In duplex DNA, the continuous sugar phosphate backbones prevent the double helix from significant bending, but breaks in the duplex such as nicks, gaps, and flaps present points at which significant bending is possible. The conformational dynamics of these aberrant structures remains poorly understood. Two factors can maintain the duplexlike conformation of these aberrant structures, these being the hydrophobic and aromatic stacking interactions of the nucleobases, and the electrostatic repulsion of the negatively charged backbones. Using confocal single-molecule Förster resonance energy transfer on nicked and gapped DNA structures, we compare the relative contributions of these two factors by modulating the electrostatic repulsion through mono- and divalent cation concentrations. Base stacking interactions dominate the dynamics of nicked DNA, making it behave essentially like duplex DNA. Gapped structures have weaker base stacking and thus backbone electrostatic repulsion becomes important, and shielding from cations results in an average increase in bending around the gap. This bending of gapped structures could be interpreted by increased flexibility of unstacked structures, transient unstacking events, or a combination of the two. Burst variance analysis (BVA) and analysis by photon-by-photon hidden Markov modeling (H²MM), methods capable of detecting submillisecond dynamics of single molecules in solution, only revealed a single state, indicating that dynamics are occurring at time scales shorter than microseconds.

中文翻译：

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碱基堆积和静电排斥对DNA缺口和缺口的相对贡献

在双链体DNA中，连续的糖磷酸主链可防止双螺旋显着弯曲，但双链体中的断裂（如缺口，缺口和襟翼）则存在可能发生显着弯曲的点。这些异常结构的构象动力学仍然知之甚少。两个因素可以维持这些异常结构的双链状构象，它们是核碱基的疏水和芳族堆积相互作用，以及带负电荷的主链的静电排斥。使用在有缺口和有缺口的DNA结构上共聚焦单分子Förster共振能量转移，我们通过调节单价和二价阳离子浓度的静电排斥来比较这两个因素的相对贡献。碱基堆叠相互作用主导着刻痕DNA的动力学，使它的行为基本上像双链DNA。带间隙的结构的碱基堆积较弱，因此骨架的静电排斥变得很重要，而对阳离子的屏蔽会导致间隙周围弯曲的平均增加。间隙结构的这种弯曲可以通过未堆叠结构的灵活性增加，瞬态未堆叠事件或两者的组合来解释。爆发方差分析（BVA）和通过光子逐个光子隐马尔可夫建模（H 或两者结合。爆发方差分析（BVA）和通过光子逐个光子隐马尔可夫建模（H 或两者结合。爆发方差分析（BVA）和通过光子逐个光子隐马尔可夫建模（H能够检测溶液中单个分子的亚毫秒动态变化的方法（仅² MM）仅显示一种状态，这表明动态发生的时间尺度短于微秒。