Computational RNA Nanodesign

计算RNA纳米设计

• 批准号: 7733458
• 负责人: Bruce Shapiro
• 金额: $ 51.29万
• 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/7733458
• 关键词: Accounting; Algorithms; Back; Base Pairing; Biological; Categories; Closure; Complex; Computer software; Computing Methodologies; Crystallography; Databases; Detection; Development; Dimensions; Disease; Docking; Engineering; Environment; Functional RNA; Generations; Genetic; Goals; Graph; Guanine + Cytosine Composition; Helix (Snails); Indium; Individual; Language; Legal patent; Length; Malignant Neoplasms; Manuals; Measures; Methods; Modeling; Molecular; Molecular Conformation; Mutate; Mutation; Nanostructures; Object Attachment; Pattern; Philosophy; Placement; Process; Property; Protein Binding; Proteins; Purpose; RNA; RNA Databases; Range; Receptor Cell; Running; Scanning; Score; Shapes; Specific qualifier value; Standards of Weights and Measures; Structure; System; Tail; Testing; Therapeutic; To specify; Tube; aptamer; base; catalyst; combinatorial; concept; database design; design; desire; dimer; ear helix; graphical user interface; improved; molecular dynamics; molecular mechanics; nanobiology; nanodevice; nanoparticle; nanosensors; programs; satisfaction; self assembly; software systems; synthetic biology; three dimensional structure; three-dimensional modeling

;RNAJunction Database: The design of RNA based nanostructures is at least partially reliant on the components that comprise the individual building blocks. A good way of determining these components is by utilizing naturally occurring RNA motifs. Using this philosophy we developed the RNAJunction relational database, which consists of the PDB (Protein Data Base) representations of over 13,000 RNA kissing loops and n-way junctions. The database is available from our website http://www.ccrnp.ncifcrf.gov/bshapiro/. These junctions were found by scanning the entire PDB database of RNA structures using our JunctionScanner algorithm. This algorithm relies on results that are obtained by running the RNAview software that parses the PDB structure into standard Watson/Crick base pairs as well as several other non-canonical base interactions. The results from this parse are then used to determine the connectivity of the junctions and kissing loops. The database itself is divided into six sub-databases each of which can be searched in a multitude of ways. Three of these sub-databases categorize the motifs based upon the degree of well-formedness of the projecting helical stubs. The other categories reduce redundancy by clustering motifs based upon the criteria that each cluster must contain motifs with the same sequences and each of the motifs must be conformationally very similar to each other. Several search modes are available to the user. One mode of search that has proven to be very useful involves searching for motifs that have specific angle ranges between their helical stubs. Using this information, it is possible to add A-form helical connectors to attach these found motifs to others, ultimately forming a desired shape. The existence of this database has proven to be very valuable for the manual and combinatoric generation of RNA based nanostructures. RNA Hexagonal Nanoring and Nanotube: One of our goals is to design functional RNA nanoparticles that can be used, for example, for therapeutic purposes, as substrates for crystallography or for nanosensors. One of our first designs was of an RNA hexagonal ring and RNA nanotube (patent pending). Besides elucidating the properties of the RNA that forms such structures, the ring and tube may