级支架的形成，该纳米级支架可以从RNA（也是DNA和RNA/DNA杂种）自组装，并精确控制其形状，大小和组成。这些立方纳米镜的直径仅为13 nm，由短寡核苷酸组成，使其与化学合成，点修饰和进一步的功能化。纳米管组件通过凝胶测定，动态光散射和低温电子显微镜进行了验证。还通过使用仅在全RNA组件上最佳活性的荧光RNA适体的使用也证明了功能性RNA纳米接管的形成。我们表明，在体外转录过程中，RNA纳米镜可以在等热条件下（37摄氏度）自组装，为生物医学应用开放了构建传感器，可编程包装和货物输送系统的途径。基于RNA I/II逆接吻复合物与相关siRNA相关的逆接吻复合物的自组装RNA纳米构造我们通过生化和生物物理方法的实验表征，使用计算方法是由我们设计的。基于几种促进多边形自组装的能力，基于几种RNAi/II接吻复合物的变体产生了高度可编程的纳米素。这种依靠弯曲接吻复合物的特定几何形状的自组装策略具有开发多价干扰RNA递送剂的潜力。通过用6个siRNA组装纳米，可以验证这一点。然后证明这些构建体是由DICER处理的，DICER是RNAi沉默途径的一部分的酶。用于用于自动化纳米医学的siRNA功能化RNA颗粒的设计和自组装方案的规范我们指定了三种装配方案，用于生成两种不同类型的RNA自组装功能NP，使用完全自动化的过程。这些NP是基于两种纳米型工具设计（Nanoring和Nanocube）设计的，它们是多个siRNA的载体。通过延伸多达6个带有siRNA双链体的脚手架链的NP通过伸展而功能化。组装方案产生了功能化的RNA NP，我们表现出与人类重组迪切尔在体外相互作用以产生siRNA的相互作用。我们的设计策略表明，我们可以提供适合临床前开发的无内毒素治疗RNA NP的快速，经济和易于控制的生产。在基于RNA的纳米技术的新兴领域中，在纳米结构建模中使用RNA结构灵活性数据，需要自动化结构设计过程。我们的目标是开发用于协助此过程的计算机方法。我们的RNA结数据库包含数千个RNA连接，可以用作构建RNA纳米颗粒的构件。我们开发的两个程序，分别是Nanotiler和RNA2D3D，可以将这些构件与A-Corm螺旋的理想化片段相结合，以产生所需的3D纳米结构。最初，构建块被视为刚性对象。但是，实验数据表明，RNA适应了较大结构环境的约束。我们将构建块的灵活性包括在整个设计过程中。通过使用实验验证的系统RNA TectoSquare，我们表明，考虑到其螺旋区域中其接吻环基序的灵活性以及在其螺旋区域中的扭曲似乎是实现现实设计的必要条件。了解将碳环糖糖限制在北方和南方构象上对RNA纳米设计相对较新类型的改性核苷酸的类型，即被约束至北或南构型的碳环糖糖，可用于RNA纳米颗粒设计，以通过固化其结构和稳定性来控制核试验物质，并改善核试验的构图。通过分子动力学（MD）模拟研究了两个RNA结构，一个RNA十二焦和一个HIV接吻环复合物，其中几种核苷酸被北部或南约束糖代替。十二焦点中取代的南约束核苷酸扩大了主要的凹槽，并缩小并加深了小凹槽，从而诱导了类似于B形DNA螺旋的局部构象变化。在HIV接吻环复合体中，将南北约束的核苷酸取代为侧面和茎。修改后的HIV接吻环复合物的RMSD值低于正常的接吻循环复合物。总体扭曲角度也改变了，其标准偏差减小。此外，通过主成分分析（PCA）和转导的分子动力学（SMD），修饰的RNA DodeCamer和HIV接吻环复合物的特征是。 PCA结果表明，受约束的糖稳定了总体运动。 SMD模拟的结果表明，随着主链三角角通过伸长的增加，由于糖类似物的约束，将更多的力应用于修饰的RNA。鉴于此类结构的大小，用于分子动力学模拟的RNA纳米结构的粗晶片是基于RNA的纳米结构的建模和表征是一项艰巨的任务。充其量，此类分子的所有原子分子动力学研究都可以获得几纳秒持续时间的轨迹，这是对此类结构进行全面表征的有限时间尺度。已经开发了一系列粗粒模型，以研究RNA纳米结构的分子动力学。该系列中的模型每个核苷酸具有一到三个珠子，并包含不同量的详细结构信息。这种处理使我们能够达到数千个核苷酸的系统，即微秒的时间尺度，从而在Bionanotechnology的背景下启用大型RNA聚合物的模拟。我们发现，只有几个通用参数描述的每三个核苷酸模型能够描述不同的RNA构象，并且在结构上的精度与模型相当，在这些模型中，包括从参考结构中获得的骨架p-c4'二脑的详细值。第一次关于RNA纳米技术的国际会议举行了一次会议，我是一名共同组织者，重点介绍了在俄亥俄州克利夫兰举行的第一次RNA纳米技术和治疗学国际会议上提出的RNA纳米技术的最新进展。该会议是第一个将来自法国，瑞典，韩国，中国以及整个美国的RNA纳米技术发言人汇集的邀请发言人，讨论RNA纳米技术及其应用。它为学术界，政府和制药行业的研究人员提供了一个平台，以分享该领域的现有知识，愿景，技术和挑战，并促进有兴趣推进这一新兴科学学科的研究人员的合作。会议涵盖了一系列主题，包括用于表征RNA纳米结构的生物物理和单分子方法；通过化学或生化方法，RNA纳米粒子结构的化学或生化方法，计算，预测和建模对RNA纳米颗粒的结构研究； RNA纳米颗粒组装的方法； RNA合成，结合和标记的化学； RNA纳米颗粒在治疗剂中的应用。