Conformation dependent electronic transport in a DNA double-helix

Abstract

In this work we report the study of conformation dependent electronic transport properties of DNA double-helix within tight-binding framework including its helical symmetry. We have studied the changes in localization properties of DNA as we alter the number of stacked bases within a pitch of the double-helix keeping the total number of nucleotides in the DNA chain fixed. We take three DNA sequences, two of them are periodic and one is random and observe that localization length increases as we increase the radius of DNA double-helix i.e., number of nucleotides within a pitch. We have also investigated the effect of backbone energetic on the I-V response of the system and we find that in presence of helical symmetry, depending on the interplay of conformal variation and disorder strength DNA can be found in either metallic or semiconducting and even in an insulating phase, which in turn successfully explain all the experimental findings by a single model.

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

“…A similar transition has been reported by introducing conformal variation at the helical symmetry as well as backbone disorder into a FLM [121]. Helical symmetry is taken into account via the inclusion of hopping integrals between bases in adjacent pitches (i.e., turns of the helix).…”

“…For strong disorder, the current is considerably enhanced with increasing n, giving a insulator to metal transition. Reproduced from Ref [121],. S. Kundu and S. N. Karmakar, Conformation dependent electronic transport in a DNA double-helix, AIP Adv.…”

“…S. Kundu and S. N. Karmakar, Conformation dependent electronic transport in a DNA double-helix, AIP Adv. 2015, 5, 107122[121] http://dx.doi. org/10.1063/1.4934507, CC BY 3.0.…”

Detection of base-pair mismatches in DNA using graphene-based nanopore device

“…Whereas interstrand hopping between nucleobases is taken as v=0.035 eV, one order of magnitude less than the intrastrand hopping. These values are consistent with previous reports [42,43,44,45,46]. Fig.…”

Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials

“…Furthermore, hydration around the DNA strands increases stiffness [125], and salt interactions determine the length-scale of this hydration layer resulting in significant swelling of DNA fibers in the absence of salt [60]. Salts act as counterions to stabilize the negative charge of the DNA backbone and govern hole transfer along dsDNA, while the conformational state is responsible for electronic coupling through π-orbital base stacking [126][127][128][129] This mechano-electronic coupling has been utilized to develop a FRET-based nanosensor for mercury [130] and demonstrated an order of magnitude increase in conductivity for A-form DNA relative to its B-form [131]. An alternative mechanoelectric DNA-based probe was developed for potassium detection based on the conformational transition of DNA into a G-quadruplex [132].…”