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Counter-ion effects of A- and B-type poly(dG)·Poly(dC) and poly(dA)·Poly(dT) DNA by elongation method

Authors

  • Peng Xie,

    1. Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
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  • Kai Liu,

    1. Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
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  • Fenglong Gu,

    Corresponding author
    1. Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631, China
    2. Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama 332-0012, Japan
    • Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631 China
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  • Yuriko Aoki

    Corresponding author
    1. Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
    2. Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama 332-0012, Japan
    • Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama 332-0012, Japan
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Abstract

The elongation method was developed to calculate the local density of states (LDOS) at ab initio molecular orbital (MO) level. This method is performed on eight types of DNA molecules: namely, a pitch of A- and B- type poly(dA)·poly(dT) and poly(dG)·poly(dC), and they are neutralized by H+ and Na+, respectively. The difference of total energy between elongation and conventional calculations in each step is considerably small in the order of 10−9 hartree/atom for 20 units of B-type poly(dA)·poly(dT) model. When the figures of total DOS of each model was compared, the energy gap of model containing Na+ is smaller than that of corresponding model containing H+. The LDOS for each model estimated by elongation method can well reproduce the results by conventional method. The LDOS figures show that the valence bands in A- and B-type DNA are formed by the highest occupied MOs (HOMOs) of adenine/guanine. Na+ can greatly decrease the energy of lowest unoccupied MO (LUMO) and consequently decrease the energy gap between LUMO and HOMO. The electron transfer between stacking adenine/guanine and sodium would play an important role in the conductivity of A- and B-type DNA. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

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