be engineered to include functional entities such as siRNAs, molecular beacons or aptamers. The existence of the RNAJunction database made it possible to computationally design an RNA hexameric nanoring and ultimately an RNA nanotube. A significant issue was to find a motif that could form approximately a 120 degree angle at each of six corners. By scanning the RNAJunction database the Col E1 kissing loop motif was discovered to have a 122 degree angle. This kissing loop structure was determined by NMR (one half designated as RNAIi and the other half as RNAIIi). Two forms of the building blocks were computationally designed. One form consists of two building block components (Nanoring A+B). The first component contains an RNAIi loop on both ends and the other contains an RNAIIi loop at both ends. The other form contains an RNAIi loop on one end and an RNAIIi loop on the other (self-dimer). The concept of the hexagonal nanoring was extended by adding appropriately engineered dangling ends oriented perpendicular to the ring plane in alternating patterns. This permitted the placement of multiple rings on top of each other by utilizing complementary dangling ends. The placement of these stacked rings result in the RNA based nanotube. NanoTiler - Software for RNA Nanostructure Design: To better facilitate the design of RNA based nanoparticles an extensive software system, NanoTiler, has been developed that permits RNA nanodesign at several different conceptual levels. The user can interface with the system via a graphical user interface or with a scripting language. A key feature of NanoTiler is its ability to accomplish combinatorial search of 3D RNA structure spaces by utilizing motifs derived from the RNAJunction database. A specified set of motifs can be placed in space and joined with A-form helix connectors. The connector lengths can be varied. This leads to a large combinatorial space of structures. Some of these structures form closed rings; others can form dendrimer-like conformations. Ring-formation can be detected automatically. Constraint satisfaction methods are also applied to improve ring closure and proper fit of connected helices. In addition, a graph that indicates the desired topology can be input into the design process of a structure. A graph matching algorithm is used to determine when a designed structure matches the desired topology. Once a desired topology is realized, NanoTiler can then be focused on producing a set of sequences that can be experimentally tested for the formation of the designed structure. A sequence-fusing algorithm connects fragments that were used in the generation of the conformational topologies. Next the sequence optimization algorithm can be applied in order to limit the amount of cross talk between the designed sequences. Sequences are repeatedly mutated, except for the portions that have to be maintained to preserve important motifs such as those obtained from the RNAJunction database, scoring each set of mutated sequences. NanoTiler in conjunction with other programs measures the degree of hybridization that occurs between the sequences and the degree of folding into the target secondary structure. Limitations on GC content and repetitious runs of sequence are also taken into account in the score. Once an optimized set of sequences is generated, mutations are substituted back into the 3D structure. This is accomplished by an algorithm in NanoTiler that searches known structures for the same base pairs that have a conformation similar to that needed in the generated structure. Once all fragments are designed, they