Sundar Rajan Vinoth, Levin Sune, McCauley Micah J, Williams Mark C, Rouzina Ioulia, Wilhelmsson L Marcus, Westerlund Fredrik
Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
Nucleic Acids Res. 2025 Jan 7;53(1). doi: 10.1093/nar/gkae1183.
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.
人们普遍认识到，双链DNA（dsDNA）在细胞中会受到强大且动态的机械力作用。在不断增加的张力下，B-DNA（DNA最稳定的双链形式）会协同伸长，转变为S-DNA和单链DNA（ssDNA）的混合物。尽管付出了巨大努力，但S-DNA的结构、能量学、动力学及生物学作用仍不清楚。我们在此使用光镊拉伸具有可变数量三环胞嘧啶（tC）修饰的60个碱基对（bp）的dsDNA寡核苷酸。我们观察到B-DNA和S-DNA之间存在多个快速协同且可逆的双态转变。值得注意的是，tC修饰增加了转变力，同时由于dsDNA末端的磨损逐渐增加，降低了转变延伸和自由能。我们量化了经历B到S转变的碱基对平均数量以及自由能和速率。这使我们能够在没有力的情况下重建B到S的自由能分布。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解链快得多。我们推测S-DNA可能作为一种瞬时中间体，例如在分子马达诱导的局部dsDNA链分离中发挥作用。
