Theoretical studies of GC-specific photocleavage of DNA via electron transfer: Significant lowering of ionization potential and 5'-localization of HOMO of stacked GG bases in B-form DNA
Theoretical studies of GC-specific photocleavage of DNA via electron transfer: Significant lowering of ionization potential and 5'-localization of HOMO of stacked GG bases in B-form DNA
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DOI：
10.1021/ja9609821
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发表时间：
1996-07-31
影响因子：
15
通讯作者：
Saito, I
中科院分区：
文献类型：
--
作者：
Sugiyama, H;Saito, I
在 3-21G(*) 和 6-31G* 水平上对堆叠的 DNA 碱基进行从头算分子轨道计算，以阐明在电子接受光敏剂存在下 DNA 光裂解的 5'-GG-3' 序列特异性的起源。电离势 (IF) 被估计为 B 形几何中 16 组两个堆叠核碱基和七组堆叠核碱基对系统的库普曼定理值。结果发现，GG/CC 系统是 10 个可能的堆叠核碱基对中最低的，并且大约 70% 的 HOMO 位于 5'-GG-3' 的 5'-G 上。这些计算表明5'-GG-3'的5'-G是B DNA中最多电子供给位点，并且表明从DNA到电子受体的单电子转移在5'-GG-3'位点最有效地发生，这与实验数据完全一致。为了了解阳离子自由基的命运，估计了七个堆叠核碱基对的垂直 IP。结果发现，GG/CC体系具有最小的垂直IP，并且阳离子自由基位于5'-GG-3'的5'-G上。这些结果意味着 5'-GG-3' 的 5'-G 是通过 DNA 的“空穴”迁移中的一个汇点，即，在 B 型 DNA 中产生的电子损失中心将主要最终位于 5'-GG-3' 的 5'-G 上，并且表明不仅初始光电离的碱基特异性，而且随后的能量上有利于空穴迁移到最低 5'-GG-3' 位点的起源都是5'-GG-3' 特异性切割。还检查了具有各种几何形状的堆叠 GG 的计算，包括 A 型和 Z 型 DNA 的方向。
Ab initio molecular orbital calculations of stacked DNA bases were performed at the 3-21G(*) and 6-31G* levels to elucidate the origin of the 5'-GG-3' sequence specificity for the photocleavage of DNA in the presence of electron-accepting photosensitizers. Ionization potentials (IF) were estimated as Koopman's theorem values for 16 sets of two stacked nucleobases and seven sets of stacked nucleobase pair systems in a B-form geometry. It was found that the GG/CC system is the lowest among the 10 possible stacked nucleobase pairs and that approximately 70% of the HOMO is localized on the 5'-G of 5'-GG-3'. These calculations indicate that the 5'-G of 5'-GG-3' is the most electron donating site in B DNA and suggest that one-electron transfer from DNA to an electron acceptor occurs most effectively at 5'-GG-3' sites which are fully consistent with the experimental data. In order to know the fate of the cation radical, the vertical IPs were estimated for seven stacked nucleobase pairs. It was found that the GG/CC system possesses the smallest vertical IP and that the cation radical is localized on the 5'-G of 5'-GG-3'. These results imply that the 5'-G of 5'-GG-3' is a sink in ''hole'' migration through DNA, i.e., an electron-loss center created in a B-form DNA will end up predominantly on the 5'-G of 5'-GG-3', and suggest that not only the base specificity for initial photoionization but also subsequent energetically favored hole migration to the lowest 5'-GG-3' site are the origin of the 5'-GG-3' specific cleavage. Calculations of stacked GGs with various geometries including orientations of A- and Z-form DNA were also examined.