Predicting the Torsional Dynamics of DNA

虽然DNA的双螺旋结构是众所周知的，但关于其结构如何影响其生物学功能的基本问题仍然存在。通过结构，我们指的是这种惊人的长而灵活的生物聚合物的形状和应力随时间的变化。理解DNA的结构-功能关系取决于分子的扭转动力学的量化，因为扭转涉及所有主要的DNA功能，包括压缩、转录、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揭示DNA在单分子水平上的扭转动力学，从而解决了这一需求。特别是，我们介绍了一种新的检测方法，采用磁性光调制珠（磁-月亮）来测量拴在这些珠上的DNA分子的动态扭曲。同时，我们扩展了一个计算棒模型，该模型描述了栓系DNA-头系统的耦合非线性动力学，使模型能够从伴随的单分子DNA实验中得到验证。我们对DNA扭转动力学的研究对医学和物理科学有更广泛的影响。考虑到特定的抗癌药物（例如拓扑替康）靶向蛋白质（例如拓扑异构酶I），这些蛋白质可以缓解DNA复制过程中扭转应力和超级线圈的积累。通过实质上阻断DNA的扭转松弛，这些药物抑制了患病细胞的分裂（因此繁殖）。提高这些化疗药物的疗效取决于首先了解它们对扭转应力DNA的作用。我们断言，通过系统的实验/理论努力，这种理解最终可能来自DNA扭转力学的基本知识。我们的实验还引入了一种新的分子？捻探测器?以月亮的形状出现。虽然对单分子DNA研究明显有利，但这种新技术可能会转化为其他生物分子系统或纳米级设备的应用，其中分子旋转起主要作用（例如分子马达蛋白，分子轮，轮烷，细菌鞭毛，ATP合成酶，RecA）。

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).