FREE ENERGY PROFILES OF SINGLE STRANDED DNA

单链 DNA 的自由能谱

• 批准号: 7601514
• 负责人: IOAN ANDRICIOAEI
• 金额: $ 0.03万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7601514
• 关键词: Base Pairing; Computer Retrieval of Information on Scientific Projects Database; Condition; DNA; Free Energy; Funding; Future; Grant; Institution; Methods; Research; Research Personnel; Resources; Single-Stranded DNA; Source; Temperature; United States National Institutes of Health; base; melting; molecular dynamics; research study; single molecule

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. Recent single molecule experiments on single stranded DNA have shown that the form the DNA takes is dependent on its method of formation. Our collaborator Mara Prentiss has shown that slow thermal melting creates ?short? single strands that have a base separation of 0.54 nm while unzipping creates a ?long? form with base separation of 0.7-0.8 nm. We propose to study these experiments by using molecular dynamics to calculate free energy profiles of single stranded DNA as a function of base pair separation. This may require multiple free energy profiles as we study the effects of temperature and initial conditions on the extension. In addition we would like to take this opportunity to explore the Teragrid resources for future requests for allocations.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目及 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 最近对单链 DNA 进行的单分子实验表明，DNA 的形式取决于其形成方法。我们的合作者 Mara Prentiss 已经证明，缓慢的热熔化会造成“短路”。碱基间隔为 0.54 nm 的单链，在解压缩时会产生“长”链。形成碱基间距为 0.7-0.8 nm 的形式。我们建议通过使用分子动力学来计算单链 DNA 的自由能分布作为碱基对分离的函数来研究这些实验。当我们研究温度和初始条件对延伸的影响时，这可能需要多个自由能分布。此外，我们想借此机会探索 Teragrid 资源，以供未来的分配请求。