RUI: Investigating DNA Deformation Induced by Cation Binding Using Computational Analysis of X-ray Crystal Structures

众所周知，DNA含有构建活生物体的指令。不太为人所知的是，这些指令中的许多并没有直接使用。实际使用的指令部分取决于DNA的弯曲和折叠方式。因此，了解DNA变形的机制对于理解DNA在遗传信息存储和表达中的功能是非常重要的。这个项目研究了阳离子结合扭曲DNA的趋势。该项目的实验重点包括使用计算分析来测试阳离子诱导两种类型DNA变形的能力：(1)在弯曲和凹槽变窄时发生的磷酸盐拥挤；(2)离子通过阳离子-圆周率相互作用与碱基面相互作用而使碱基脱栈。分析了单价阳离子蛋白质侧链在DNA/蛋白质复合体晶体结构中诱导DNA磷酸拥挤的能力。该项目还将通过对DNA晶体结构的计算分析来表征DNA中的阳离子-pi相互作用，并确定与各种二价阳离子的DNA络合物的晶体结构。广泛影响：从事这一跨学科研究的学生将学习在实验上确定晶体结构的重要技能，以及分析数据库中可用结构信息的计算技能。本文描述的项目将培养科学思维技能和编程技能，当与实际结构确定技能相结合时，将给学生提供结构生物学这些共生方面的全面体验。通过与两个主要研究机构密切合作并前往两个主要研究机构收集和分析结晶学数据，学生的教育将进一步扩大。

It is well known that DNA contains the instructions for building live organisms. Less well known is that many of these instructions are not used directly. Which instructions are actually used is partially determined by how the DNA is bent and folded. Therefore, understanding the mechanisms by which DNA is deformed is important to understanding the function of DNA in the storage and expression of genetic information. This project investigates the tendency of cation binding to distort DNA. The experimental focus of the project involves using computational analysis to test the ability of cations to induce two types of DNA deformation: (1) phosphate crowding that occurs in bending and groove narrowing; and (2) base unstacking by ions interacting with base faces via cation-pi interactions. The ability of monovalent cationic protein side chains to induce DNA phosphate crowding in crystal structures of DNA/protein complexes will be analyzed. The project will also characterize cation-pi interactions in DNA by computational analysis of DNA crystal structures as well as determines the crystal structures of DNA complexes with various divalent cations.Broader Impacts: Students engaged in this interdisciplinary research will learn skills important in experimentally determining crystal structures as well as computational skills to analyze structural information available in databases. The projects described herein will develop scientific thinking skills and programming skills that when combined with practical structure determination skills, will give the student well-rounded experience of these symbiotic aspects of structural biology. The students' education will be further expanded by close collaboration with and travel to two major research institutions to collect and analyze crystallographic data.