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We study electronic transport in long DNA chains using the tight-binding approach for a ladder-like model of DNA. We find insulating behavior with localizaton lengths xi ~ 25 in units of average base-pair seperation. Furthermore, we observe small, but significant differences between lambda-DNA, centromeric DNA, promoter sequences as well as random-ATGC DNA.
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We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases $A$ and $C$, which has been shown previously to have different interactions with the pore. We study DNA with repeating blocks $A_nC_n$ for various values of $n$, and find that the translocation time depends strongly on the {em block length} $2n$ as well as on the {em orientation} of which base entering the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences are contained in the periodicity of the residence time of the individual nucleotides inside the pore.
We study the elastic properties of a single A/B copolymer chain with a specific sequence. We predict a rich structure in the force extension relations which can be addressed to the sequence. The variational method is introduced to probe local minima on the path of stretching and releasing. At given force, we find multiple configurations which are separated by energy barriers. A collapsed globular configuration consists of several domains which unravel cooperatively. Upon stretching, unfolding path shows stepwise pattern corresponding to the unfolding of each domain. While releasing, several cores can be created simultaneously in the middle of the chain resulting in a different path of collapse.
The question of whether DNA conducts electric charges is intriguing to physicists and biologists alike. The suggestion that electron transfer/transport in DNA might be biologically important has triggered a series of experimental and theoretical investigations. Here, we review recent theoretical progress by concentrating on quantum-chemical, molecular dynamics-based approaches to short DNA strands and physics-motivated tight-binding transport studies of long or even complete DNA sequences. In both cases, we observe small, but significant differences between specific DNA sequences such as periodic repetitions and aperiodic sequences of AT bases, lambda-DNA, centromeric DNA, promoter sequences as well as random-ATGC DNA.
We propose a model Hamiltonian for describing charge transport through short homogeneous double stranded DNA molecules. We show that the hybridization of the overlapping pi orbitals in the base-pair stack coupled to the backbone is sufficient to predict the existence of a gap in the nonequilibrium current-voltage characteristics with a minimal number of parameters. Our results are in a good agreement with the recent finding of semiconducting behavior in short poly(G)-poly(C) DNA oligomers. In particular, our model provides a correct description of the molecular resonances which determine the quasi-linear part of the current out of the gap region.
In this study, we compare the charge transport properties of multiple (double stranded) dsRNA sequences with corresponding dsDNA sequences. Recent studies have presented a contradictory picture of relative charge transport efficiencies in A-form DNA:RNA hybrids and dsDNA. Using a multiscale modelling framework, we compute conductance of dsDNA and dsRNA using Landauer formalism in coherent limit and Marcus-Hush theory in the incoherent limit. We find that dsDNA conducts better than dsRNA in both the charge transport regimes. Our analysis shows that the structural differences in the twist angle and slide of dsDNA and dsRNA are the main reasons behind the higher conductance of dsDNA in the incoherent hopping regime. In the coherent limit however, for the same base pair length, the conductance of dsRNA is higher than that of dsDNA for the morphologies where dsRNA has smaller end-to-end length relative to that of dsDNA.
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