Genetic information is encoded in the DNA double helix, which, in its physiological milieu, is characterized by the iconical Watson-Crick nucleo-base pairing. Recent NMR relaxation experiments revealed the transient presence of an alternative, Hoogsteen (HG) base pairing pattern in naked DNA duplexes, and estimated its relative stability and lifetime. In contrast with DNA, such structures were not observed in RNA duplexes. Understanding HG base pairing is important because the underlying "breathing" motion between the two conformations can significantly modulate protein binding. However, a detailed mechanistic insight into the transition pathways and kinetics is still missing. We performed enhanced sampling simulation (with combined metadynamics and adaptive force-bias method) and Markov state modeling to obtain accurate free energy, kinetics, and the intermediates in the transition pathway between Watson-Crick and HG base pairs for both naked B-DNA and A-RNA duplexes. The Markov state model constructed from our unbiased MD simulation data revealed previously unknown complex extrahelical intermediates in the seemingly simple process of base flipping in B-DNA. Extending our calculation to A-RNA, for which HG base pairing is not observed experimentally, resulted in relatively unstable, single-hydrogen-bonded, distorted Hoogsteen-like bases. Unlike B-DNA, the transition pathway primarily involved base paired and intrahelical intermediates with transition timescales much longer than that of B-DNA. The seemingly obvious flip-over reaction coordinate (i.e., the glycosidic torsion angle) is unable to resolve the intermediates. Instead, a multidimensional picture involving backbone dihedral angles and distance between hydrogen bond donor and acceptor atoms is required to gain insight into the molecular mechanism.

中文翻译：

---

DNA 与 RNA 中 Hoogsteen 碱基配对的自由能景观和构象动力学

遗传信息编码在 DNA 双螺旋中，在其生理环境中，其特征是标志性的 Watson-Crick 核碱基配对。最近的 NMR 弛豫实验揭示了在裸 DNA 双链体中存在替代 Hoogsteen (HG) 碱基配对模式的瞬时存在，并估计了其相对稳定性和寿命。与 DNA 相比，在 RNA 双链体中没有观察到这种结构。了解 HG 碱基配对很重要，因为两种构象之间的潜在“呼吸”运动可以显着调节蛋白质结合。然而，仍然缺乏对过渡途径和动力学的详细机制洞察。我们执行了增强的采样模拟（结合元动力学和自适应力偏置方法）和马尔可夫状态建模以获得准确的自由能，动力学，以及裸 B-DNA 和 A-RNA 双链体的 Watson-Crick 和 HG 碱基对之间过渡途径中的中间体。根据我们的无偏 MD 模拟数据构建的马尔可夫状态模型在 B-DNA 中看似简单的碱基翻转过程中揭示了以前未知的复杂螺旋外中间体。将我们的计算扩展到 A-RNA，在实验中未观察到 HG 碱基配对，导致相对不稳定、单氢键、扭曲的 Hoogsteen 样碱基。与 B-DNA 不同，过渡途径主要涉及碱基配对和螺旋内中间体，其过渡时间比 B-DNA 长得多。看似明显的翻转反应坐标（即糖苷扭转角）无法解析中间体。反而，