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折叠的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3D折叠结构RNA的吸收是加深我们对生命过程的理解的关键要求[3]。我们将使用在英国道尔顿坎布里安设施(DCF)独有的快氦离子。这些离子在亚纳米尺度上产生小颗粒状的损伤，可以有效地切割折叠的RNA。当单个离子穿过RNA结构时，折叠的RNA的邻近部分更有可能碎裂在一起。因此，出现的片段更常见地表明折叠结构中相互靠近的部分。学生将开发一种新的程序来利用这种现象：1)照射简单的RNA结构并分析碎片以确定最佳化学条件，2)优化和确定将Poly-A尾巴放在离子损伤末端的效率作为下一代测序的先决条件，3)完善磁珠捕鱼以去除不包含相同邻近信息的分离末端片段，4)将以上步骤1-3与下一代测序相结合，产生可推断邻近图和折叠结构的数据。这一过程将对日益复杂的结构重复，从Add1-适体和RNA拼图收集开始，5)开发分析技术来获取测序数据，并将其转换为RNA不同部分之间的接近程度的地图。从事此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，并将有机会为结构生物学的重大突破做出贡献。1]Richardson等人2019年生物化学DOI：10.1021/acs.BioChem.9b0053[2]Kim等人2020年NAT。COM。DOI 10.1038/s41467-019-13942-4[3]Masayuki和Corey 10.1038 NAT。药品发现版本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