DNA Melting in Solution

描述（由申请人提供）：DNA融化机制的细节是生物学和生物技术许多方面的基础。最近，实验表明，即使相对较短的结构也至少有三种状态。为了阐明DNA熔融转变的反应坐标和机理，我们建议采用理论和计算方法。我们将模拟在高于序列特定熔化温度的温度下，游离低聚物和发夹在明确的盐水中的熔化过程。对轨迹的分析将揭示在不同时间尺度上发生的各种生物化学重要过程。通过理论技术，我们将使用坐标来绘制自由能面。这项研究的一个结果将是确定熔化转变的合理反应坐标。这些不同几何形状（自由寡聚物与发夹等）和序列的差异将有助于识别在复制，转录，重组和DNA修复以及生物技术应用中发生的各种相关状态和动力学陷阱。

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.