Calculation of hopping conductivity in aperiodic nucleotide base stacks

Ye, Y.-J.; Chen, R.-S.; Roldan, Alberto; Otto, P.; Ladik, J.

doi:10.1016/s0038-1098(99)00312-9

Cited by 53 publications

(55 citation statements)

References 30 publications

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“…Theoretical studies showed that the external backbone in helical nucleotide structures is not involved in transport phenomena [16]. Thus, we believe that our calculations for the G4 stacks are well representative of principal electronic features of real systems.…”

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confidence: 54%

G-quartet biomolecular nanowires

Calzolari

Felice

Molinari

et al. 2002

Applied Physics Letters

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We present a first-principle investigation of quadruple helix nanowires, consisting of stacked planar hydrogen-bonded guanine tetramers. Our results show that long wires form and are stable in potassium-rich conditions. We present their electronic bandstructure and discuss the interpretation in terms of effective wide-bandgap semiconductors. The microscopic structural and electronic properties of the guanine quadruple helices make them suitable candidates for molecular nanoelectronics.

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confidence: 54%

G-quartet biomolecular nanowires

Calzolari

Felice

Molinari

et al. 2002

Applied Physics Letters

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“…[12][13][14][15][16][55][56][57][58][59][63][64][65][66][67][68][69]78,79,[82][83][84][85][86][87][88] with that of Kurita 25 (see Section 6.3). Thus, although compared to the ab initio calculations 18-27 our approach could be considered even too simplified and anyway purely phenomenological, it is still worth its using for the research in the DNA problem even nowadays when high performance supercomputers are available.…”

Section: 4849mentioning

confidence: 99%

Π-Electrons IN a SINGLE STRAND OF DNA: A PHENOMENOLOGICAL APPROACH

Iguchi¹

2004

Int. J. Mod. Phys. B

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We revisit the problem of the electronic properties of a single strand of DNA, formulating the Hückel approximation for π-electrons in both the sugar-phosphate backbone chain and the π-stacking of nitrogenous bases in a single strand of DNA where the nitrogenous bases are adenine (A), guanine (G), cytosine (C) and thymine (T), respectively. We calculate the electronic band structure of π-electrons: (i) in the single nitrogenous base molecules such as A, G, C and T, (ii) in the single sugar-phosphate molecule, (iii) in the single nucleotide systems such as A, G, C, T with the single sugar-phosphate group, and (iv) in the system of a single strand of DNA with an infinite repetition of a nucleotide such as A, G, C and T, respectively. We find the following: In the case of (i), there is an energy gap between the energy levels for the HOMO and LUMO in the nitrogenous base. This guarantees the semiconducting character of the bases as a mother material. In the case of (ii), there are the HOMO localized at the oxygen site with a double bond and the LUMO localized around the phosphorus atom, which have a quite large energy gap. In the case of (iii), the energy levels for the HOMO and LUMO of the nitrogenous base remain almost the same as those of the nucleotide, while those of the sugar-phosphate group remain the same as well. The HOMO of the sugar-phosphate group exists right below the HOMO of the nitrogenous base. Therefore, comparing the energy levels for the HOMOs of the nitrogenous base group with those of the sugar-phosphate group, the nitrogenous base group behaves as a donor while the sugar-phosphate group behaves as an acceptor. In the case of (iv), there are energy bands and band gaps for the extended states in the nitrogenous base group and the sugar-phosphate group as well as the discrete levels for the localized states at the phosphate site in the spectrum. There is a transition from semiconductor to semimetal as the π-electron hopping between the nitrogenous bases of nucleotide is increased. The details of the above will be discussed in the present paper. Thus, we show the powerfulness of the Hückel theory in the study of DNA as well, although this theory is, at the first glance, oversimplified and purely phenomenological.

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“…However, charge transport results through DNA are still controversial 3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21 . Experimentally it is found that DNA can either be a good conductor 3 , a semi-conductor 4,5 or even an insulator 6 .…”

Section: Introductionmentioning

confidence: 99%

“…Experimentally it is found that DNA can either be a good conductor 3 , a semi-conductor 4,5 or even an insulator 6 . Theoretically, while the exact charge transport mechanism is not clear, band transport, 5,8,9,10 polaronic transport, 4,11 fluctuation facilitated charge migration, 12,13 and multi-step hopping 14,15 have been investigated. The narrowing down of the precise charge transport mechanism has been difficult because the base pairs are weakly coupled due to the large inter-base separation of ∼ 3.4Å.…”

Section: Introductionmentioning

confidence: 99%

Interbase electronic coupling for transport through DNA

2005

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We develop a new approach to derive single state tight binding (SSTB) model for electron transport in the vicinity of valence-conduction bands of poly(G)-poly(C) and poly(A)-poly(T) DNA. The SSTB parameters are derived from first principles and are used to model charge transport through finite length DNA. We investigate the rigor of reducing the full DNA Hamiltonian to SSTB model to represent charge transport in the vicinity of valence-conduction band. While the transmission coefficient spectrum is preserved, its position shifts in energy. Thymine is poorly represented and its peak height is substantially reduced. This is attributed to the abstraction of the HOMO-LUMO coupling to other eigen-states in the nearest neighbor DNA bases, and can be corrected within 2 nd order time independent perturbation theory. Inter-strand charge transport has also been analyzed and it is found that hopping to the nearest neighbor in the complementary strand is the most important process except in the valence band of poly(G)-poly(C), where hopping to the second nearest neighbor between 3 ′ −ends is the most dominant process. As a result, transport between 3 ′ −ends and 5 ′ −ends in the vicinity of valence band of polyG-polyC is asymmetric.

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Calculation of hopping conductivity in aperiodic nucleotide base stacks

Cited by 53 publications

References 30 publications

G-quartet biomolecular nanowires

G-quartet biomolecular nanowires

Π-Electrons IN a SINGLE STRAND OF DNA: A PHENOMENOLOGICAL APPROACH

Interbase electronic coupling for transport through DNA

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