BioSystems and Micromechanics, Singapore-MIT Alliance for Research and Technology , Singapore 138602, Singapore.
J Am Chem Soc. 2014 Nov 12;136(45):16073-80. doi: 10.1021/ja5090805. Epub 2014 Nov 4.
Double-stranded DNA can exist in multiple structures, including three recently identified overstretched structures (peeled ssDNA, DNA bubble, and S-DNA) for torsion-unconstrained DNA under large tension. Here, we report systematic studies of interconversion between these overstretched DNA structures induced by changing NaCl concentration at constant force. At forces above 70 pN where DNA exists in one of the overstretched states, direct interconversions between S-DNA and DNA bubble for the end-closed DNA construct, as well as interconversions between S-DNA and peeled ssDNA for the end-opened DNA construct, were observed to involve stepwise extension changes. Interestingly, compared to other conversions, the conversion from peeled ssDNA to S-DNA has ultraslow kinetics, which can be explained by formation of secondary hairpin structures on a relaxed strand of peeled ssDNA. Our findings provide important insights into the structures of torsion-unconstrained DNA under large force.
双链 DNA 可以存在于多种结构中，包括三种最近确定的超拉伸结构（去缠绕 ssDNA、DNA 泡和 S-DNA），用于在大张力下对无扭转限制的 DNA。在这里，我们报告了在恒定力下通过改变 NaCl 浓度诱导这些超拉伸 DNA 结构之间相互转换的系统研究。在力大于 70 pN 时，DNA 存在于超拉伸状态之一，对于端封闭的 DNA 结构，直接在 S-DNA 和 DNA 泡之间以及对于端开口的 DNA 结构，直接在 S-DNA 和去缠绕 ssDNA 之间进行的相互转换都涉及逐步的延伸变化。有趣的是，与其他转换相比，从去缠绕 ssDNA 到 S-DNA 的转换具有超慢的动力学，这可以通过在去缠绕 ssDNA 的松弛链上形成二级发夹结构来解释。我们的发现为大张力下无扭转限制的 DNA 结构提供了重要的见解。
