It is widely appreciated that double stranded DNA (dsDNA) is subjected to strong and dynamic mechanical forces in cells. Under increasing tension B-DNA, the most stable double-stranded (ds) form of DNA, undergoes cooperative elongation into a mixture of S-DNA and single stranded DNA (ssDNA). Despite significant effort, the structure, energetics, kinetics and the biological role of S-DNA remains obscure. We here stretch 60 base pair (bp) dsDNA oligonucleotides with a variable number of tricyclic cytosine, tC, modifications using optical tweezers. We observe multiple fast cooperative and reversible two-state transitions between B-DNA and S-DNA. Notably, tC modifications increase the transition force, while reducing the transition extension and free energy due to progressively increasing fraying of the dsDNA ends. We quantify the average number of bps undergoing the B-to-S transition, as well as the free energies and rates. This allows us to reconstruct the B-to-S free energy profiles in absence of force. We conclude that S-DNA is an entirely force-induced state, and that the B-to-S transition is much faster than internal dsDNA melting. We hypothesize that S-DNA may have a role as a transient intermediate in, for example, molecular motor-induced local dsDNA strand separation.

中文翻译：

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用于 DNA 过度拉伸的力诱导熔解和 S-DNA 通路表现出不同的动力学


人们普遍认为，双链 DNA （dsDNA） 在细胞中受到强大的动态机械力的影响。在张力增加的情况下，B-DNA 是最稳定的双链 （ds） 形式的 DNA，它经历协同延伸，成为 S-DNA 和单链 DNA （ssDNA） 的混合物。尽管付出了巨大的努力，但 S-DNA 的结构、能量、动力学和生物学作用仍然不清楚。我们在这里使用光镊拉伸 60 个碱基对 （bp） dsDNA 寡核苷酸和可变数量的三环胞嘧啶 tC 修饰。我们观察到 B-DNA 和 S-DNA 之间的多个快速协作和可逆的双态转换。值得注意的是，tC 修饰增加了过渡力，同时由于 dsDNA 末端的磨损逐渐增加，减少了过渡延伸和自由能。我们量化了 B-to-S 过渡的平均 bps 数量，以及自由能源和费率。这使我们能够在没有力的情况下重建 B 到 S 自由能分布。我们得出结论，S-DNA 是一种完全由力诱导的状态，并且 B 到 S 的转变比内部 dsDNA 熔解快得多。我们假设 S-DNA 可能在例如分子马达诱导的局部 dsDNA 链分离中起到瞬时中间体的作用。