Computational study of the role of counterions and solvent dielectric in determining the conductance of B-DNA

Abstract

DNA naturally exists in a solvent environment, comprised of water and salt molecules such as sodium, potassium, magnesium, etc. Along with the sequence, the solvent conditions become a vital factor determining DNA structure and thus its conductance. Over the last two decades, researchers have measured DNA conductivity both in hydrated and almost dry (dehydrated) conditions. However, due to experimental limitations (the precise control of the environment), it is very difficult to analyze the conductance results in terms of individual contributions of the environment. Therefore, modeling studies can help us to gain a valuable understanding of various factors playing a role in charge transport phenomena. DNA naturally has negative charges located at the phosphate groups in the backbone, which provides both the connections between the base pairs and the structural support for the double helix. Positively charged ions such as the Sodiumion (Na + ), one of the most commonly used counterions, balance the negative charges at the backbone. This modeling study investigates the role of counterions both with and without the solvent (water) environment on charge transport through double-stranded DNA. Our computational experiments show that in dry DNA, the presence of counterions affects electron transmission at the lowest unoccupied molecular orbital energies. However, in solution, the counterions have a negligible role in transmission. Using the polarizable continuum model calculations, we demonstrate that the transmission is significantly higher at both the highest occupied and lowest unoccupied molecular orbital energies in a water environment as opposed to in a dry one. Moreover, calculations also show that the energy levels of neighboring bases are more closely aligned to ease electron flow in the solution.

Electronic Properties of DNA Origami Nanostructures Revealed by In Silico Calculations

“…Next, we carry out Green’s function-based charge transport calculations by following the methods used in our previous studies. , From the DFT calculations, we obtain the Fock, H 0 , and overlap matrices, S 0 . Then, we use the Löwdin transformation to convert H 0 into a Hamiltonian, H orthogonal , where the diagonal elements represent the energy levels at each atomic orbital, and the off-diagonal elements correspond to the coupling between the different atomic orbitals: H orthogonal = S 0 − 1 2 H 0 S 0 − 1 2 …”

Intra-strand phosphate-mediated pathways in microsolvated double-stranded DNA

“…However, the phosphate groups in DNA molecules are not covalently bind to hydrogen atoms but are surrounded by water molecules and counterions. To address the possible role of phosphate-mediated charge transport, it is necessary to perform QC computations of hydrogenuncapped dsDNA molecules, where the QM part will include both the uncapped phosphates and the inner solvation shell of dynamically generated water molecules and counterions [2,12,27,[41][42][43][44][45].…”

“…For a more realistic description of dry dsDNA electronic structure, the inner-solvation shell of MD generated water molecules and counterions should be included in the QM part of the computations [2,12,27,[41][42][43][44][45]. To this end, we perform DFT computations on several MD snapshots of the inhomogeneous intact structure.…”

“…To explore dynamical-disorder effects, we first perform MD simulations on the 100 bp sequences studied in the experiment, both intact and nicked, under different levels of solvation, and with end constraints to mimic the binding to the leads. To fully address the role of the backbone in charge transport, we also perform quantum chemical (QC) computations on MD snapshots of hydrogen-uncapped DNA, where the quantum mechanical (QM) part includes both the uncapped phosphates and the inner solvation shell of dynamically generated water molecules and counterions [2,12,27,[41][42][43][44][45]. The DFT computations are very demanding and are done on different small DNA-solvent segments taken from several 100 bp snapshots.…”