Predicting the Torsional Dynamics of DNA

预测 DNA 的扭转动力学

• 批准号: 0825488
• 负责人: Noel Perkins
• 金额: $ 36万
• 依托单位: Regents of the University of Michigan - Ann Arbor
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2012-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0825488&HistoricalAwards=false
• 关键词: Predicting; Torsional; Dynamics; DNA

While the double-helical form of DNA is well-known, fundamental questions remain concerning how its biological functions are influenced by its structure. By structure, we refer to the time-dependent shape and stress of this amazingly long and flexible biopolymer. Understanding DNA structure-function relations rests on quantifying the torsional dynamics of the molecule as torsion is implicated in all major DNA functions including compaction, transcription, replication, gene regulation, gene repair, etc. Our project addresses this need by proposing new experimental and theoretical methods for revealing the torsional dynamics of DNA at the single molecule level. In particular, we introduce a novel detection method employing a magnetic, optically modulated bead (mag-MOON) to measure the dynamic twisting of DNA molecules tethered to these beads. Simultaneously, we extend a computational rod model describing the coupled nonlinear dynamics of the tethered DNA-bead system that enables model validation from the companion single-molecule DNA experiments.Our research on DNA torsional dynamics has broader implications for the medical and physical sciences. Consider that specific anti-cancer drugs (e.g., Topotecan) target proteins (e.g., Topoisomerase I) that relieve the build up of torsional stress and supercoils during DNA replication. By essentially blocking the torsional relaxation of DNA, these drugs inhibit the division (hence propagation) of diseased cells. Increasing the efficacy of these chemotherapeutic drugs rests on first understanding their action on torsionally-stressed DNA. We assert that such understanding may ultimately grow from fundamental knowledge of the torsional mechanics of DNA as achieved through systematic experimental/theoretical efforts. Our experiments also introduce a novel molecular ?twist detector? in the form of a mag-MOON bead. While clearly advantageous for single-molecule DNA studies, this novel technique may translate to uses in other biomolecular systems or nano-scale devices where molecular rotation plays a major role (e.g., molecular motor proteins, molecular wheels, rotaxanes, bacterial flagella, ATP synthase, RecA).

尽管DNA的双螺旋形式是众所周知的，但基本问题仍然涉及其生物学如何受其结构影响。根据结构，我们指的是这种漫长而灵活的生物聚合物的时间相关的形状和压力。理解DNA结构功能关系取决于量化分子的扭转动力学，因为扭转涉及所有主要的DNA函数，包括压实，转录，复制，复制，基因调控，基因修复等。我们的项目通过提出新的实验和理论方法来解决这种需求。特别是，我们采用磁性的，光学调制的珠（Mag-Moon）引入了一种新颖的检测方法，以测量束缚在这些珠子上的DNA分子的动态扭曲。同时，我们扩展了一个计算杆模型，该模型描述了束缚的DNA孔系统的耦合非线性动力学，该模型可以从伴随的单分子DNA实验中验证模型验证。我们对DNA扭转动力学的研究对医学和物理科学具有更广泛的含义。考虑一下特定的抗癌药物（例如拓扑替康）靶蛋白（例如，拓扑异构酶I），可在DNA复制过程中缓解扭转胁迫和超级螺旋的累积。通过基本上阻止DNA的扭转松弛，这些药物抑制了患病细胞的分裂（因此）。 这些化学治疗药物的疗效提高基于首先了解它们对扭转压力DNA的作用。我们断言，这种理解最终可能会从对DNA扭转力学的基本知识中增长，这些知识是通过系统的实验/理论努力实现的。我们的实验还引入了一种新颖的分子？扭曲检测器？以mag-moon珠子的形式。尽管对于单分子DNA研究显然有利，但这种新技术可以转化为其他生物分子系统或纳米尺度设备的用途，其中分子旋转起着主要作用（例如，分子运动蛋白，分子车轮，旋转车轮，旋转型，细菌鞭毛，细菌鞭毛，ATP合酶，Reca）。