Radiolytic hydrogen production in heterogenous systems with plant relevance: Generic computational and experimental models.

结构生物学的主要挑战是确定三维折叠RNA结构[1,2]。该项目计划开发一种创新的方法来确定这些结构。虽然我们的一小部分RNA编码蛋白质，但更多的作用是编排生命的分子过程，因此确定RNA所采用的3D折叠结构是进一步了解生命过程的关键要求。我们将使用快速氦离子，这在英国道尔顿坎布里亚设施（DCF）是独一无二的。这些离子在亚纳米尺度上产生小颗粒状损伤，可以有效地解剖折叠的RNA。当单个离子穿过RNA结构时，折叠RNA的邻近部分更有可能分裂在一起。因此，经常出现的碎片表明折叠结构的部分紧密相连。学生将开发一种新的程序来利用这一现象：1)照射简单的RNA结构并分析碎片以确定最佳的化学条件；2)优化并确定将poly-A尾部置于离子损伤末端的效率，作为下一代测序的先决条件；3)完善磁珠钓鱼，去除不包含相同接近信息的分离端片段；4)将上述步骤1-3与下一代测序相结合，产生可以推断接近图和折叠结构的数据。这个过程将在越来越复杂的结构中重复，从add1适体和RNA谜题收集开始，5)开发分析技术来获取测序数据并将其转换为RNA不同部分的接近度图。参与该项目的学生将有机会在国际领先的多学科合作团队中工作，并有机会为结构生物学的重大突破做出贡献。[1] Richardson et al . 2019《生物化学》doi: 10.1021/acs.biochem。[00:53 . 00]金等。Masayuki and Corey 2016 Nat. Rev. Drug Discovery doi 10.1038/nrd.2016.117

The major challenge of structural biology is determining 3D folded RNA structures [1,2]. This project plans to develop an innovative way to determine these structures. Whilst a small amount of our RNA codes for proteins, much more acts to choreograph the molecular processes of life so determining the 3D folded structures RNA takes-up is a key requirement for furthering our understanding of the processes of life [3].We will use the fast helium ions, uniquely available in the UK at the Dalton Cumbrian Facility (DCF). These ions produce gimlet-like damage on the sub-nanometre scale, which can effectively dissect folded RNA. Near-by parts of the folded RNA are more likely to fragment together as a single ion passes through the RNA structure. Hence fragments which occur more commonly indicate parts of the folded structure which are close together.The student will develop a new procedure to exploit this phenomenon by:1) irradiating simple RNA structures and analysing the fragmentation to determine the best chemical conditions, 2) optimising and determining the efficiency of putting poly-A tails on to ion-damaged ends as a prerequisite for next-gen sequencing,3) perfecting magnetic bead-fishing to remove separate off the end-fragments which do not contain the same proximity information,4) combining the steps 1-3 above with next-gen sequencing to produce data from which proximity maps and the folded structure can be deduced. This process will be repeated for increasingly complex structures, starting with the Add1-aptamer and the RNA puzzles collection, and5) developing analytical techniques to take the sequencing data and transform it into a map of the proximity of different parts of the RNA.The student working on this project will have the opportunity to work within an internationally leading, multidisciplinary collaborative team and will have the chance to contribute to a major break-through in structural biology.1] Richardson et al 2019 Biochemistry doi: 10.1021/acs.biochem.9b0053[2] Kim et al 2020 Nat. Com. doi 10.1038/s41467-019-13942-4[3] Masayuki and Corey 2016 Nat. Rev. Drug Discovery doi 10.1038/nrd.2016.117