DNA Melting in Solution

描述（由申请人提供）：DNA解链机制的细节对于生物学和生物技术的许多方面都是至关重要的。最近，实验表明，即使对于相对较短的结构，也至少涉及三个状态。为了帮助澄清的反应坐标和机制的熔融转变的DNA，我们建议使用理论和计算方法。我们将在高于序列特异性解链温度的温度下模拟游离寡聚物双链体和发夹在显式盐水中的解链过程。对轨迹的分析将揭示在不同时间尺度上发生的各种重要的生化过程。用理论技巧来增强这一点，我们将使用坐标来绘制自由能表面。这项研究的结果将是确定合理的反应坐标的熔融过渡。不同几何形状的这些差异（游离低聚物与发夹等）和序列将可用于鉴定在复制、转录、重组和DNA修复过程中发生的各种相关状态和动力学陷阱以及生物技术应用。 公共卫生相关性DNA熔解是双链DNA通过生物手段或加热或引入某些化学物质分离成单链的过程。对DNA链如何偶联和解偶联的基础研究与公共卫生问题有着巨大的相关性，因为这种机制对于理解DNA错配、疾病表达和相关基因治疗非常重要。对DNA熔解的研究直接应用于开发和治疗灾难性疾病，如癌症，糖尿病和其他遗传性疾病，以及设计基于基因的诊断工具，如DNA微阵列。

DESCRIPTION (provided by applicant): The details of the mechanism for DNA melting are fundamental to many aspects of biology and biotechnology. Recently, it has been shown experimentally that there are at least three states involved even for relatively short structures. To help clarify the reaction coordinate and mechanism of the melting transition of DNA we propose to use theoretical and computational methods. We will simulate the melting process for both free oligomer duplexes and hairpins in explicit salt water at temperatures above the sequence specific melting temperature. Analysis of the trajectories will reveal the various biochemically important processes that occur on different time scales. Augmenting this with theoretical techniques we will use the coordinates to map out free energy surfaces. An outcome of this research will be to identify plausible reaction coordinates for the melting transition. How these differ for various geometries (free oligomers vs hairpins etc.) and sequences will be useful in identifying various relevant states and kinetic traps that occur during replication, transcription, recombination, and DNA repair as well as in biotechnological applications. PUBLIC HEALTH RELEVANCE DNA melting is the process by which double-stranded DNA separates into single strands by biological means or heat or the introduction of certain chemicals. Basic research into how DNA strands couple and uncouple has tremendous relevance to issues of public health as this mechanism is important for understanding DNA mismatches, disease expression, and associated gene therapies. Research into DNA melting has direct application to the development and treatment of catastrophic diseases such as cancer, diabetes, and other genetically inherited diseases, as well as the design of gene based diagnostic tools, like DNA microarrays.