Dramatic changes in DNA Conductance with stretching: Structural Polymorphism at a critical extension

TL;DR

This study uses multiscale modeling to explore how mechanical stretching induces structural changes in DNA that dramatically alter its electrical conductance, revealing protocol-dependent conductance jumps linked to base pair hydrogen bond breaking.

Contribution

It provides the first detailed multiscale analysis of DNA conductance changes during mechanical stretching, highlighting the impact of pulling protocol on conductance behavior.

Findings

Abrupt conductance jump occurs at 17% stretching for 5'end1-5'end2 pulling.

Significantly longer stretching (84%) is needed for a similar jump in 3'end1-3'end2 pulling.

Different pulling protocols cause distinct conductance behaviors due to hydrogen bond breaking patterns.

Abstract

In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out multiscale modeling, to predict the conductance of dsDNA as it is mechanically stretched to promote various structural polymorphisms. We calculate the current along the stretched DNA using a combination of molecular dynamics simulations, non-equilibrium pulling simulations, quantum mechanics calculations, and kinetic Monte Carlo simulations. For 5'end1-5'end2 attachments we find an abrupt jump in the current within a very short stretching length (6 $ \AA $ or 17 %) leading to a melted DNA state. In contrast, for 3'end1-3'end2 pulling it takes almost 32$ \AA $ (84 %) of stretching to cause a similar jump in the current. Thus, we demonstrate that charge transport in DNA can occur over stretching lengths of several nanometers. We find that this unexpected behaviour in the B to S conformational DNA transition arises from highly inclined base pair geometries that result from this pulling protocol. We find that the dramatically different conductance behaviors for two different pulling protocols arise from the nature of how hydrogen bonds of DNA base pairs break.