Theoretical Study on the Structure, Stability, and Electronic Properties of the Guanine-Zn-Cytosine Base Pair in M-DNA

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• 作者：Miguel Fuentes-Cabrera ; Bobby G. Sumpter ; Judit E. <img src="http ; //pubs.acs.org/images/entities/Scaron.gif" border="0">poner ; Ji<img src="http ; //pubs.acs.org/images/entities/rcaron.gif" border="0">&i
• 刊名：Journal of Physical Chemistry B
• 出版年：2007
• 出版时间：February 1, 2007
• 年：2007
• 卷：111
• 期：4
• 页码：870 - 879
• 全文大小：473K
• 年卷期：v.111,no.4(February 1, 2007)
• ISSN：1520-5207

文摘

M-DNA is a type of metalated DNA that forms at high pH and in the presence of Zn, Ni, and Co, with themetals placed in between each base pair, as in G-Zn-C. Experiments have found that M-DNA could be apromising candidate for a variety of nanotechnological applications, as it is speculated that the metal d-statesenhance the conductivity, but controversy still clouds these findings. In this paper, we carry out a comprehensiveab initio study of eight G-Zn-C models in the gas phase to help discern the structure and electronic propertiesof Zn-DNA. Specifically, we study whether a model prefers to be planar and has electronic properties thatcorrelate with Zn-DNA having a metallic-like conductivity. Out of all the studied models, there is only onewhich preserves its planarity upon full geometry optimization. Nevertheless, starting from this model, onecan deduce a parallel Zn-DNA architecture only. This duplex would contain the imino proton, in contrast towhat has been proposed experimentally. Among the nonplanar models, there is one that requires less than 8kcal/mol to flatten (both in gas and solvent conditions), and we propose that it is a plausible model forbuilding an antiparallel duplex. In this duplex, the imino proton would be replaced by Zn, in accordance withexperimental models. Neither planar nor nonplanar models have electronic properties that correlate with Zn-DNA having a metallic-like conductivity due to Zn d-states. To understand whether density functional theory(DFT) can describe appropriately the electronic properties of M-DNAs, we have investigated the electronicproperties of G-Co-C base pairs. We have found that when self-interaction corrections (SIC) are not includedthe HOMO state contains Co d-levels, whereas these levels are moved below the HOMO state when SIC areconsidered. This result indicates that caution should be exercised when studying the electronic properties ofM-DNAs with functionals that do not account for strong electronic correlations.