Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States.
Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States.
J Phys Chem B. 2019 Mar 14;123(10):2291-2304. doi: 10.1021/acs.jpcb.8b12172. Epub 2019 Feb 28.
Molecular dynamics (MD) simulations of 2-aminopurine (2Ap)-labeled DNA dinucleoside monophosphates (DNMPs) were performed to investigate the hypothesis that base stacking dynamics occur on timescales sufficiently rapid to influence the emission signals measured in time-resolved fluorescence experiments. Analysis of multiple microsecond-length trajectories shows that the DNMPs sample all four coplanar stacking motifs. In addition, three metastable unstacked conformations are detected. A hidden Markov-state model (HMSM) was applied to the simulations to estimate transition rates between the stacked and unstacked states. Transitions between different stacked states generally occur at higher rates when the number of nucleobase faces requiring desolvation is minimized. Time constants for structural relaxation range between 1.6 and 25 ns, suggesting that emission from photoexcited 2Ap, which has an excited-state lifetime of 10 ns, is sensitive to base stacking kinetics. A master equation model for the excited-state population of 2Ap predicts multiexponential emission decays that reproduce the sub-10 ns emission decay lifetimes and amplitudes seen in experiments. Combining MD simulations with HMSM analysis is a powerful way to understand the dynamics that influence 2Ap excited-state relaxation and represents an important step toward using observed emission signals to validate MD simulations.
对 2-氨基嘌呤（2Ap）标记的 DNA 二核苷酸单磷酸（DNMP）进行了分子动力学（MD）模拟，以研究碱基堆积动力学是否发生在足够快的时间尺度上，从而影响时间分辨荧光实验中测量的发射信号这一假说。对多个微秒长度轨迹的分析表明，DNMP 可以采样所有四个共面堆积模式。此外，还检测到了三种亚稳态去堆积构象。隐马尔可夫状态模型（HMSM）被应用于模拟，以估计堆叠和去堆叠状态之间的转换速率。当需要去溶剂化的核碱基面数量最小时，不同堆叠状态之间的转换通常以更高的速率发生。结构弛豫的时间常数在 1.6 和 25 ns 之间，这表明具有 10 ns 激发态寿命的光激发 2Ap 的发射对碱基堆积动力学敏感。2Ap 激发态布居的主方程模型预测了多指数发射衰减，该模型再现了实验中观察到的亚 10 ns 发射衰减寿命和幅度。将 MD 模拟与 HMSM 分析相结合，是理解影响 2Ap 激发态弛豫的动力学的有效方法，也是利用观察到的发射信号验证 MD 模拟的重要步骤。