are subjected to molecular mechanics minimization to fix bond lengths and angles. If desired, the entire structure or portions of the structure are subjected to molecular dynamics to characterize the dynamical qualities of the designed nanostructure. RNA2D3D - Software for RNA Nanostructure Exploration and RNA 3D Modeling: We developed another software package, RNA2D3D, that is being used for exploratory design of RNA based nanoparticles. An example of its use was illustrated in the design of a tecto-square and teco-mesh, which have been shown experimentally by others to be capable of self-assembly. Part of the modeling process allows the definition of a kissing loop interaction by the appropriate sculpting of the hairpins involved in the kissing loop. A pair of complementary bases can be specified allowing the loops to dock in a coaxial fashion. A list of these loop-loop interactions can be specified in a file that indicates the connectivity. In this way, one can establish the docked elements of, in this case, the four L-shaped components that make up the tecto-square. A similar approach can be taken to specify the base pairing interactions that make up the single stranded tails that bring multiple squares together to form a mesh. Modeling these components in this fashion immediately indicates that treating the building blocks as rigid bodies does not produce a closed ring [summary truncated at 7800 characters]

; RNAJunction数据库：基于RNA的纳米结构的设计至少部分依赖于组成单个构建块的组件。确定这些组件的一种好方法是利用天然存在的RNA图案。利用这种理念，我们开发了RNA开19个关系数据库，该数据库由PDB（蛋白质数据库）表示，该数据库的表示超过13,000个RNA接吻循环和N向连接。该数据库可从我们的网站http://www.ccrnp.ncifcrf.gov/bshapiro/获得。通过使用我们的JunctionsCanner算法扫描RNA结构的整个PDB数据库，可以找到这些连接。该算法依赖于通过运行将PDB结构解析为标准Watson/Crick Base对以及其他几种其他非典型基础相互作用的RNAview软件获得的结果。然后，该分析的结果用于确定连接和接吻循环的连通性。数据库本身分为六个子数据库，每个数据库可以通过多种方式搜索。这些子数据库中的三个根据投射螺旋存根的良好程度对基序进行分类。其他类别通过基于每个群集必须包含具有相同序列的基序的标准来减少冗余，并且每个基序都必须在彼此之间非常相似。用户可以使用几种搜索模式。事实证明，一种非常有用的搜索模式涉及搜索其螺旋存根之间具有特定角度范围的图案。使用此信息，可以添加A形式的螺旋连接器将这些图案连接到其他图案，最终形成所需的形状。事实证明，该数据库的存在对于基于RNA的纳米结构的手册和组合生成非常有价值。 RNA六边形纳米型和纳米管：我们的目标之一是设计功能性RNA纳米颗粒，例如用于治疗目的，作为晶体学或纳米传感器的底物。我们的第一个设计之一是RNA六角环和RNA纳米管（申请专利）。除了阐明形成这种结构的RNA的性能外，环和管还可以设计为包括功能实体，例如siRNA，分子信标或适体。 RNAJuntion数据库的存在使得可以在计算上设计RNA六聚体nanoring并最终是RNA纳米管。一个重要的问题是找到一个可能在六个角中每个角形成大约120度角的基序。通过扫描RNAJuntion数据库，发现Col E1接吻环图案具有122度角。这种接吻循环结构由NMR（一个指定为RNAII，另一半称为RNAIII）确定。两种形式的构建块是计算设计的。一种形式由两个构件组件（Nanoring A+B）组成。 第一个组件在两端都包含一个RNAII循环，而另一个组件在两端都包含一个RNAIII循环。另一种形式在一端包含一个RNAII循环，另一端包含一个RNAIII循环（自动二聚体）。通过以交替的模式添加适当设计的悬挂端垂直于环平面的定向悬挂端，扩展了六角形纳米纳的概念。 这允许通过使用互补的悬挂端将多个环放在彼此之上。这些堆叠环的放置导致基于RNA的纳米管。 Nanotiler- RNA纳米结构设计的软件：为了更好地促进基于RNA的纳米颗粒的设计，已经开发了一种广泛的软件系统，即纳米动物，它允许在几个不同的概念级别上进行RNA纳米设计。用户可以通过图形用户界面或脚本语言与系统接口。纳米动物的一个关键特征是它通过利用源自RNAJunction数据库的图案来完成对3D RNA结构空间的组合搜索的能力。可以将指定的一组图案放置在太空中，并与A形螺旋螺旋连接器连接。连接器长度可以变化。这导致了较大的结构组合空间。这些结构中的一些形成了封闭环。其他人可以形成类似树状聚合物的构象。可以自动检测到环形成。 还采用约束满意度方法来改善环形螺旋的闭合和适当的拟合。此外，指示所需拓扑的图可以输入结构的设计过程。图形匹配算法用于确定设计的结构何时与所需的拓扑匹配。一旦实现了所需的拓扑结构，就可以将纳米动物专注于产生一组序列，这些序列可以通过实验测试，以形成设计的结构。序列式算法连接用于生成构象拓扑的片段。接下来，可以应用序列优化算法，以限制设计序列之间的交叉谈话量。序列反复突变，除了必须维护以保留重要基序的部分，例如从RNAJuntion数据库获得的部分，对每组突变的序列进行了评分。与其他程序结合使用纳米叶剂，测量序列与折叠程度之间发生的杂交程度。在分数中还考虑了GC内容和重复运行序列的限制。一旦生成了优化的序列集，将突变替换回3D结构。这是通过纳米构算法中的算法来完成的，该算法搜索已知结构的相同碱基对，其构象与生成结构中所需的构象相似。一旦设计了所有片段，它们就会受到分子力学的最小化，以固定键长和角度。如果需要，结构的整个结构或部分都会受到分子动力学的影响，以表征设计纳米结构的动力学品质。 RNA2D3D-用于RNA纳米结构勘探和RNA 3D建模的软件：我们开发了另一个软件包RNA2D3D，该软件包用于基于RNA的纳米粒子的探索设计。在Tecto-Square和Teco-Mesh的设计中说明了其使用的一个例子，而其他人则在实验中显示了能够自组装。建模过程的一部分允许通过适当的接吻循环中的发夹来定义接吻循环相互作用。可以指定一对互补的基础，允许循环以同轴方式对接。可以在指示连接性的文件中指定这些循环循环交互的列表。这样，就可以建立构成Tecto平方的四个L形组件的对接元素。可以采用类似的方法来指定构成单个绞合尾巴的基本配对相互作用，这些尾巴将多个正方形融合在一起以形成网格。以这种方式对这些组件进行建模，立即表明将构件作为刚体将块状物体视为不会产生封闭环[摘要以7800个字符截断]