Efficient and accurate calculations on the electronic structure of B -type poly(dG)poly(dC) DNA by elongation method

First step toward the understanding of the biological properties of aperiodic DNA

Yuuichi Orimoto, Feng Long Gu, Akira Imamura, Yuriko Aoki

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

Elongation method was applied to determine the electronic structures of B -type poly(dG)poly(dC) DNA at the ab initio molecular orbital level as a first step toward the calculation of aperiodic DNA. The discrepancy in total energy between the elongation method and a conventional calculation was negligibly small in the order of 10-8 hartreeat. for 14 G-C base pair model. The local density of states for 10 G-C base pair model estimated by the elongation method well reproduced the results by the conventional calculation. It was found that the band gap of the whole system is mainly due to the energy difference between the valence band of guanine and the conduction band of cytosine. Moreover, the electron transfer path through stacking G-C base pairs rather than sugar-phosphate backbones has been confirmed by the authors' calculations.

Original languageEnglish
Article number215104
JournalJournal of Chemical Physics
Volume126
Issue number21
DOIs
Publication statusPublished - Jun 13 2007

Fingerprint

elongation
Electronic structure
Elongation
deoxyribonucleic acid
electronic structure
DNA
Sugar Phosphates
guanines
Cytosine
Guanine
Molecular orbitals
sugars
Valence bands
Conduction bands
molecular orbitals
phosphates
electron transfer
conduction bands
Energy gap
valence

All Science Journal Classification (ASJC) codes

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

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title = "Efficient and accurate calculations on the electronic structure of B -type poly(dG)poly(dC) DNA by elongation method: First step toward the understanding of the biological properties of aperiodic DNA",
abstract = "Elongation method was applied to determine the electronic structures of B -type poly(dG)poly(dC) DNA at the ab initio molecular orbital level as a first step toward the calculation of aperiodic DNA. The discrepancy in total energy between the elongation method and a conventional calculation was negligibly small in the order of 10-8 hartreeat. for 14 G-C base pair model. The local density of states for 10 G-C base pair model estimated by the elongation method well reproduced the results by the conventional calculation. It was found that the band gap of the whole system is mainly due to the energy difference between the valence band of guanine and the conduction band of cytosine. Moreover, the electron transfer path through stacking G-C base pairs rather than sugar-phosphate backbones has been confirmed by the authors' calculations.",
author = "Yuuichi Orimoto and Gu, {Feng Long} and Akira Imamura and Yuriko Aoki",
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T1 - Efficient and accurate calculations on the electronic structure of B -type poly(dG)poly(dC) DNA by elongation method

T2 - First step toward the understanding of the biological properties of aperiodic DNA

AU - Orimoto, Yuuichi

AU - Gu, Feng Long

AU - Imamura, Akira

AU - Aoki, Yuriko

PY - 2007/6/13

Y1 - 2007/6/13

N2 - Elongation method was applied to determine the electronic structures of B -type poly(dG)poly(dC) DNA at the ab initio molecular orbital level as a first step toward the calculation of aperiodic DNA. The discrepancy in total energy between the elongation method and a conventional calculation was negligibly small in the order of 10-8 hartreeat. for 14 G-C base pair model. The local density of states for 10 G-C base pair model estimated by the elongation method well reproduced the results by the conventional calculation. It was found that the band gap of the whole system is mainly due to the energy difference between the valence band of guanine and the conduction band of cytosine. Moreover, the electron transfer path through stacking G-C base pairs rather than sugar-phosphate backbones has been confirmed by the authors' calculations.

AB - Elongation method was applied to determine the electronic structures of B -type poly(dG)poly(dC) DNA at the ab initio molecular orbital level as a first step toward the calculation of aperiodic DNA. The discrepancy in total energy between the elongation method and a conventional calculation was negligibly small in the order of 10-8 hartreeat. for 14 G-C base pair model. The local density of states for 10 G-C base pair model estimated by the elongation method well reproduced the results by the conventional calculation. It was found that the band gap of the whole system is mainly due to the energy difference between the valence band of guanine and the conduction band of cytosine. Moreover, the electron transfer path through stacking G-C base pairs rather than sugar-phosphate backbones has been confirmed by the authors' calculations.

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