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.

核磁共振光谱（NMR）对于DNA和RNA的表征非常重要，它包含了各种方法，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基本见解。尽管核磁共振在这一领域的杰出贡献，一些基本的工具和方法（通常可用于蛋白质）仍然缺乏核酸，需要进一步的发展或微调。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是必不可少的，以阐明更准确和高质量的良好分辨NMR结构。这种方法需要用充分表征的RNA和DNA参考系统进行验证。我们的目标是改进目前建立的方法和协议，并提供高质量的数据，以优化力场参数化。在这方面，我们已经阐明了两个RNA发夹模型系统（四环UUCG和CUUG）的结构，使用了丰富的结构数据，并纳入优化的潜力，在水中细化。UUCG结构目前被认为是力场优化和评估的黄金标准，通过与其他方法和经验数据的交叉验证。我们目前正在研究额外的四环（GCAA，GAAG）的结构和动力学。此外，我们从我们目前对RNA病毒（Covid-19和西尼罗河病毒）基因组元件以及其他小DNA和RNA基序和重复序列的广泛研究中提供了额外的合适模型靶标。在我们的奋进来描述合奏的RNA结构的特点，现实的，我们研究了CUUG四环系统，它原来的特点是大量的动力学，尽管它的高热稳定性。因此，我们最近结合NMR与分子动力学模拟，以探测潜在的构象景观，并提供合适的结构合奏。在本申请中，我们将包括较大的RNA和DNA分子，G-四链体和RNA/DNA三链体。对于它们的结构测定，我们将收集额外的全球，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并改进工具和方案。此外，我们的目标是包括最重要的和发生的RNA和DNA的修改，以及几个离子和计划采用和开发的构象合奏的结构计算的方法。这些新的和改进的参数和方法将在已建立的软件中提供给结构NMR社区，并通过在我们现有的NMR结构测定门户网站服务中实施。此外，我们将在合适的开源数据库、期刊和平台上发布结果。