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

该子项目是利用 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得主要资金， 因此可以在其他CRISP条目中表示。列出的机构是 中心，不一定是研究者的机构。 我们要求计算资源的自由能计算两个不同的系统，拓扑异构酶和DNA与聚酰胺胺（PAMAM）树枝状大分子的相互作用的DNA超螺旋的松弛。这两个系统都涉及理解纳米尺寸的物体（即分别是酶和树枝状聚合物）影响长段DNA的机械化学的能力背后的驱动力。拓扑异构酶是对细胞过程至关重要的酶，并且是重要的化学治疗靶标。我们正在计算的自由能档案松弛的DNA超螺旋由人类拓扑异构酶I与和没有有效的抗癌药物拓扑替康。PAMAM树枝状聚合物显示出作为用于治疗目的的基因递送至细胞的潜在系统的前景。我们计划使用分子动力学模拟来研究第三代PAMAM树状聚合物和24个碱基对的双链DNA之间的相互作用。而不是从与DNA复合的树枝状聚合物开始，伞形取样将用于将树枝状聚合物拉向DNA链，以观察相互作用是如何开始的。这些模拟的反应坐标将是两个分子质心之间的距离。先前对树枝状聚合物和带负电荷的表面之间的相互作用的模拟表明，随着纳米颗粒接近表面，树枝状聚合物的形态发生变化。因此，我们预计最终的树状聚合物-DNA复合物将涉及树状聚合物和DNA的结构变化。采用加权直方图分析法对反应坐标的分布函数进行去偏处理，生成自由能分布。将计算树枝状聚合物的非球形度，以分析树枝状聚合物接近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.