Modeling the Molecular Forces Driving the Structure, Folding, and Misfolding of Nucleic Acids

南加州大学的Chi H. Mak获得了化学学部化学理论、模型和计算方法项目的奖励，研究决定核酸结构的分子驱动力。核酸DNA和RNA是细胞生命周期的核心。双螺旋结构在人类基因组中普遍存在，但当基因数据以双链形式保存时，DNA在复制、转录、重组和修复过程中也呈现出多种多样的、短暂的单链结构。在细胞中，DNA和RNA浸泡在周围的水溶剂环境中，与周围的带电物质（如Mg+2）一起。该项目的重点是开发和应用一个准确和有效的模型，以了解和量化这种环境在确定驱动DNA和RNA折叠和错误折叠的力量中的作用。利用该模型设计了一种新的计算算法，可以直接模拟折叠和展开过程，具有原子级精度，大大提高了数值计算效率。这使得全面的结构动力学模拟能够研究dna、rna及其杂交体在双链和单链形式之间转换过程中的错误折叠，这是理解它们在细胞中的功能和调控的关键过程。该项目的教育和推广部分旨在将基于发现的科学的一些自然兴奋恢复到本科化学课程中。正在开发一个可扩展的虚拟平台，用于数字数据共享和学生协作，以增加和增强学生的亲自实验室体验。作为项目的一部分，一个在iOS和Android设备以及标准网络浏览器上运行的移动应用程序将为基于云的协作环境提供一个接口。该平台将用于南加州当地的初高中学生的推广工作，并将提供采用低成本、易得、无害材料的实验设计，用于学生和教师之间可扩展的虚拟协作和互动。该项目的目标是制定严格的理论和有效的计算策略，以了解决定核酸如何折叠的基本驱动力，以及当它们错误折叠时导致的异常功能。项目中开发的折叠算法基于麦教授开发的磷酸糖主链构象自由能的分析公式，使用分析和半分析模型来描述溶剂和反作用力对核酸结构的影响，为从头折叠dna和rna提供了一个计算效率高、遍历性高的数值平台。这些研究的重点是理解和量化溶剂和反离子诱导的三种特定类型的相互作用：碱基堆叠力、反向配对相互作用及其衍生的互补识别机制，以及离子诱导的特异性和非特异性链内吸引力。分析理论和数值模拟都被用来揭示和量化这些力量。将这些相互作用模型集成到新的蒙特卡罗折叠算法中，该项目将重点研究与ssDNA和RNA生理学相关的两个具体问题：(1)基因组中过度扩增的三核苷酸（CNG）或六核苷酸（GGGGCC）重复序列转录的mrna上的非规范二级结构；(2)r环的过度积累与移位的单链DNA的序列和环长度以及RNA/DNA杂交的稳定性以及结合这些r环的上下游双链DNA的超卷曲有关。教育和推广活动包括开发一个可访问网络的、可扩展的虚拟环境，以实现实验设计和数据的共享，并促进学生和教师之间的协作互动，在化学实验课程和课程中鼓励和发展基于探究的科学。

Chi H. Mak of the University of Southern California is supported by an award from the Chemical Theory, Models and Computational Methods program in the Chemistry Division to study the molecular driving forces that determine the structures of nucleic acids. The nucleic acids DNA and RNA are central to the life cycle of the cell. The double helix is ubiquitous in the human genome, but while genetic data is safeguarded in double-stranded form, DNA also assumes diverse, transient, single-stranded structures during replication, transcription, recombination, and repair processes. In the cell, DNA and RNA are immersed in a surrounding water solvent environment, together with ambient charged species such as Mg+2. This project focuses on developing and applying an accurate and efficient model to understand and quantify the role of this environment in determining the forces that drive the folding and misfolding of DNA and RNA. The model is used to design a new computational algorithm that can directly simulate folding and unfolding processes with atomic-level accuracy and significantly improved numerical efficiency. This enables full-scale structural dynamical simulations to study misfolding of DNAs, RNAs and their hybrids during transitions between double-stranded and single-stranded forms, processes critical to understanding their function and regulation in the cell. The education and outreach component of the project is aimed at restoring some of the natural excitement of discovery-based science into the undergraduate chemistry curriculum. A scalable virtual platform for digital data-sharing and student collaboration is being developed to augment and enhance the student in-person laboratory experience. A mobile app designed as part of the project and running on iOS and Android devices and standard web browsers will provide an interface to the cloud-based collaborative environment. The platform will be utilized in outreach efforts to middle school and high school students in the local Southern California region, and will make available experimental designs that employ low-cost, readily-available, non-hazardous materials for scalable virtual collaboration and interactions among students and their teachers.The goal of this project is to formulate rigorous theories and efficient computational strategies to understand the fundamental driving forces that dictate how nucleic acids fold, and the aberrant functions that result when they misfold. Based on an analytical formula for the conformational free energy of the sugar-phosphate backbone developed by Professor Mak, the folding algorithm developed in the project uses analytical and semi-analytical models to describe solvent- and counterion-mediated forces dictating the structures of nucleic acids, yielding a computationally efficient and highly ergodic numerical platform for folding DNAs and RNAs from scratch. These studies focus on understanding and quantifying three specific types of solvent- and counterion-induced interactions: base stacking forces, back pairing interactions and complementary recognition mechanisms derived from them, and ion-induced specific and nonspecific intra-chain attractions. Both analytical theories and numerical simulations are being used to unravel and quantify these forces. With these interaction models integrated into a new Monte Carlo folding algorithm, the project focuses on studying two specific problems related to ssDNA and RNA physiology: (1) noncanonical secondary structures on mRNAs transcribed from overexpanded trinucleotide (CNG) or hexanucleotide (GGGGCC) repeats in the genome, and (2) the overaccumulation of R-loops as a function of sequence and loop length of the displaced single-stranded DNA as well as stability of the RNA/DNA hybrid and supercoiling in the upstream or downstream double-stranded DNA bounding these R-loops. Educational and outreach activities include the development of a web-accessible, scalable virtual environment to enable sharing of experimental designs and data, and facilitate collaborative interactions among students and instructors, to encourage and develop the excitement of inquiry-based science within chemistry laboratory courses and curricula.