Single-Molecule Study of Biopolymers in Complex Solutions

ID：MPS/DMR/BMAT(7623)1006737 PI：Saleh，Omar ORG：加州大学圣巴巴拉分校题目：复杂溶液中生物聚合物的单分子研究该项目将研究不同序列的单链DNA分子在各种溶液条件下的弹性，并量化多价反离子和聚集剂对生物聚合物结构动态方面的影响。这项研究计划旨在得出明确的、定量的物理原理，管理离子生物聚合物在生物细胞中遇到的那种拥挤、富盐环境中的行为。等电点将直接量化不同序列的单链DNA的物理参数，并试图解决关于单链DNA局部刚性的序列相关性的相互矛盾的结果。他将研究单链DNA碱基堆积产生棒状统计单体的能力；棒状聚合物已被预测(尽管尚未证明)具有新的弹性行为。多价溶液静电学是一个尚未解决的重大理论问题，对不同价态盐的影响的研究将为溶液静电学的复杂问题提供清晰的数据。该方法将提供可能验证或无效某些理论的数据。分子拥挤是一种普遍的、非特异性的相互作用，它促进紧密的生物分子构象，从而影响折叠生物聚合物的稳定性和大分子结合平衡。这些都是基本的和普遍存在的生物分子过程，对这个问题提出的实验方法将为这个重要问题提供基本的见解。具体地说，PI将测量拥挤溶液中单个聚合物的构象，并将直接测试最近预测不同拥挤浓度下压实程度的理论。所有的实验都旨在帮助验证PI和同事最近在聚合物的比例图和单分子拉伸实验之间建立的联系。建议的实验是基于PI实验室独特的低力拉伸能力。聚合物的低力弹性对单体之间的短程和长程相互作用都直接敏感，因此可以全面地探索聚合物的微观物理。在这方面，假设低力技术优于传统的高力方法，也可能比常用的散射技术有优势。BROADER影响：单链DNA的机械性能是各种生物、生物技术和生物材料问题的基础。任何模型，包括非结构的单链DNA，都必须准确地描述未折叠状态的序列依赖的构象。该项目的数据将为这些模型提供基本的输入参数，从而影响我们对分子生物学过程(例如RNA折叠)以及dsDNA的气泡形成和变性转变的理解。此外，对单链DNA的机械响应的测量可能导致它们在基于DNA的纳米结构中的合理使用和更好的分子信标设计。最后，这项工作的一部分将被用作本科生实习生的暑期项目，实习生将从校园项目中招募，这些项目针对的是传统上在物理学科中代表性较低的学生。实习生将直接与研究生一起工作在这个项目上。他们将学习与这种跨学科努力相适应的各种技能，包括生物分子合成、耦合化学以及定量数据获取和分析。实习生将参加小组会议，做报告，并就他们的工作写一篇期末论文。因此，他们将在开展尖端跨学科研究所需的广泛活动中获得大量接触和经验。最后，指导研究生将获得作为教师和研究项目主任的宝贵经验；这将直接为他作为研究小组组长的未来科学职业生涯做好准备，并通过更好地理解如何将日常研究与大局目标联系起来来提高他目前工作的质量。

ID: MPS/DMR/BMAT(7623) 1006737 PI: Saleh, Omar ORG: University of California, Santa BarbaraTitle: Single-Molecule Study of Biopolymers in Complex SolutionsINTELLECTUAL MERIT: The project will study the elasticity of single-stranded DNA (ssDNA) molecules of various sequences in a variety of solution conditions, and quantify the effects of multivalent counterions and crowding agents on dynamic aspects of biopolymer structure. The research program is designed to result in clear, quantitative physical principles governing ionic biopolymer behavior in the kind of crowded, salt-rich environments encountered in biological cells. The PI will directly quantify the physical parameters of ssDNA of various sequences, and attempt to resolve conflicting results on the sequence-dependence of ssDNA's local stiffness. He will investigate the ability of ssDNA base-stacking to create rod-like statistical monomers; rod-like polymers have been predicted (though not demonstrated) to have novel elasticity behaviors. Multivalent solution electrostatics represents a major unsolved theoretical problem, and this study of the effect of salts of various valencies will give clear data on complex issues of solution electrostatics. The approach will provide data that may validate or invalidate certain theories. Molecular crowding is a universal and non-specific interaction that promotes compact biomolecular conformations, thus affecting the stability of folded biopolymers and macromolecular binding equilibria. These are fundamental and ubiquitous biomolecular processes, and the proposed experimental approach to this problem will provide basic insight into this important problem. Specifically, the PI will measure the conformation of individual polymers in a crowded solution and will directly test recent theories that predict the magnitude of compaction at various crowded concentrations. All of the experiments are designed to help validate the link recently forged by the PI and coworkers between the scaling picture of polymers and single-molecule stretching experiments. The proposed experiments are based on the unique low-force stretching capabilities of the PI's lab. A polymer's low-force elasticity is directly sensitive to both the short- and long-range interactions between the monomers and thus can comprehensively probe the microscopic physics of the polymer. In this respect, the low-force technique is hypothesized to outperform traditional high-force methods, and may also have advantages over commonly-used scattering techniques.BROADER IMPACTS: The mechanical properties of ssDNA underlie a variety of biological, biotechnological, and biomaterials problems. Any model including unstructured ssDNAs must accurately describe the sequence-dependent conformation of the unfolded state. Data from this project will provide basic input parameters for such models, and thus will impact our understanding of processes in molecular biology (e.g. RNA folding) and bubble formation and denaturation transitions of dsDNA. Further, the measurements of the mechanical response of ssDNAs could lead to their rational use within DNA-based nanostructures and better design of molecular beacons. Finally, parts of this work will be used as a summer project for undergraduate interns, who will be recruited from on-campus programs for students traditionally under-represented in the physical sciences. The interns will work directly alongside the graduate student working on this project. They will learn a wide variety of skills appropriate to this interdisciplinary effort, including biomolecular synthesis, coupling chemistries, and quantitative data acquisition and analysis. The interns will attend group meetings, give presentations, and write a final paper on their work. Thus, they will gain significant exposure and experience to a wide range of activities needed to carry out cutting-edge interdisciplinary research. Finally, the mentoring graduate student will receive invaluable experience as a teacher and director of a research project; this should directly prepare him for a future scientific career as a research group leader, as well as improve the quality of his present work through a better understanding of how to relate day-to-day research with big-picture goals.