MODELING THE FORCED EXTENSION OF NICKED DNA

这个子项目是许多研究子项目中的一个 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来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 我们请求Teragrid资源用于我们对切口DNA链强制延伸的理论研究。由短寡核苷酸自组装的带切口的DNA链最近已经由co-PI之一进行了实验研究（Kersey等人，J. Am.化学会，126：3038-3039，2004）。在强制延伸过程中，切口链的行为被发现与连续DNA的行为显著不同（参见图1）。Strick等人，Ann. Rev. Bioph.生物分子结构：29：523-543，2000; Harris等人，生物J.，88：1684-1691，2004）。我们试图揭示缺口DNA强制延伸的结构机制，并可能通过操纵DNA序列来学习编程不同延伸机制的方法。所获得的知识可能会促进纳米技术应用的缺口DNA链，并推进我们对关键生物过程的理解，如DNA修复和复制。在一系列转向分子动力学（SMD）模拟中对切口DNA的延伸进行建模（Isralewitz et. al，Curr. Opin. 11：224-230，2001），使用经典MD软件NAMD和AMBER。该模型系统由大约4.5万个原子组成。初步的研究揭示了几种可能的情况下，在强制延伸的切口DNA的结构变化。需要额外的计算资源来收集这些场景的足够的统计样本，探测不同的延伸速度，并研究不同的切口DNA序列。我们要求在Teragrid机器上安装3万个SU。使用NAMD基准测试（http：//www.ks.uiuc.edu/Research/namd/performance.html），我们估计，当在Cray XT 3的16到64个CPU上运行时，10-20纳秒（ns）的典型SMD模拟需要大约4，000 - 8，000个SU;在更快的BlueGene/L机器上只需要1，000 - 2，000个SU。因此，我们的要求相当于在较慢的Teragrid机器上运行5-8次额外的SMD，使我们能够在探测的扩展速度下将目前积累的数据采样大约增加一倍。在更快的Teragrid机器上，分配将相当于20-30次SMD运行，这将使我们能够探测另一个DNA序列，并使用不同的力场重复原始模拟。如果结果令人鼓舞，将向MRAC提交一份继续进行研究的更广泛的建议。

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 Teragrid resources for our theoretical study of the forced extension of nicked DNA chains. Nicked DNA chains, self-assembled from short oligonucleotides, have been recently studied experimentally by one of the co-PIs (Kersey et al., J. Am. Chem. Soc., 126:3038-3039, 2004). The behavior of the nicked chains during the forced extension was found to be remarkably different from that of continuous DNA (cf. Strick et al., Ann. Rev. Bioph. Biomol. Struct., 29:523-543, 2000; Harris et al., Bioph. J., 88:1684-1691, 2004). We seek to uncover the structural mechanism of the nicked DNA forced extension and, perhaps, learn the ways to program different extension regimes by manipulating the DNA sequence. The obtained knowledge may foster nanotechnology applications of nicked DNA chains and advance our understanding of key biological processes, such as DNA repair and replication. The extension of nicked DNA is modeled in a series of steered molecular dynamics (SMD) simulations (Isralewitz et. al, Curr. Opin. Struct. Biol. 11:224-230, 2001), using the classical MD software NAMD and AMBER. The model system consists of around 45 thousand atoms. The preliminary studies reveal several possible scenarios of structural changes of nicked DNA during the forced extension. Additional computational resources are needed to collect a sufficient statistical sampling of these scenarios, probe different extension velocities, and study different sequences of nicked DNA. We request 30,000 SUs on Teragrid machines. Using NAMD benchmarks (http://www.ks.uiuc.edu/Research/namd/performance.html), we estimate that our typical SMD simulation of 10-20 nanoseconds (ns) requires about 4,000-8,000 SUs when run on 16 to 64 CPUs of Cray XT3; only 1,000-2,000 SUs would be required on a faster BlueGene/L machine. Therefore, our request amounts to 5-8 additional SMD runs on slower Teragrid machines, allowing us to approximately double our presently accumulated data sampling at the probed extension velocities. On faster Teragrid machines, the allocation would be equivalent to 20-30 SMD runs, which would enable us to also probe another DNA sequence and repeat the original simulations with a different forcefield. In case of encouraging results, a more extended proposal for continuing the studies will be submitted to MRAC.