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。确定这些成分的一个好方法是利用天然存在的RNA基序。利用这一理念，我们开发了RNAJunction关系数据库，该数据库由超过13,000个RNA亲吻环和n向连接的PDB（蛋白质数据库）表示组成。该数据库可从我们的网站http://www.ccrnp.ncifcrf.gov/bshapiro/获得。这些连接是通过使用我们的JunctionScanner算法扫描整个RNA结构的PDB数据库发现的。该算法依赖于运行RNAview软件获得的结果，该软件将PDB结构解析为标准的Watson/Crick碱基对以及其他几种非规范碱基相互作用。这种分析的结果随后被用来确定连接和接吻环的连通性。数据库本身分为六个子数据库，每个子数据库都可以通过多种方式进行搜索。其中三个子数据库根据突出的螺旋存根的格式良好的程度对图案进行分类。其他类别通过基于每个簇必须包含具有相同序列的基元和每个基元必须在构象上彼此非常相似的标准聚类基元来减少冗余。有几种搜索模式可供用户使用。一种被证明非常有用的搜索模式包括搜索在它们的螺旋存根之间有特定角度范围的图案。利用这些信息，可以添加a形螺旋连接器，将这些找到的图案连接到其他图案上，最终形成所需的形状。该数据库的存在已被证明对基于RNA的纳米结构的手工和组合生成非常有价值。RNA六边形纳米环和纳米管：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。我们最初的设计之一是RNA六边形环和RNA纳米管（正在申请专利）。除了阐明形成这种结构的RNA的特性外，环和管可以被设计成包括功能实体，如sirna，分子信标或适体。RNAJunction数据库的存在使得计算设计RNA六聚体纳米环和最终的RNA纳米管成为可能。一个重要的问题是找到一个图案，可以形成大约120度的角度在每六个角。通过扫描RNAJunction数据库，发现cole1吻环基序具有122度角。这种亲和环结构通过核磁共振（NMR）确定（一半指定为RNAIi，另一半指定为RNAIIi）。通过计算设计了两种形式的构建模块。一种形式由两个构建块组件组成（纳米环A+B）。第一个组件在两端包含一个RNAIi循环，另一个组件在两端包含一个RNAIIi循环。另一种形式在一端包含RNAIi环，在另一端包含RNAIIi环（自二聚体）。六角形纳米环的概念通过添加适当的工程悬垂末端来扩展，这些末端以交替的模式垂直于环平面。这允许多个环放置在彼此的顶部，利用互补的悬垂末端。这些堆叠环的放置形成了基于RNA的纳米管。NanoTiler - RNA纳米结构设计软件：为了更好地促进基于RNA的纳米颗粒的设计，已经开发了一个广泛的软件系统，NanoTiler，允许在几个不同的概念水平上进行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进行交互。NanoTiler的一个关键特征是它能够利用来自RNAJunction数据库的基序来完成3D RNA结构空间的组合搜索。一组特定的图案可以放置在空间中，并与A型螺旋连接器连接。连接器的长度可以改变。这导致了一个大的结构组合空间。其中一些结构形成闭合环；其他的可以形成树突状构象。环状结构可以自动检测。约束满足方法也被用于改善环闭合和连接螺旋的适当配合。此外，还可以在结构的设计过程中输入指示所需拓扑的图形。图匹配算法用于确定设计的结构何时与期望的拓扑匹配。一旦实现了理想的拓扑结构，NanoTiler就可以专注于产生一组序列，这些序列可以通过实验测试来形成所设计的结构。序列融合算法将用于生成构象拓扑的片段连接起来。其次，可以应用序列优化算法来限制设计序列之间的串扰量。序列重复突变，除了那些必须保持重要基序的部分（如从RNAJunction数据库中获得的那些基序），对每组突变序列进行评分。NanoTiler与其他程序一起测量序列之间发生的杂交程度和折叠成目标二级结构的程度。对GC内容的限制和序列的重复运行也被考虑在分数中。一旦生成了一组优化的序列，突变就会被替换回3D结构中。这是通过NanoTiler中的一种算法完成的，该算法在已知结构中搜索具有与生成结构中所需构象相似的相同碱基对。一旦所有的片段都设计好了，它们就会受到分子力学最小化的影响，以固定键的长度和角度。如果需要，整个结构或部分结构将受到分子动力学的影响，以表征所设计纳米结构的动态特性。RNA2D3D—RNA纳米结构探索和RNA 3D建模软件：我们开发了另一个软件包RNA2D3D，用于RNA纳米颗粒的探索性设计。其应用的一个例子是在tecto-square和teco-mesh的设计中，已经被其他人实验证明能够自组装。建模过程的一部分允许通过适当的雕刻在接吻环中涉及的发夹来定义接吻环的相互作用。可以指定一对互补的碱基，允许环路以同轴方式停靠。可以在指示连接性的文件中指定这些循环交互的列表。通过这种方式，人们可以建立对接的元素，在这种情况下，组成tecto-square的四个l形组件。可以采用类似的方法来指定构成单链尾部的碱基配对相互作用，这些单链尾部将多个正方形聚集在一起形成网格。以这种方式对这些组件进行建模立即表明，将构建模块视为刚体不会产生闭合环[摘要截断为7800个字符]