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

Peng Xie, Kai Liu, Fenglong Gu, Yuriko Aoki

    Research output: Contribution to journalArticle

    10 Citations (Scopus)

    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)A·poly(dT) and poly(dG)A·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)A·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.

    Original languageEnglish
    Pages (from-to)230-239
    Number of pages10
    JournalInternational Journal of Quantum Chemistry
    Volume112
    Issue number1
    DOIs
    Publication statusPublished - Jan 1 2012

    Fingerprint

    Poly dA-dT
    Radiation counters
    elongation
    Elongation
    counters
    deoxyribonucleic acid
    DNA
    guanines
    adenines
    Guanine
    Molecular orbitals
    Adenine
    ions
    molecular orbitals
    Energy gap
    DOS
    Valence bands
    electron transfer
    Sodium
    sodium

    All Science Journal Classification (ASJC) codes

    • Atomic and Molecular Physics, and Optics
    • Condensed Matter Physics
    • Physical and Theoretical Chemistry

    Cite this

    Counter-ion effects of A- and B-type poly(dG)A·Poly(dC) and poly(dA)A·Poly(dT) DNA by elongation method. / Xie, Peng; Liu, Kai; Gu, Fenglong; Aoki, Yuriko.

    In: International Journal of Quantum Chemistry, Vol. 112, No. 1, 01.01.2012, p. 230-239.

    Research output: Contribution to journalArticle

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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)A·poly(dT) and poly(dG)A·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)A·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.",
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