FREE ENERGY PROFILES OF SINGLE STRANDED DNA

单链 DNA 的自由能谱

• 批准号: 7723251
• 负责人: IOAN ANDRICIOAEI
• 金额: $ 0.05万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2009-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7723251
• 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.

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。 最近对单链DNA的单分子实验表明，DNA的形式取决于其形成方法。我们的合作者玛拉·普伦蒂斯已经证明了缓慢的热熔化会产生？短的？单链具有0.54纳米的基础分离，而解链创建一个？很长时间？形成0.7- 0.8nm的碱分离。我们建议通过使用分子动力学来研究这些实验，以计算作为碱基对分离的函数的单链DNA的自由能分布。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，我们想借此机会探讨Teragrid资源，以备将来的拨款要求。