Albrecht Christian H, Neuert Gregor, Lugmaier Robert A, Gaub Hermann E
Applied Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, 80799 Munich, Germany.
Biophys J. 2008 Jun;94(12):4766-74. doi: 10.1529/biophysj.107.125427. Epub 2008 Mar 13.
Strand separation of double-stranded DNA is a crucial step for essential cellular processes such as recombination and transcription. By means of a molecular force balance, we have analyzed the impact of different pulling directions and different force-loading rates on the unbinding process of short double-stranded DNA. At loading rates above 9 x 10(5) pN/s, we found a marked difference in rupture probability for pulling the duplex in 3'-3' direction compared to a 5'-5' direction, indicating different unbinding pathways. We propose a mechanism by which unbinding at low loading rates is dominated by nondirectional thermal fluctuations, whereas mechanical properties of the DNA become more important at high loading rates and reveal the asymmetry of the phosphoribose backbone. Our model explains the difference of 3'-3' and 5'-5' unbinding as a kinetic process, where the loading rate exceeds the relaxation time of DNA melting bubbles.
双链DNA的链分离是重组和转录等基本细胞过程的关键步骤。通过分子力平衡，我们分析了不同拉伸方向和不同力加载速率对短双链DNA解链过程的影响。在高于9×10⁵ pN/s的加载速率下，我们发现与5'-5'方向相比，沿3'-3'方向拉伸双链时的断裂概率存在显著差异，这表明解链途径不同。我们提出了一种机制，即低加载速率下的解链由非定向热涨落主导，而在高加载速率下DNA的力学性质变得更为重要，并揭示了磷酸核糖骨架的不对称性。我们的模型将3'-3'和5'-5'解链的差异解释为一个动力学过程，其中加载速率超过了DNA熔解泡的弛豫时间。
