Coarse-Graining DNA Energy Landscapes for the Analysis of Hybridization Kinetics

用于杂交动力学分析的粗粒 DNA 能量图

• 批准号: 0506468
• 负责人: Niles Pierce
• 金额: $ 89.63万
• 依托单位: California Institute of Technology
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-09-01 至 2008-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0506468&HistoricalAwards=false
• 关键词: Coarse; Graining; DNA; Energy; Landscapes

DNA is best known as the genetic storage medium for life. However, its unique structural properties make it attractive for engineering nanoscale structures and devices. Remarkably, synthetic DNA systems can be programmed to self-assemble into complex objects implementing dynamic mechanical tasks by appropriately designing the sequence of bases (A,C,G and T) comprising the constituent DNA strands. When mixed, the strands "hybridize" in prescribed ways by forming "base-pairs" between complementary bases (A with T, C with G). DNA nanotechnology explores and develops these capabilities for applications in nanorobotics, nanofabrication, biomolecular computation, biosensing, nanoelectronics and nanomedicine. In principle, equilibrium and kinetic properties of a DNA strand can be characterized by the features of its "free energy landscape". Likely equilibrium structures correspond to deep valleys in the landscape, and the rate of conversion between two structures depends on the nature of the valleys and ridges separating them. The dynamics of a folding DNA strand define a path somewhat analogous to a ball rolling over the landscape. To analyze functional DNA systems with moving parts, it is important to identify large-scale landscape features that dominate experiments. Unfortunately, in practical problems, existing physical models define landscapes with fine-grained detail that obscures the large-scale features. For example, DNA systems commonly have theoretical landscapes containing more states than there are atoms in the universe, though experiments suggest that a small number of features dominate the landscape. The project will develop algorithms for efficiently exploring large landscapes that cannot be enumerated explicitly, including coarse-graining approaches to simulate the temporal evolution of physically meaningful "macrostates" without having to simulate full "microstate" landscapes. These macrostate predictions will guide and interpret experimental studies of DNA systems of fundamental interest to current nanorobotics and biosensing efforts. Custom-built fluorescence instruments will probe free energy landscapes at the level of single molecules. While our expertise in DNA nanotechnology motivates our experiments on synthetic DNA, the new coarse-graining theory, computational algorithms, and experimental methods will be equally applicable to analysis of natural RNA molecules (such as the mutant of human telomerase RNA that is thought to cause dyskeratosis congenita by altering the free energy landscape of a conformational switch). Our research objectives are integral with an education program dedicated to training undergraduates, graduate students, and postdocs in distinctly interdisciplinary research groups that currently involve Applied & Computational Mathematics, Applied Physics, Biochemistry, Bioengineering, Biology, Chemistry, Chemical Engineering, Computer Science, Computation & Neural Systems, and Physics. This is coupled with an outreach program that brings local high school science students to Caltech to discover DNA nanotechnology, meet with lab members in small informal groups, and generate enthusiasm for pursuing careers in science and engineering. We will also continue our policy of freely distributing the source code for our analysis and design software.

DNA被认为是生命的遗传储存媒介。然而，其独特的结构特性使其对工程纳米结构和器件具有吸引力。值得注意的是，合成DNA系统可以通过适当设计构成DNA链的碱基（A、C、G和T）的序列来编程以自组装成执行动态机械任务的复杂物体。当混合时，链通过在互补碱基之间形成“碱基对”（A与T，C与G）以规定的方式“杂交”。 DNA纳米技术探索和发展这些能力，应用于纳米机器人，纳米纤维，生物分子计算，生物传感，纳米电子学和纳米医学。 原则上，DNA链的平衡和动力学性质可以通过其“自由能景观”的特征来表征。可能的平衡结构对应于景观中的深谷，两种结构之间的转换率取决于分隔它们的山谷和山脊的性质。 折叠DNA链的动力学定义了一条有点类似于球在景观上滚动的路径。为了分析具有运动部件的功能DNA系统，重要的是要识别主导实验的大规模景观特征。 不幸的是，在实际问题中，现有的物理模型定义的景观与细粒度的细节，掩盖了大规模的功能。例如，DNA系统通常具有包含比宇宙中原子更多的状态的理论景观，尽管实验表明少数特征主导景观。 该项目将开发算法，用于有效地探索无法明确枚举的大型景观，包括粗粒化方法来模拟物理上有意义的“宏观状态”的时间演变，而不必模拟完整的“微观状态”景观。这些宏观预测将指导和解释DNA系统的基本利益，目前的纳米机器人和生物传感的努力的实验研究。定制的荧光仪器将在单分子水平上探测自由能景观。虽然我们在DNA纳米技术方面的专业知识激发了我们对合成DNA的实验，但新的粗粒化理论，计算算法和实验方法同样适用于分析天然RNA分子（例如人类端粒酶RNA的突变体，被认为通过改变构象开关的自由能景观导致先天性角化不良）。 我们的研究目标是一个教育计划，致力于培养本科生，研究生和博士后在明显的跨学科研究小组，目前涉及应用计算数学，应用物理，生物化学，生物工程，生物学，化学，化学工程，计算机科学，计算神经系统和物理学。与此同时，还开展了一项外展计划，将当地高中理科学生带到加州理工学院，探索DNA纳米技术，与实验室成员在小型非正式小组中会面，并激发他们追求科学和工程职业的热情。我们还将继续我们的政策，免费分发我们的分析和设计软件的源代码。