The A/B transition is a basic element of DNA conformational change. Because of its involvement in the sensing of the ionic conditions by DNA and in specific protein–DNA interactions, this transition is important for biological functions of DNA. Therefore, accurate modeling of the A/B equilibrium by means of empirical force fields is of utmost interest. In this work, we examine the A/B equilibrium in three AMBER force fields, including the recent bsc1 and OL15 modifications, using much longer MD simulations than attempted before. Special attention is paid to the coupling of the A/B equilibrium with the south/north (S/N) transition of the sugar pucker. We found that none of the tested force fields provided a satisfactory description of the A/B equilibrium because the B-form was predicted to be much too stable and the A-form was predicted to be almost absent even in concentrated trifluoroethanol solutions. Based on comparison with NMR data for duplexes and single nucleosides, we hypothesize that this problem arose from the incorrect description of the S/N equilibrium of sugar pucker, where the south conformation is much too stable, thus stabilizing the B-form. Because neither the A/B equilibrium in duplexes nor the S/N equilibrium in nucleosides was described accurately, further refinements of the AMBER DNA force fields are needed.

中文翻译：

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AMBER力场中A到B-DNA的转变及其与糖折叠的耦合

A / B转换是DNA构象变化的基本要素。由于它参与了DNA对离子条件的感应以及特定的蛋白质-DNA相互作用，因此这种转变对于DNA的生物学功能非常重要。因此，利用经验力场对A / B平衡进行精确建模非常重要。在这项工作中，我们使用比以前尝试的更长的MD模拟来检查三个AMBER力场（包括最近的bsc1和OL15修改）中的A / B平衡。特别要注意A / B平衡与制糖器的南/北（S / N）过渡的耦合。我们发现，没有测试的力场能提供令人满意的A / B平衡描述，因为即使在浓三氟乙醇溶液中，B形式也非常稳定，而A形式却几乎不存在。基于与双链体和单核苷的NMR数据比较，我们假设此问题源于对糖皱纹的S / N平衡的错误描述，其中南构象过于稳定，因此稳定了B型。由于没有准确描述双链体中的A / B平衡或核苷中的S / N平衡，因此需要进一步完善AMBER DNA力场。我们假设这个问题是由于对糖皱纹的S / N平衡的错误描述引起的，那里的南构象太稳定了，因此稳定了B型。由于没有准确描述双链体中的A / B平衡或核苷中的S / N平衡，因此需要进一步完善AMBER DNA力场。我们假设这个问题是由于对糖皱纹的S / N平衡的错误描述引起的，那里的南构象太稳定了，因此稳定了B型。由于没有准确描述双链体中的A / B平衡或核苷中的S / N平衡，因此需要进一步完善AMBER DNA力场。