Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, 332-0012 Japan.
J Phys Chem B. 2009 Dec 24;113(51):16384-92. doi: 10.1021/jp9054582.
We examined the ionization potential (IP) corresponding to the free energy of a hole on duplex DNA by semiempirical molecular orbital theory with a continuum solvent model. As for the contiguous guanines (a guanine run), we found that the IP in the gas phase significantly decreases with the increasing number of nucleotide pairs of the guanine run, whereas the IP in water (OP, oxidation potential) only slightly does. The latter result is consistent with the experimental result for DNA oligomers in water. This decrease in the IP is mainly due to the attractive electrostatic interaction between the hole and a nucleotide pair in the duplex DNA. This interaction is reduced in water, which results in the small decrease in the IP in water. This mechanism explains the discrepancy between the experimental result and the previous computational results obtained by neglecting the solvent. As for the chemically modified guanine, the previous work showed that the removal of some solvent (water) molecules due to the attachment of a neutral functional group to a guanine in a duplex DNA stabilizes the hole on the guanine. One might naively have expected the opposite case, since a polar solvent usually stabilizes ions. This mechanism also explains this unexpected stabilization of a hole as follows. When some water molecules are removed, the attractive electrostatic interaction stabilizing the hole increases, and thus, the hole is stabilized. In order to design the hole energetics by a chemical modification of DNA, this mechanism has to be taken into account and can be used.
我们通过带有连续溶剂模型的半经验分子轨道理论研究了双链 DNA 上空穴的自由能对应的电离势 (IP)。对于连续的鸟嘌呤（鸟嘌呤序列），我们发现气相中的 IP 随着鸟嘌呤序列的核苷酸对数量的增加而显著降低，而水中的 IP（氧化势）仅略有降低。后一种结果与水中 DNA 寡聚物的实验结果一致。这种 IP 的降低主要是由于空穴与双链 DNA 中核苷酸对之间的吸引力静电相互作用。这种相互作用在水中会减弱，导致水中 IP 的微小降低。该机制解释了实验结果与之前忽略溶剂的计算结果之间的差异。对于化学修饰的鸟嘌呤，之前的工作表明，由于中性官能团附着在双链 DNA 中的鸟嘌呤上，一些溶剂（水）分子的去除稳定了鸟嘌呤上的空穴。人们可能会天真地期望相反的情况，因为极性溶剂通常会稳定离子。该机制还解释了这种空穴的意外稳定，如下所示。当一些水分子被去除时，稳定空穴的吸引力静电相互作用增加，因此空穴被稳定。为了通过 DNA 的化学修饰来设计空穴能态，必须考虑到这种机制，并可以使用它。
