ENERGETICS OF THE MECHANO-CHEMICAL COUPLING IN DNA ON THE NANOMETER LENGTH SCAL

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 我们要求计算资源用于两个不同体系的自由能计算，即DNA超螺旋的拓扑异构酶松弛和DNA与聚酰胺胺(PAMAM)树枝状大分子的相互作用。这两个系统都涉及了解纳米尺寸物体(即分别是酶和树枝状大分子)影响长片段DNA机械力化学能力背后的驱动力。拓扑异构酶是细胞过程中最重要的酶，也是重要的化疗靶点。我们正在计算在有和没有强力抗癌药物拓扑替康的情况下，人类拓扑异构酶I对DNA超螺旋松弛的自由能分布。PAMAM树枝状大分子显示出作为一种潜在的将基因输送到细胞用于治疗目的的系统的前景。我们计划用分子动力学模拟方法研究第三代PAMAM树状大分子与24个碱基对的dsDNA之间的相互作用。不是从与DNA复合的树状大分子开始，而是使用伞状取样将树状大分子拉向DNA链，以了解相互作用是如何启动的。这些模拟的反应坐标将是两个分子的质心之间的距离。以往对树枝状大分子与带负电表面相互作用的模拟表明，随着纳米粒子接近表面，树枝状大分子的形态会发生变化。因此，我们预计最终的树状大分子-DNA复合体将涉及树状大分子和DNA的结构变化。利用加权直方图分析方法，对反应坐标的分布函数进行去偏处理，生成自由能函数。将计算树枝状大分子的非球形度，以分析树枝状大分子接近DNA时的形态。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We request computational resources for the free energy calculations of two distinct systems, the relaxation of DNA supercoils by topoisomerase and the interaction of DNA with Polyamidoamine (PAMAM) dendrimers. Both systems involve understanding the driving forces behind the ability of nanometer sized objects (i.e. an enzyme and a dendrimer respectively) to affect the mechano-chemistry of long stretches of DNA. Topoisomerases are enzymes of quintessential importance to cellular processes and are an important chemotherapeutic target. We are calculating the free energy profiles of relaxation of DNA supercoils by Human Topoisomerase I with and without the potent anti-cancer drug Topotecan. PAMAM dendrimers show promise as a potential system for delivery of genes to cells for therapeutic purposes. We plan to study the interactions between a generation 3 PAMAM dendrimer and a 24 base-pair dsDNA using molecular dynamics simulations. Rather than start with the dendrimer complexed with the DNA, umbrella sampling will be used to pull a dendrimer toward the strand of DNA in order to see how the interaction is initiated. The reaction coordinate for these simulations will be the distance between the centers of mass of the two molecules. Previous simulations on the interactions between dendrimers and negatively charged surfaces show that the morphology of the dendrimer changes as the nanoparticle approaches the surface. We expect, therefore, that the final dendrimer-DNA complex will involve structural changes in both the dendrimer and the DNA. The weighted histogram analysis method will be used to unbias the distribution function of the reaction coordinate and generate a free energy prole. Asphericity of the dendrimer will be calculated to analyze the morphology of the dendrimer as it approaches the DNA.