Pathway analysis on DNA charge transfer through adenine and guanine bridges

Heeyoung Kim, One Choi, Eunji Sim

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Long-range DNA charge transfer dynamics of 5'-GAnGA mG3-3' (n = 1, 2, m = 1-3) sequences have been explored on a quantitative basis. First, the degree of coherence was determined in terms of coherence length. Second, relative contribution of charge transfer mechanisms such as incoherent (nearest-neighbor) hopping, through-bridge, and superexchange as well as G-hopping mechanism was assessed by the density matrix decomposition based on the path integral formalism. Finally, time evolution of individual trajectory contribution was investigated through pathway analysis. Although G-hopping pathways were indeed found to be crucial, we have also shown that the initial transfer is driven by the nearest-neighbor hopping pathways through energetically less favored adenines followed by G-hopping pathways. Therefore, not only the G-hopping pathways but also the through-adenine pathways govern the overall long-range DNA charge transfer. By placing guanines no farther than two adenines apart, one can fully utilize efficient tunneling between guanines for long-range DNA charge transfer.

Original languageEnglish
Pages (from-to)20394-20400
Number of pages7
JournalJournal of Physical Chemistry C
Volume114
Issue number48
DOIs
Publication statusPublished - 2010 Dec 9

Fingerprint

guanines
adenines
Guanine
Adenine
Charge transfer
DNA
deoxyribonucleic acid
charge transfer
Trajectories
trajectories
formalism
Decomposition
decomposition

All Science Journal Classification (ASJC) codes

  • Electronic, Optical and Magnetic Materials
  • Energy(all)
  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films

Cite this

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abstract = "Long-range DNA charge transfer dynamics of 5'-GAnGA mG3-3' (n = 1, 2, m = 1-3) sequences have been explored on a quantitative basis. First, the degree of coherence was determined in terms of coherence length. Second, relative contribution of charge transfer mechanisms such as incoherent (nearest-neighbor) hopping, through-bridge, and superexchange as well as G-hopping mechanism was assessed by the density matrix decomposition based on the path integral formalism. Finally, time evolution of individual trajectory contribution was investigated through pathway analysis. Although G-hopping pathways were indeed found to be crucial, we have also shown that the initial transfer is driven by the nearest-neighbor hopping pathways through energetically less favored adenines followed by G-hopping pathways. Therefore, not only the G-hopping pathways but also the through-adenine pathways govern the overall long-range DNA charge transfer. By placing guanines no farther than two adenines apart, one can fully utilize efficient tunneling between guanines for long-range DNA charge transfer.",
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Pathway analysis on DNA charge transfer through adenine and guanine bridges. / Kim, Heeyoung; Choi, One; Sim, Eunji.

In: Journal of Physical Chemistry C, Vol. 114, No. 48, 09.12.2010, p. 20394-20400.

Research output: Contribution to journalArticle

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AU - Kim, Heeyoung

AU - Choi, One

AU - Sim, Eunji

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N2 - Long-range DNA charge transfer dynamics of 5'-GAnGA mG3-3' (n = 1, 2, m = 1-3) sequences have been explored on a quantitative basis. First, the degree of coherence was determined in terms of coherence length. Second, relative contribution of charge transfer mechanisms such as incoherent (nearest-neighbor) hopping, through-bridge, and superexchange as well as G-hopping mechanism was assessed by the density matrix decomposition based on the path integral formalism. Finally, time evolution of individual trajectory contribution was investigated through pathway analysis. Although G-hopping pathways were indeed found to be crucial, we have also shown that the initial transfer is driven by the nearest-neighbor hopping pathways through energetically less favored adenines followed by G-hopping pathways. Therefore, not only the G-hopping pathways but also the through-adenine pathways govern the overall long-range DNA charge transfer. By placing guanines no farther than two adenines apart, one can fully utilize efficient tunneling between guanines for long-range DNA charge transfer.

AB - Long-range DNA charge transfer dynamics of 5'-GAnGA mG3-3' (n = 1, 2, m = 1-3) sequences have been explored on a quantitative basis. First, the degree of coherence was determined in terms of coherence length. Second, relative contribution of charge transfer mechanisms such as incoherent (nearest-neighbor) hopping, through-bridge, and superexchange as well as G-hopping mechanism was assessed by the density matrix decomposition based on the path integral formalism. Finally, time evolution of individual trajectory contribution was investigated through pathway analysis. Although G-hopping pathways were indeed found to be crucial, we have also shown that the initial transfer is driven by the nearest-neighbor hopping pathways through energetically less favored adenines followed by G-hopping pathways. Therefore, not only the G-hopping pathways but also the through-adenine pathways govern the overall long-range DNA charge transfer. By placing guanines no farther than two adenines apart, one can fully utilize efficient tunneling between guanines for long-range DNA charge transfer.

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