Hydrogen bonding revisited: Geometric selection as a principal determinant of DNA replication fidelity
Hydrogen bonding revisited: Geometric selection as a principal determinant of DNA replication fidelity
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DOI：
10.1073/pnas.94.20.10493
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发表时间：
1997-09-30
影响因子：
11.1
通讯作者：
Goodman, MF
中科院分区：
文献类型：
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作者：
Goodman, MF
氢键在形成沃森-克里克（W-C）AT和GC碱基对中发挥着核心作用，这是自1953年发现DNA结构以来的基本范式。除了链间氢键，链内碱基堆积和链间交叉堆积相互作用在保持碱基沿DNA主链沿着长度的堆积结构中是重要的。一般来说，W-C碱基对之间的H键被认为是“信息”，而碱基堆积的相互作用被认为是“非信息”，仅仅是稳定双螺旋。因此，通常认为，将A与T配对以及将G与C配对的H键主要负责DNA聚合酶以高保真度合成DNA的能力。二氟甲苯是胸腺嘧啶（T）的非极性等排类似物，在嘧啶环上含有氟原子代替氧，因此不能与A（1）形成氢键。然而，AF碱基对几乎与AT碱基对一样由大肠杆菌校对缺陷DNA聚合酶I（KF exo）形成，如Moran et al. (2)报告在这一期的会议记录[的化学结构的F和T和空间填充模型的每一个显示在莫兰等人。(2)，图1]。当F作为DNA上的模板碱基（3）或作为dFTP底物（2）存在时，KF exo不能强烈区分AF对的观察结果适用。显然不可避免的结论是，氢键不是聚合酶选择性地形成W-C碱基对所绝对需要的。这些结果提供了一个动力，重新考虑氢键实际上在稳定DNA和增强DNA聚合酶保真度中发挥的作用。双链DNA寡聚体中的错配碱基对确实会导致DNA解链温度显著降低（4）。F取代T后H键的丢失具有这种类型的不稳定效应（2）。然而，在许多教科书中发现的仅H键将DNA双螺旋的两条链保持在一起的概念似乎是不够的。当考虑到双链体交替共聚物聚d（A，T）或聚d（G，C）在水溶液中具有与它们各自的均聚物对应物聚dApoly dT或聚dGpoly dC显著不同的熔融温度时，变得清楚的是，碱基堆积相互作用对双链体稳定性具有重要的、可能是主导的序列依赖性影响。从解链数据推导出的匹配和错配碱基对之间的自由能差（G 0）在约0.2- 4.0kcal/mol（4-6）的范围内，这取决于错配的同一性、周围的序列环境及其在中心附近或在DNA末端的位置。在溶液中测量的这些G 0值不足以解释几乎所有聚合酶的高核苷酸插入重复性，包括那些似乎特别“容易出错”的聚合酶，如真核生物Poll酶（7）或HIV-1逆转录酶（8-10）。例如，对于天然碱基对AT对AC（6）测得的G 0 3.7 kcal/mol应导致AC错误插入频率约为2
That hydrogen bonds play a central role in forming Watson–Crick (W–C) AT and GC base pairs is a fundamental paradigm dating from the discovery of the structure of DNA in 1953. In addition to interstrand H bonding, intrastrand base-stacking and interstrand cross-stacking interactions are important in maintaining the bases in a stacked structure along the length of the DNA backbone. In general, H bonds between W–C base pairs are viewed as ‘‘informational,’’whereas the base-stacking interactions are regarded as ‘‘noninformational,’’merely stabilizing the double helix. Consequently, it is a common perception that the H bonds pairing A with T and G with C are primarily responsible for the ability of DNA polymerases to synthesize DNA with high fidelity. Difluorotoluene, a nonpolar isosteric analog of thymine (T), contains fluorine atoms in place of oxygens on the pyrimidine ring and thus cannot form H bonds with A (1). Nevertheless, AF base pairs are formed almost as well as AT pairs by Escherichia coli proofreading-defective DNA polymerase I (KF exo), as Moran et al.(2) report in this issue of the Proceedings [the chemical structures of F and T and spacefilling models of each are shown in Moran et al.(2), figure 1]. The observation that KF exo fails to discriminate strongly against AF pairs applies when F is present either as a template base on DNA (3) or as a dFTP substrate (2). The apparently inescapable conclusion is that H bonds are not absolutely required for polymerase to form W–C base pairs selectively. These results provide an impetus to reconsider what role H bonds actually play in stabilizing DNA and enhancing DNA polymerase fidelity. Mismatched base pairs in a duplex DNA oligomer do cause marked reductions in DNA melting temperatures (4). The loss of H bonds upon replacement of T with F has this type of destabilizing effect (2). However, the notion that H bonds alone keep the two strands of a DNA double helix together, which is found in many textbooks, seems inadequate. When one considers that duplex alternating copolymers poly d (A, T) or poly d (G, C) have melting temperatures in aqueous solution that differ substantially from their respective homopolymer counterparts poly dApoly dT or poly dGpoly dC, it becomes clear that base-stacking interactions have an important, perhaps dominant, sequence-dependent effect on duplex stability.Furthermore, the free-energy differences (G0) between matched and mismatched base pairs deduced from melting data are in a range of about 0.2–4.0 kcal/mol (4–6), depending on the identity of the mispair, the surrounding sequence context, and its location near the center or at the DNA terminus. These G0 values, as measured in solution, are insufficient to account for the high nucleotide insertion fidelities of virtually all polymerases, including those that seem to be especially ‘‘error prone’’such as eukaryotic Pol ß (7) or HIV-1 reverse transcriptase (8–10). For example, G0 3.7 kcal/mol measured for the natural base pairs AT versus AC (6) should result in an AC misinsertion frequency of about 2