He Yichen, Shang Yazhuo, Liu Yu, Zhao Shuangliang, Liu Honglai
State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237 China.
State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237 China.
Springerplus. 2015 Dec 15;4:777. doi: 10.1186/s40064-015-1581-7. eCollection 2015.
DNA melting has attracted much attention due to its importance in understanding the life-reproduction and metabolism and in the applications of modern DNA-based technologies. While numerous works have been contributed to the determination of melting profiles in diverse environments, the understanding of DNA melting dynamics is still limited. By employing three-site-per-nucleotide (3SPN) double-stranded DNA (dsDNA) model, we here demonstrate the melting dynamics of an isolated short dsDNA under different conditions (different temperatures, ionic concentrations and DNA chain lengths) can be accessed by coarse-grained simulation studies. We particularly show that at dilute ionic concentration the dsDNA, regardless being symmetric or asymmetric, opens at both ends with roughly equal probabilities, while at high ionic concentration the asymmetric dsDNA chain opens at the A-T-rich end. The comparisons of our simulation results to available data are discussed, and overall good agreements have been found.
由于DNA解链在理解生命繁殖与代谢以及现代基于DNA的技术应用方面具有重要意义，它已备受关注。尽管已有众多研究致力于确定不同环境下的解链曲线，但对DNA解链动力学的理解仍较为有限。通过采用每核苷酸三位点（3SPN）双链DNA（dsDNA）模型，我们在此证明，通过粗粒度模拟研究，可以了解不同条件（不同温度、离子浓度和DNA链长度）下孤立短双链DNA的解链动力学。我们特别表明，在稀离子浓度下，双链DNA无论对称与否，两端打开的概率大致相等，而在高离子浓度下，不对称双链DNA链在富含A-T的一端打开。我们讨论了模拟结果与现有数据的比较，总体上发现吻合度良好。
