Single-Molecule Study of Biopolymers in Complex Solutions

ID：MPS/DMR/BMAT（7623）1006737 PI：萨利赫、奥马尔 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智力优势：该项目将研究各种序列的单链DNA（ssDNA）分子在各种溶液条件下的弹性，并量化多价抗衡离子和拥挤剂对生物聚合物结构动态方面的影响。 该研究计划旨在产生明确的，定量的物理原理，控制生物细胞中遇到的拥挤，富盐环境中的离子生物聚合物行为。PI将直接量化各种序列的ssDNA的物理参数，并试图解决ssDNA的局部刚度的序列依赖性上的矛盾结果。 他将研究ssDNA碱基堆积产生棒状统计单体的能力;棒状聚合物已被预测（尽管未被证明）具有新颖的弹性行为。 多价溶液静电学是一个尚未解决的重大理论问题，本研究的各种化合价的盐的影响将提供明确的数据解决静电学的复杂问题。 该方法将提供可能验证或否定某些理论的数据。 分子拥挤是一种普遍的和非特异性的相互作用，促进紧凑的生物分子构象，从而影响折叠的生物聚合物和大分子结合平衡的稳定性。 这些都是基本且普遍存在的生物分子过程，针对该问题提出的实验方法将为这一重要问题提供基本见解。 具体来说，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各种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缩放图和单分子拉伸实验之间建立的联系。 拟议的实验是基于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直接敏感，因此可以全面探测聚合物的微观物理。 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techniques.BROADER IMPLEMENTATION：ssDNA的机械性能的基础上的各种生物，生物技术和生物材料的问题。 任何包括非结构化ssDNA的模型都必须准确描述未折叠状态的序列依赖性构象。 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，ssDNAs的机械响应的测量可以导致它们在基于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实习生的暑期项目，他们将从传统上在物理科学中代表性不足的学生的校园计划中招募。 实习生将直接与研究生一起从事这个项目。 他们将学习各种各样的技能，适合这种跨学科的努力，包括生物分子合成，耦合化学，定量数据采集和分析。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，他们将获得大量的接触和经验，以开展尖端的跨学科研究所需的广泛活动。 最后，指导研究生将获得宝贵的经验，作为教师和研究项目的主任;这应该直接为他未来的科学生涯做好准备，作为一个研究小组的领导者，以及通过更好地理解如何将日常研究与大局目标相联系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.