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3D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RNA中有少量编码蛋白质，但更多的行为是设计生命的分子过程，因此确定RNA的3D折叠结构是进一步了解生命过程的关键要求[3]。我们将使用快速氦离子，这是英国道尔顿坎布里亚设施（DCF）唯一可用的。这些离子在亚纳米尺度上产生类似于螺丝刀的损伤，可以有效地切割折叠的RNA。当单个离子穿过RNA结构时，折叠RNA的邻近部分更有可能一起断裂。因此，更常见的碎片表示折叠结构中靠在一起的部分。学生将开发一个新的程序来利用这一现象：1）照射简单的RNA结构并分析片段化以确定最佳化学条件，2）优化并确定将聚腺苷酸尾置于离子损伤末端上的效率，作为下一代测序的先决条件，3）完善磁珠钓取以去除分离不包含相同邻近信息的末端片段，4）将上述步骤1-3与下一代测序组合以产生数据，从该数据可以推断出邻近图和折叠结构。对于越来越复杂的结构，将重复此过程，从Add 1-适体和RNA谜题收集开始，并5）开发分析技术，以获取测序数据并将其转换为RNA不同部分的邻近图。从事该项目的学生将有机会在国际领先的，[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

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