Improvement of the NMR structural quality for RNA and DNA

提高 RNA 和 DNA 的 NMR 结构质量

• 批准号: 537258662
• 负责人: Professor Dr. Harald Schwalbe
• 金额: --
• 依托单位: Institut für Organische Chemie und Chemische Biologie
• 依托单位国家: 德国
• 项目类别: Research Grants
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/537258662?language=en
• 关键词: Improvement; NMR; structural; quality; RNA

Nuclear Magnetic Resonance spectroscopy (NMR) is very important for the characterization of DNA and RNA, encompassing a variety of methods that offer essential insight on the structure, function, interactions and conformational dynamics of these biomolecules. Despite the eminent contribution of NMR in this field, some essential tools and approaches (which are routinely available for proteins) are still missing for nucleic acids and require further development or fine-tuning. Notably, the parametrization of forcefields used for the structure determinations of nucleic acids still lacks behind. Advancing the development in this area is therefore indispensable to elucidate more accurate and high-quality well resolved NMR structures. Such approach requires verification with well characterized RNA and DNA reference systems. Our objective is to improve the currently established methods and protocols and provide high quality data to optimize the forcefield parametrization. In this respect, we already elucidated the structure of two RNA hairpin model systems (the tetraloops UUCG and CUUG) using a wealth of structural data and incorporated optimized potentials for refinement in water. The UUCG structure is currently considered to be the gold standard for forcefield optimizations and assessment by cross-validation with other methods and empirical data. We currently investigate the structure and dynamics of additional tetraloops (GCAA, GAAG). Moreover, we provide additional suitable model targets from our current extensive investigations of elements from the genome of RNA viruses (Covid-19 and West Nile Virus) and other small DNA and RNA motifs and repeats. In our endeavor to describe the ensemble characteristic of RNA structures realistically, we studied the CUUG tetraloop system, which turned out to feature substantial dynamics despite its high thermal stability. Thus, we have recently combined NMR with molecular dynamic simulations to probe the underlying conformational landscape and provide suitable structural ensembles. In this application, we will include larger RNA and DNA molecules, G-Quadruplexes, and RNA/DNA triplexes. For their structure determination, we will gather additional global, long-range structural, orientational and dynamic restraint data and utilize 3D structure prediction and homology modeling for evaluation of the nucleic acid forcefield and improvement of tools and protocols. Moreover, we aim to include the most important and occurring RNA and DNA modifications as well as several ions and plan to employ and develop approaches for the structure calculation of conformational ensembles. These new and improved parameters and methods will be made available for the structural NMR community in established software and through implementation in our existing web-portal service for NMR structure determination. In addition, we will publish the results in suitable open source databases, journals and platforms.

核磁共振波谱 (NMR) 对于 DNA 和 RNA 的表征非常重要，它涵盖了多种方法，可以提供对这些生物分子的结构、功能、相互作用和构象动力学的重要见解。尽管核磁共振在这一领域做出了杰出的贡献，但对于核酸来说，一些基本的工具和方法（通常可用于蛋白质）仍然缺失，需要进一步开发或微调。值得注意的是，用于核酸结构测定的力场参数化仍然缺乏。因此，推进这一领域的发展对于阐明更准确、高质量、高分辨率的 NMR 结构至关重要。这种方法需要使用特征良好的 RNA 和 DNA 参考系统进行验证。我们的目标是改进当前建立的方法和协议，并提供高质量的数据来优化力场参数化。在这方面，我们已经利用大量的结构数据阐明了两个 RNA 发夹模型系统（四环 UUCG 和 CUUG）的结构，并结合了在水中精炼的优化潜力。 UUCG 结构目前被认为是通过与其他方法和经验数据交叉验证进行力场优化和评估的黄金标准。我们目前研究其他四环（GCAA、GAAG）的结构和动力学。此外，我们还通过目前对 RNA 病毒（Covid-19 和西尼罗病毒）基因组元素以及其他小 DNA 和 RNA 基序和重复序列的广泛研究，提供了其他合适的模型靶标。在我们努力真实地描述 RNA 结构的整体特征的过程中，我们研究了 CUUG 四环系统，该系统尽管具有很高的热稳定性，但仍具有显着的动力学特征。因此，我们最近将核磁共振与分子动力学模拟相结合，以探测潜在的构象景观并提供合适的结构整体。在此应用中，我们将包括较大的 RNA 和 DNA 分子、G-四链体和 RNA/DNA 三链体。为了确定它们的结构，我们将收集额外的全局、远程结构、方向和动态约束数据，并利用 3D 结构预测和同源建模来评估核酸力场以及改进工具和协议。此外，我们的目标是包括最重要和发生的 RNA 和 DNA 修饰以及几种离子，并计划采用和开发构象系综的结构计算方法。这些新的和改进的参数和方法将在已建立的软件中供结构 NMR 社区使用，并通过我们现有的用于 NMR 结构测定的门户网站服务中的实施来提供。此外，我们还将在合适的开源数据库、期刊和平台上发布结果。