Methylation effect on the ohmic resistance of a poly-GC DNA-like chain

Moura, F. A. B. F. de; Lyra, M. L.; Almeida, M.L. de; Ourique, G.S.; Fulco, U. L.; Albuquerque, E.L.

doi:10.1016/j.physleta.2016.07.069

Cited by 7 publications

(7 citation statements)

References 35 publications

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“…In Ref. [112], a poly(CG) single-stranded segment is considered, with methyl groups randomly connected with the 5-carbon of C bases (forming the so-called 5-methylcytosine), again, with probability p. For completely unmethylated or methylated segments, the DOS consists of two smooth bands, derived by the on-site energy of G and C, for p = 0, and of G and 5-methylcytosine for p = 1, respectively; the only difference is in the energy intervals of the allowed states. For 0 < p < 1, the smooth profile of the DOS is degraded, since the presence of randomly distributed methyl groups along the chain introduces a small disorder, which in turn leads to an enhancement in the effective resistance that can reach one order of magnitude.…”

Section: Energy Structure Of Nucleic Acid Wiresmentioning

confidence: 99%

Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport

Lambropoulos

Simserides

2019

Symmetry

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This review is devoted to tight-binding (TB) modeling of nucleic acid sequences like DNA and RNA. It addresses how various types of order (periodic, quasiperiodic, fractal) or disorder (diagonal, non-diagonal, random, methylation et cetera) affect charge transport. We include an introduction to TB and a discussion of its various submodels [wire, ladder, extended ladder, fishbone (wire), fishbone ladder] and of the process of renormalization. We proceed to a discussion of aperiodicity, quasicrystals and the mathematics of aperiodic substitutional sequences: primitive substitutions, Perron–Frobenius eigenvalue, induced substitutions, and Pisot property. We discuss the energy structure of nucleic acid wires, the coupling to the leads, the transmission coefficients and the current–voltage curves. We also summarize efforts aiming to examine the potentiality to utilize the charge transport characteristics of nucleic acids as a tool to probe several diseases or disorders.

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Section: Energy Structure Of Nucleic Acid Wiresmentioning

confidence: 99%

Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport

Lambropoulos

Simserides

2019

Symmetry

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“…It is worth noting that epigenetic processes such as methylation (the addition of a methyl group (-CH

) to one of the bases) will modify the on-site nucleobase energy and its effective mass alike, thereby changing both the mass ratio parameter

among nucleotides and their

parameter value. While the role of methylation-related on-site energy changes has been discussed in several recent works [ 43 , 44 , 45 ], the role of methylation-related dynamical effects in the CT efficiency has not. Due to the presence of both an on-site energy term (

) and a transfer integral term (

) in the diagonal term of the effective Hamiltonian given by Equation ( 16 ), one should expect the possible existence of resonance effects involving both electronic and dynamical physical parameters in an intertwined fashion.…”

Section: Dna Model Hamiltonianmentioning

confidence: 99%

Base-Pairs’ Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules

Maciá

2020

Materials

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By introducing a suitable renormalization process, the charge carrier and phonon dynamics of a double-stranded helical DNA molecule are expressed in terms of an effective Hamiltonian describing a linear chain, where the renormalized transfer integrals explicitly depend on the relative orientations of the Watson–Crick base pairs, and the renormalized on-site energies are related to the electronic parameters of consecutive base pairs along the helix axis, as well as to the low-frequency phonons’ dispersion relation. The existence of synchronized collective oscillations enhancing the π-π orbital overlapping among different base pairs is disclosed from the study of the obtained analytical dynamical equations. The role of these phonon-correlated, long-range oscillation effects on the charge transfer properties of double-stranded DNA homopolymers is discussed in terms of the resulting band structure.

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“…Отметим, что теоретические и экспериментальные исследования различных модификаций ДНК, направленные на изучение свойств транспорта зарядов, развиваются в последнее время очень активно. Изучаются детали механизмов взаимодействия электронов с возмущениями цепочки нуклеотидов [23][24][25], рассчитываются вольт-амперные характеристики молекулы ДНК [26,27], анализируются способы управления характеристиками транспорта зарядов [28,29], исследуется влияние внешней среды [30], рассматриваются как перспективные сложные модификации, включающие ДНК [31][32][33][34][35][36], описываются различные прикладные возможности [37]. В настоящей же работе изучается взаимодействие электрона с мобильным бризером, возбужденным в небольшой группе смежных нуклеотидных пар у одного из закрепленных концов молекулы за счет начальных смещений нуклеотидов или возмущений их скорости.…”

Section: Introductionunclassified

Trapping and transport of charges in DNA by mobile discrete breathers

Chetverikov¹,

Sergeev²,

Лахно³

2018

Math.Biol.Bioinf.

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Аннотация. С использованием модели Пейрарда-Бишопа-Доксуа-Холстейна проведено численное моделирование захвата и транспорта заряда (электрона или дырки) в молекуле ДНК мобильными дискретными бризерами, возбуждаемыми начальными возмущениями скоростей или координат смежных нуклеотидных пар, дислоцированных около закрепленного конца молекулы. Показано, что эффективное образование стабильной квазичастицы «мобильный дискретный бризер + электрон» достигается при возмущении нескольких нуклеотидных пар, расположенных на конце молекулы. Бризеры могут быть возбуждены при возмущениях координат и скорости частиц как направленных к оси, так и от оси молекулы. Волновая функция электрона должна быть вначале локализована в области возмущения молекулы. Установлено, что метастабильная квазичастица может перемещаться на дистанцию до 200 межпарных расстояний. Описанный механизм транспорта заряженной частицы не требует наложения внешнего электрического поля и может рассматриваться как альтернативный поляронному механизму.

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Methylation effect on the ohmic resistance of a poly-GC DNA-like chain

Cited by 7 publications

References 35 publications

Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport

Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport

Base-Pairs’ Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules

Trapping and transport of charges in DNA by mobile discrete breathers

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