Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores

Abstract

Mechanical manipulation of DNA, by forced extension, can lead to a structural transformation of double-stranded DNA (dsDNA) from a helical form to a linear zipper-like form. By employing classical molecular dynamics and quantum mechanical non-equilibrium Greens function-based transport simulations, we show the ability of graphene nanopores to discern different dsDNA conformations, in a helical to zipper transition, using transverse electronic conductance. In particular, conductance oscillations due to helical dsDNA vanish as dsDNA extends from helical to zipper form as it is transported through the nanopore. The predicted ability to detect conformational changes in dsDNA, via transverse electronic conductance, can widen the potential of graphene-based nanosensors for DNA detection.

Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores

“…For each snapshot, the electric potential induced by the charge distribution of ssDNA was determined by means of the self-consistent Poisson−Boltzmann equation. 30 , 31 Then the transverse conductance across the graphene sheet was calculated employing for the relevant electronic degrees of freedom a tight binding Hamiltonian and evaluating the current through the associated nonequilibrium Green’s function. 30 , 31 …”

“…Given the MD trajectory snapshots of translocating ssDNA defining the charge density ρ DNA ( r ) through the coordinates of all atoms and their partial charges, the electric potential φ( r ) was calculated using the Poisson−Boltzmann equation 30 , 31 In this calculation, the charges due to solute ions were described assuming a Boltzmann equilibrium, namely through Here, C K + ( r ) and C Cl – ( r ) are the local ion concentrations of K + and Cl – , and C 0 is the molar concentration in the solution which we have set to 1 M. Equations 3 – 5 were solved iteratively until convergence. The system was discretized into a 129 × 129 × 129 point grid, spanning a box of dimension 10 × 10 × 13 nm 3 .…”

“…Given the Hamiltonian ( eq 6 ), we employed the nonequilibrium Green’s function method 30 , 31 to calculate the transmission function T ( E ). The conductance for a given source-drain bias across the graphene ribbon is given by where h is the Planck constant, and f 1 ( E ) and f 2 ( E ) are the Fermi–Dirac distributions at source and drain, respectively.…”

Detection and mapping of DNA methylation with 2D material nanopores

“…Another advantage of electrically active 2D materials as nanopore membranes is the capability to measure in-plane transverse electronic sheet current, 42–44 in addition to the ionic current. 36–38,45 In our prior studies, we showed that a graphene layer with a nanopore in the center of an electric constriction is capable of detecting the conformational transition of a helical double-stranded DNA to a zipper DNA 46 as well as counting nucleotides in a single stranded DNA. 47,48 …”

Monte Carlo simulation algorithm for B‐DNA

“…The various techniques currently used for modeling DNA include user-directed modifications of all-atom models, [16,15,[19] ab initio modeling using dummy spheres, [20,21] rigid body modeling, [22,23] coarse-grained (CG) simulations, [24][25][26][27][28][29][30][31][32][33][34][35][36][37] and allatom molecular dynamics (MD). [38][39][40][41][42][43][44] Each of these modeling techniques has different advantages and disadvantages, but only CG and all-atom simulations incorporate physics of the DNA molecule. While all-atom MD is the most exhaustive, the large number of atoms in nucleosomes and nucleosome arrays, over 25,000 atoms per nucleosome, make this method intractable using commodity hardware.…”