Meng He, Bosman Johan, van der Heijden Thijn, van Noort John
Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands.
Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands.
Biophys J. 2014 Mar 4;106(5):1174-81. doi: 10.1016/j.bpj.2014.01.017.
DNA responds to small changes in force and torque by over- or undertwisting, forming plectonemes, and/or melting bubbles. Although transitions between either twisted and plectonemic conformations or twisted and melted conformations have been described as first-order phase transitions, we report here a broadening of these transitions when the size of a topological domain spans several kilobasepairs. Magnetic tweezers measurements indicate the coexistence of three conformations at subpicoNewton force and linking number densities ∼-0.06. We present a statistical physics model for DNA domains of several kilobasepairs by calculating the full partition function that describes this three-state coexistence. Real-time analysis of short DNA tethers at constant force and torque shows discrete levels of extension, representing discontinuous changes in the size of the melting bubble, which should reflect the underlying DNA sequence. Our results provide a comprehensive picture of the structure of underwound DNA at low force and torque and could have important consequences for various biological processes, in particular those that depend on local DNA melting, such as the initiation of replication and transcription.
DNA通过过度扭曲或欠扭曲、形成超螺旋以及/或者解链泡来响应力和扭矩的微小变化。尽管扭曲构象与超螺旋构象之间或扭曲构象与解链构象之间的转变已被描述为一级相变，但我们在此报告，当拓扑结构域的大小跨越几千碱基对时，这些转变会变宽。磁镊测量表明，在亚皮牛顿力和大约-0.06的连环数密度下，三种构象共存。我们通过计算描述这种三态共存的完整配分函数，提出了一个针对几千碱基对的DNA结构域的统计物理模型。在恒定力和扭矩下对短DNA链进行实时分析，显示出离散的伸长水平，代表解链泡大小的不连续变化，这应该反映了潜在的DNA序列。我们的结果提供了在低力和扭矩下负超螺旋DNA结构的全面图景，并且可能对各种生物学过程产生重要影响，特别是那些依赖于局部DNA解链的过程，例如复制和转录的起始。
