Electrical conductance in duplex DNA: Helical effects and low-frequency vibrational coupling

Maciá, Enrique

doi:10.1103/physrevb.76.245123

Cited by 30 publications

(29 citation statements)

References 53 publications

(68 reference statements)

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“…31 Subsequently, the combined effect of helical structure and bps twist motion on charge transfer through more realistic duplex DNA at low temperatures was considered. 32 The physical picture emerging from that work was that although an ensemble of bps twisting back and forth around the helix axis generally results in a degraded charge-transfer efficiency, a significant improvement of charge migration can occur via charge coupling to certain lattice modes at low temperatures, in line with several works suggesting that structural fluctuations may facilitate charge transfer in DNA. 9,33,34 In fact, recent quantum-mechanics/ molecular-dynamics studies of a duplex ͑GT͒ 15 oligomer have shown the presence of large fluctuations of t 2 ͑the magnitude determining the charge-transfer rate͒ about one order of magnitude larger than the averaged ͗t 2 ͘ value, occurring every 1 ps on the average.…”

Section: Introductionsupporting

confidence: 63%

“…Thus, effective model Hamiltonians can be expressed as the sum of two main contributions H = H e + H l , where H e describes the charge dynamics over the -stacked electronic system and H l describes the duplex DNA dynamics. The electronic degrees of freedom of a double-stranded DNA ͑including sugar-phosphate and environmental effects͒ are described in terms of the effective Hamiltonian, 32,42,43 …”

Section: Dna Model Descriptionmentioning

confidence: 99%

“…In order to visualize the corresponding patterns we will assume that, for small enough relative displacements, the Euclidean distance between two neighboring bases can be expressed as d n,nϮ1 ͑ ͒Ӎ n,nϮ1 ͑ ͒. 32 Making use of the basic relationship d n,nϮ1…”

Section: Long-range Correlated Resonance Effectsmentioning

confidence: 99%

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π−πorbital resonance in twisting duplex DNA: Dynamical phyllotaxis and electronic structure effects

Maciá

2009

Phys. Rev. B

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The presence of synchronized, collective twist motions of the Watson-Crick base pairs in DNA duplexes ͑helicoidal standing waves͒ can efficiently enhance the -orbital overlapping between nonconsecutive base pairs via a long-range, phonon-correlated tunneling effect. The resulting structural patterns are described within the framework of dynamical phyllotaxis, providing a realistic treatment which takes into account both the intrinsic three-dimensional, helicoidal geometry of DNA, and the coupling between the electronic degrees of freedom and double-helix DNA molecular dynamics at low frequencies. The main features of the resulting electronic band structures are discussed for several resonance frequencies of interest, highlighting the possible biophysical implications of the obtained results.

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Section: Introductionsupporting

confidence: 63%

Section: Dna Model Descriptionmentioning

confidence: 99%

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π−πorbital resonance in twisting duplex DNA: Dynamical phyllotaxis and electronic structure effects

Maciá

2009

Phys. Rev. B

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“…In addition, carrier coupling to low-frequency vibrational modes may give rise to a significant improvement of the conductance. 15 Recent experiments in poly͑G͒-poly͑C͒ and poly͑A͒-poly͑T͒ DNA molecules in solution suggest that they may act as nanowires supporting high electrical current under moderate bias. 9 The nucleotide sequence in synthetic poly͑G͒-poly͑C͒ and poly͑A͒-poly͑T͒ DNA molecules is periodic.…”

Section: Introductionmentioning

confidence: 99%

Bloch-like oscillations in the Peyrard-Bishop-Holstein model

2008

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The Peyrard-Bishop-Holstein model has been previously introduced as an appropriate framework for the description of polaronic effects for charge migration in DNA. We study numerically the Peyrard-BishopHolstein model when the charge carrier is also subjected to an applied uniform electric field. We find that the polaron undergoes coherent oscillations when the electric field is applied along the stacking direction. The frequency of the oscillations is the same as in the rigid lattice ͑Bloch frequency͒ provided that the carrier-lattice coupling is not large. Increasing the coupling the single peak of the Fourier spectrum splits into side peaks around the Bloch frequency.

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“…In that case, the effective model Hamiltonian can be expressed as the sum of two main contributions H ¼ H e þ H l , where H e describes the charge carrier dynamics over the p-stacked electronic system and H l describes the duplex DNA dynamics. The electronic degrees of freedom of a double-stranded DNA (including sugar-phosphate and environmental effects) are described in terms of the effective Hamiltonian [23],…”

Section: Helical Geometry and Dynamical Effectsmentioning

confidence: 99%

Charge transfer in DNA: effective Hamiltonian approaches

Maciá¹

2009

Zeitschrift Für Kristallographie - Crystalline Materials

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Abstract. Aperiodic order plays a very significant role in biology, as it determines most informative content of genomes. Amongst the various physical, chemical or biological phenomena that might be inferred from sequence correlations, charge transfer properties deserve particular attention. Indeed, the nature of DNA-mediated charge migration has been related to the understanding of damage recognition process, protein binding, or with the task of engineering biological processes (e.g. designing nanoscale sensing of genomic mutations), opening new challenges for emerging nanobiotechnologies. Nevertheless, the solution of Schrö-dinger's equation with a potential that is given by a onedimensional array of the double-stranded DNA remains as a main open theme in solid state physics of biological macromolecules. In this contribution, I will shortly review several approaches introduced during the last few years in order to describe charge transfer migration in DNA in terms of tightbinding effective Hamiltonians. Conceptual and physical motivationsDuring the 1930s, DNA was considered to be merely a tetranucleotide composed of one unit each of deoxyadenylic, -guanilyc, -thymidylic, and -cytidilic acids (the particular order of appearance of each of these bases being considered as irrelevant). Even when it was subsequently realized that the molecular weight of DNA is actually much higher, it was still widely believed that the tetranucleotide unit was the basic repeating building block of the large DNA polymer, in which the four different kinds of nucleotides recur in periodic sequence i.e., (GACT) n [1]. Thus, DNA was originally viewed as a trivially periodic macromolecule, unable to store the amount of information required for the governance of cell function. The mystery of the nature of the genetic material attracted some physicists to genetics. Thus, Schrödinger suggested that a gene consists of a long sequence of a few repeating elements exhibiting a well defined order without the recourse of periodic repetition, and illustrated the vast combinatorial possibilities of such a structure. In this way, the notion of a one-dimensional aperiodic solid was introduced [2], and we can consider Schrödinger was the first person to put forward the notion of a linear genetic code [1]. Hence, Schrödinger's proposal of considering DNA as a one-dimensional aperiodic chain, with four different nucleotides arranged in a way able to store the required genetic information was progressively incorporated into dominant biophysical thinking. In fact, when macromolecules of biological interest are considered from the viewpoint of condensed matter physics, a fundamental question naturally arises regarding the potential role of certain physical properties on their biological functions. In particular, the role of charge migration in DNA mutation repair has been extensively discussed during the last decade, and the possible existence of correlation effects in electrical conductivity due to the presence of long-range spatial correlations in DNA ha...

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Electrical conductance in duplex DNA: Helical effects and low-frequency vibrational coupling

Cited by 30 publications

References 53 publications

π−πorbital resonance in twisting duplex DNA: Dynamical phyllotaxis and electronic structure effects

π−πorbital resonance in twisting duplex DNA: Dynamical phyllotaxis and electronic structure effects

Bloch-like oscillations in the Peyrard-Bishop-Holstein model

Charge transfer in DNA: effective Hamiltonian approaches

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