DNA: insulator or wire?

Beratan, David N.; Priyadarshy, Satyam; Risser, Steven M.

doi:10.1016/s1074-5521(97)90230-1

Cited by 176 publications

(143 citation statements)

References 26 publications

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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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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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“…It is crucial to understand how PNA͞DNA hybrids mimic the reactions and functions of duplex DNA. Of immediate importance for their application as clinical diagnostic agents is investigation of the conductivity of DNA and its PNA analogs (5,6).…”

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confidence: 99%

Peptide nucleic acid–DNA duplexes: Long range hole migration from an internally linked anthraquinone

Armitage

Ly²,

Koch³

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

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The discovery that peptide nucleic acids (PNA) mimic DNA and RNA by forming complementary duplex structures following Watson-Crick base pairing rules opens fields in biochemistry, diagnostics, and medicine for exploration. Progress requires the development of modified PNA duplexes having unique and well defined properties. We find that anthraquinone groups bound to internal positions of a PNA oligomer intercalate in the PNA-DNA hybrid. Their irradiation with near-UV light leads to electron transfer and oxidative damage at remote GG doublets on the complementary DNA strand. This behavior mimics that observed in related DNA duplexes and provides the first evidence for long range electron (hole) transport in PNA-DNA hybrid. Analysis of the mechanism for electron transport supports hole hopping.Peptide nucleic acid (PNA) oligomers are DNA͞RNA analogs (see Fig. 1) in which the natural sugar-phosphate backbone is replaced by a synthetic peptide backbone (1). PNA oligomers that contain purine and pyrimidine nucleobases hybridize with complementary DNA and RNA strands to form right-handed, double-helical complexes according to the Watson-Crick rules of hydrogen bond-mediated base pair formation (2). Although much has been learned about the structural (3) and thermodynamic (4) factors involved in hybridization, little is known about the chemical reactivity of PNA͞DNA hybrids. It is crucial to understand how PNA͞DNA hybrids mimic the reactions and functions of duplex DNA. Of immediate importance for their application as clinical diagnostic agents is investigation of the conductivity of DNA and its PNA analogs (5, 6).DNA must balance the dual requirements of chemical stability and ease of transcription and replication (7). It is clear that DNA is far from inert toward a variety of different reactive species, particularly oxidizing agents. Oxidative damage to DNA produced by normal metabolism, deep-UV laser irradiation (8), gamma rays (9), or pulse radiolysis (10) accumulates at guanine residues, an effect attributed to one-dimensional migration of a radical cation (''hole'') along the DNA helix (11). Both the low oxidation potential and reactivity of the guanine radical cation contribute to the effectiveness of guanine as a trap for the migrating hole. Because guanine lesions may be the major cause of mutations (12), intense attention is focused on understanding the conductivity properties of DNA to elucidate the mechanisms by which migration of oxidative damage occurs (13). In this regard, the recent reports by Barton and coworkers are particularly important (14, 15). They describe a system consisting of a rhodium complex that is covalently linked to one end of a DNA duplex. Irradiation caused damage to the DNA more than 30 Å from where the complex was presumed to intercalate. This observation opens up exciting opportunities to study the factors that control hole migration in nucleic acids.Photosensitizers often react with nucleic acids by single electron transfer to oxidize a base. Recent findings reveal that the...

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“…This limits the predictive power of those models in case of complex biomolecular systems. On the other hand, first-principle calculations [50][51][52][53][54][55][56][57][58][59][60][61][62][63] performed on static structures can provide accurate values for the electronic couplings but can hardly deal with the full transport problem. As a result, the development of methodologies exploiting the advantages of both approaches become highly desirable.…”

Section: Introductionmentioning

confidence: 99%

Modeling Charge Transport and Dynamics in Biomolecular Systems

Gutiérrez

Cuniberti

2023

JSAME

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Charge transport at the molecular scale builds the cornerstone of molecular electronics (ME), a novel paradigm aiming at the realization of nanoscale electronics via tailored molecular functionalities. Biomolecular electronics, lying at the borderline between physics, chemistry and biology, can be considered as a sub-field of ME. In particular, the potential applications of DNA oligomers either as template or as active device element in ME have strongly drawn the attention of both experimentalist and theoreticians in the past years. While exploiting the self-assembling and self-recognition properties of DNA based molecular systems is meanwhile a well-established field, the potential of such biomolecules as active devices is much less clear mainly due to the poorly understood charge conduction mechanisms. One key component in any theoretical description of charge migration in biomolecular systems, and hence in DNA oligomers, is the inclusion of conformational fluctuations and their coupling to the transport process. The treatment of such a problem affords to consider dynamical effects in a non-perturbative way in contrast to, e.g., conventional bulk materials. Here we present an overview of recent work aiming at combining molecular dynamic simulations and electronic structure calculations with charge transport in coarse-grained effective model R. Gutierrez and G. CunibertiHamiltonians. This hybrid methodology provides a common theoretical starting point to treat charge transfer/transport in strongly structurally fluctuating molecular-scale physical systems.

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DNA: insulator or wire?

Abstract: DNA-based electron transfer reactions are seen in processes such as biosynthesis and radiation damage/repair, but are poorly understood. What kinds of experiments might tell us how far and how fast electrons can travel in DNA? What does modern theory predict?

Cited by 176 publications

References 26 publications

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

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

Peptide nucleic acid–DNA duplexes: Long range hole migration from an internally linked anthraquinone

Modeling Charge Transport and Dynamics in Biomolecular Systems

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