Cheng Xiaolin, Kelso Catherine, Hornak Viktor, de los Santos Carlos, Grollman Arthur P, Simmerling Carlos
Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA.
J Am Chem Soc. 2005 Oct 12;127(40):13906-18. doi: 10.1021/ja052542s.
The process by which DNA repair enzymes recognize and selectively excise damaged bases in duplex DNA is fundamental to our mechanistic understanding of these critical biological reactions. 8-Oxoguanine (8-oxoG) is the most common form of oxidative DNA damage; unrepaired, this lesion generates a G:C-->T:A mutation. Central to the recognition and repair of DNA damage is base extrusion, a process in which the damaged base lesion or, in some cases, its partner disengages from the helix and is bound to the enzyme's active site where base excision takes place. The conformation adopted by 8-oxoG in duplex DNA is affected by the base positioned opposite this lesion; conformational changes may also take place when the damaged base binds to its cognate repair enzyme. We performed unrestrained molecular dynamics simulations for several 13-mer DNA duplexes. Oligomers containing G:C and 8oxoG:C pairs adopted Watson-Crick geometries in stable B-form duplexes; 8oxoG showed increased local and global flexibility and a reduced barrier to base extrusion. Duplexes containing the G:A mismatch showed much larger structural fluctuations and failed to adopt a well-defined structure. For the 8oxoG:A mismatch that is recognized by the DNA glycosylase MutY, the damaged nucleoside underwent spontaneous and reproducible anti-->syn transitions. The syn conformation is thermodynamically preferred. Steric hindrance and unfavorable electrostatics associated with the 8oxoG O8 atom in the anti conformation were the major driving forces for this transition. Transition events follow two qualitatively different pathways. The overall anti-->syn transition rate and relative probability of the two transition paths were dependent on local sequence context. These simulations indicate that both the dynamic and equilibrium behavior of the duplex change as a result of oxidation; these differences may provide valuable new insight into the selective action of enzymes on damaged DNA.
DNA修复酶识别并选择性切除双链DNA中受损碱基的过程，对于我们从机制上理解这些关键的生物反应至关重要。8-氧代鸟嘌呤（8-oxoG）是氧化性DNA损伤最常见的形式；若未得到修复，这种损伤会产生G:C→T:A突变。碱基挤出是DNA损伤识别与修复的核心过程，在这个过程中，受损的碱基损伤位点，或在某些情况下其配对碱基，从螺旋中脱离并结合到发生碱基切除的酶活性位点。双链DNA中8-oxoG所采取的构象受该损伤位点对面碱基的影响；当受损碱基与其同源修复酶结合时也可能发生构象变化。我们对几条13聚体DNA双链进行了无约束分子动力学模拟。含有G:C和8oxoG:C碱基对的寡聚体在稳定的B型双链中采用沃森-克里克几何结构；8oxoG表现出局部和整体柔性增加以及碱基挤出的势垒降低。含有G:A错配的双链表现出更大的结构波动，且未能形成明确的结构。对于被DNA糖基化酶MutY识别的8oxoG:A错配，受损核苷发生了自发且可重复的反式→顺式转变。顺式构象在热力学上更有利。反式构象中与8-oxoG的O8原子相关的空间位阻和不利静电是这种转变的主要驱动力。转变事件遵循两种性质不同的途径。整体的反式→顺式转变速率以及两条转变途径的相对概率取决于局部序列背景。这些模拟表明，双链的动态和平衡行为都会因氧化而改变；这些差异可能为酶对受损DNA的选择性作用提供有价值的新见解。
