Title: Development of simulation techniques to study co-transcriptional RNA nanostructure folding

标题：研究共转录 RNA 纳米结构折叠的模拟技术的发展

• 批准号: 2748418
• 金额: --
• 依托单位: University of Oxford
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2022
• 资助国家: 英国
• 起止时间: 2022 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2748418
• 关键词: Title; Development; simulation; techniques; study

The aim of the project is to use multi-scale simulation methods to explore the kinetics of co-transcriptional RNA folding, leading to new methods of RNA nanostructure design.Understanding the physics of biomolecular folding is a key challenge of theoretical biophysics. DNA nanostructures are assembled by annealing multiple oligonucleotides with predictable base-pairing interactions: 3D structures with >104 components can be created by rational design. In contrast, recent progress in predicting protein folding by the Alphafold2 team from Google DeepMind required input from biophysics, bioinformatics and machine learning. Co-transcriptional folding of RNA nanostructures combines the single-strand architecture of proteins with relatively predictable interactions between nucleobases and is thus a fascinating model system.Co-transcriptional folding has rich non-equilibrium physics: assembly during production of the polymer locks in metastable sub-structures. For example, formation of a double helix requires the wrapping of two strands around each other which, unless very short, is only possible if a free end is available (normally the case in multi-stranded assembly) or if the entire section is able to rotate freely. Tertiary contacts which prevent wrapping can lead to topological barriers to assembly. Key to the success of single-stranded folding is therefore control of the order of assembly of sub-structures. When a time-dependent annealing temperature is used, as is typical in DNA nanostructure assembly, order is controlled by the relative stabilities of the different elements. Under the isothermal conditions of co-transcriptional assembly one must instead exploit the order of synthesis to control assembly through design of free-energy barriers and non-equilibrium assembly pathways. To design non-equilibrium assembly pathways for nanostructure assembly we need design tools based on better understanding of the physics of co-transcriptional folding.So far, relatively simple tools have been used to understand co-transcriptional assembly. We will use the coarse-grained oxRNA model to provide more detail of free-energy landscapes for assembly and how these can be sculpted to optimize assembly pathways. oxRNA represents each nucleotide as a single rigid body with interactions parametrized empirically to reproduce structural, mechanical and thermodynamic properties of single- and double-stranded RNA. This efficient representation enables study of large structures (>104 bases) as well as rare processes such as the formation or breaking of base pairs and strand displacement. oxRNA successfully reproduces some common motifs used in RNA nanotechnology e.g. kissing loops and PX crossovers. In designing synthetic RNA nanostructures we will focus on canonical base pairing, avoiding the many non-canonical structural motifs found in biological RNA, which hugely simplifies modelling and study of folding.Fundamental insights obtained using folding simulations will be used to create and refine design tools to improve yield and to extend the size range over which co-transcriptional RNA origami nanostructures form reliably. This project will lay the foundations for the development of intracellular RNA nanostructure fabrication. Potential applications of self-assembled nanostructures within the cell include: probes of cellular function to report on cellular processes; in situ drug synthesis; intervention in natural genetic control systems or gene editing; and as a new generation of autonomous medical device, combining diagnosis and treatment with sub-cellular resolution.This project lies within cross-council priority area Synthetic Biology. It integrates research in (EPSRC) Physical Sciences - Biophysics and Soft Matter Physics.The project is supervised byProf. Andrew Turberfield and Prof. Ard Louis (Oxford Physics) and will involve close collaboration Prof. Jonathan Doye (Oxford Chemistry) and Prof. Petr Sulc (ASU).

该项目的目的是使用多尺度模拟方法来探索共转录RNA折叠的动力学，从而导致RNA纳米结构设计的新方法。理解生物分子折叠的物理学是理论生物物理学的一个关键挑战。DNA纳米结构是通过退火多个寡核苷酸与可预测的碱基配对相互作用组装的：通过合理的设计可以创建具有>104个组件的3D结构。相比之下，谷歌DeepMind的Alphafold 2团队在预测蛋白质折叠方面的最新进展需要生物物理学、生物信息学和机器学习的投入。RNA纳米结构的共转录折叠结合了蛋白质的单链结构和相对可预测的核碱基之间的相互作用，因此是一个迷人的模型系统。例如，双螺旋的形成需要两个链彼此缠绕，除非非常短，否则只有在自由端可用（通常是多链组装的情况）或整个部分能够自由旋转的情况下才可能。防止缠绕的第三接触可能导致组装的拓扑障碍。因此，单链折叠成功的关键是控制子结构的组装顺序。当使用依赖于时间的退火温度时，如在DNA纳米结构组装中典型的，顺序由不同元素的相对稳定性控制。在共转录组装的等温条件下，人们必须通过设计自由能屏障和非平衡组装途径来利用合成顺序来控制组装。为了设计纳米结构组装的非平衡组装途径，我们需要基于对共转录折叠物理机制更好理解的设计工具。我们将使用粗粒度的oxRNA模型来提供更多关于组装自由能景观的细节，以及如何塑造这些景观以优化组装途径。oxRNA将每个核苷酸表示为单个刚性体，其相互作用根据经验参数化以再现单链和双链RNA的结构、机械和热力学性质。这种高效的表示方法可以研究大型结构（>104个碱基）以及罕见的过程，如碱基对的形成或断裂以及链置换。oxRNA成功地复制了RNA纳米技术中使用的一些常见基序，例如接吻环和PX交叉。在设计合成RNA纳米结构时，我们将专注于规范碱基配对，避免在生物RNA中发现的许多非规范结构基序，这极大地简化了折叠的建模和研究。使用折叠模拟获得的基本见解将用于创建和改进设计工具，以提高产量，并扩大共同转录RNA折纸纳米结构可靠形成的尺寸范围。该项目将为细胞内RNA纳米结构制造的发展奠定基础。细胞内自组装纳米结构的潜在应用包括：细胞功能探针，用于报告细胞过程;原位药物合成;干预天然遗传控制系统或基因编辑;以及作为新一代自主医疗设备，将诊断和治疗与亚细胞分辨率相结合。该项目属于跨理事会优先领域合成生物学。它整合了物理科学（EPSRC）的研究-生物物理学和软物质物理学。Andrew Turberfield和Ard Louis教授（牛津物理学），并将与Jonathan Doye教授（牛津化学）和Petr Sulc教授（ASU）密切合作。