Yang Wei
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
DNA Repair (Amst). 2006 Jun 10;5(6):654-66. doi: 10.1016/j.dnarep.2006.02.004. Epub 2006 Mar 29.
A fundamental question in DNA repair is how a mismatched or modified base is detected when embedded in millions to billions of normal base pairs. A survey of the literature and structural database reveals a common feature in all repair protein-DNA complexes: the DNA double helix is discontinuous at a lesion site due to base unstacking, kinking and/or nucleotide extrusion. Lesions induce destabilization and distortion of short linear DNAs, and underwinding in negatively supercoiled DNA presumably could compound the reduced stability caused by a lesion. A hypothesis is thus put forward that DNA lesion recognition occurs in two steps. Repair proteins initially recognize the weakened base stacking, and thus a flexible hinge at a DNA lesion. Sampling of flexible hinges rather than all DNA base pairs can reduce the task of finding a lesion by two to three orders of magnitude, from searching millions base pairs to thousands. After the initial encounter, a repair protein scrutinizes the shape, hydrogen bonding and electrostatic potentials of bases at the flexible hinge and dissociates if it is not a correct substrate. MutS, which has a broad range of substrates, actively dissociates from non-specific binding via an ATP-dependent proofreading mechanism. A single lesion may thus be sampled by BER, NER and MMR proteins until repaired. This proposition immediately suggests a mechanism for crosstalk between different repair and signaling pathways. It also raises the possibility that sampling of a lesion by one protein could facilitate loading of another by direct protein-protein or DNA mediated interactions.
DNA修复中的一个基本问题是，当一个错配或修饰的碱基嵌入数百万至数十亿个正常碱基对中时，它是如何被检测到的。对文献和结构数据库的调查揭示了所有修复蛋白-DNA复合物的一个共同特征：由于碱基解堆叠、扭结和/或核苷酸挤出，DNA双螺旋在损伤位点处是不连续的。损伤会导致短线性DNA的不稳定和扭曲，而负超螺旋DNA中的解旋可能会加剧损伤引起的稳定性降低。因此，有人提出一个假说，即DNA损伤识别分两步进行。修复蛋白最初识别弱化的碱基堆叠，也就是DNA损伤处的一个柔性铰链。对柔性铰链而非所有DNA碱基对进行采样，可以将寻找损伤的任务减少两到三个数量级，从搜索数百万个碱基对减少到数千个。在初次相遇后，修复蛋白会仔细检查柔性铰链处碱基的形状、氢键和静电势，如果不是正确的底物就会解离。具有广泛底物范围的MutS通过一种ATP依赖的校对机制从非特异性结合中主动解离。因此，单个损伤可能会被碱基切除修复（BER）、核苷酸切除修复（NER）和错配修复（MMR）蛋白采样，直到被修复。这一观点立即暗示了不同修复和信号通路之间的串扰机制。它还提出了一种可能性，即一种蛋白对损伤的采样可能通过直接的蛋白质-蛋白质或DNA介导的相互作用促进另一种蛋白的加载。
