Sequence dependency of canonical base pair opening in the DNA double helix

The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair.DNA碱基从双螺旋结构中挤出是诸多细胞过程（如DNA复制、修饰与修复）的关键步骤。碱基对打开是碱基弹出的第一步，但其确切机制目前仍未被充分阐明。本研究针对两条DNA序列中的11种不同经典碱基对的打开过程开展了大规模经典分子动力学模拟，以此探究序列对碱基对打开过程的影响。我们采用了两款主流的生物分子力场，并通过一种全新开发的自适应采样算法，以简单距离坐标作为偏置变量对模拟施加约束，使模拟沿该坐标往复进行，从而得以捕捉多条不同的碱基对打开路径。我们将计算得到的自由能与核磁共振（Nuclear Magnetic Resonance, NMR）研究中的结果进行了对比，并对用于解析该NMR数据的模型假设进行了验证。研究结果进一步表明，相邻序列是影响打开自由能的重要因素，但同时也提示还存在其他序列相关效应发挥作用。所有观测到的碱基对均表现出朝向DNA大沟打开的倾向：对于GC碱基对而言，其优先打开的碱基为胞嘧啶；而对于AT碱基对，两种碱基间存在序列依赖性的竞争。针对AT碱基对的打开过程，我们识别出两种非经典碱基对相互作用，它们共同构成了自由能分布曲线中的一个局部极小值点。无论是AT还是CG碱基对，我们均观测到在处于开放状态的碱基对的特定位点上，会与水分子及钠离子形成长寿命的相互作用。