Dramatic changes in DNA conductance with stretching: structural polymorphism at a critical extension

Abstract

aIn 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 Å or 17%) leading to a melted DNA state. In contrast, for 3'end1-3'end2 pulling it takes almost 32 Å (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 found that the dramatically different conductance behaviors for two different pulling protocols arise from how the hydrogen bonds of DNA base pairs break.

Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA

“…S14) with OS3 scheme (and melted-DNA with OS5 scheme) is independent of DNA length. It is worth mentioning that apart from the 12 bp and 30 bp length studied here, we have also looked at the force extension behavior for 20 bp long dsDNA in our recent work [78]. All these simulations prompted us to comment that the force-extension and H-bond breaking behavior is qualitatively insensitive to DNA length.…”

DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase

“…Experimental results of Albrecht et al show that the differences in behaviour of DNA when using different pulling schemes can depend on the loading rate, with stretching forces propagating first at high pulling rates, but shearing becoming dominant at slower pulling rates (Albrecht et al 2008). Others have also shown that there are structural differences when using different pulling mechanisms (Bag et al 2016; Danilowicz et al 2009; Roe & Chaka, 2009).…”

“…The most readily available information on DNA under tension is the empirically measured force-extension curve (Rief et al 1999; Smith et al 1992), which provides the clear signal of some transition, but no atomistic-level information. This is supplemented by fluorescence and polarised-light studies (van Mameren et al 2009; Nordén et al 1992; King et al 2013), and by atomistic simulations which are able to provide explicit descriptions of the DNA but which are limited in the accessible timescales and system sizes (Bag et al 2016; Konrad & Bolonick., 1996; Lebrun & Lavery, 1996; Li & Gisler, 2009; Roe & Chaka, 2009).…”

Stacking Effects on Charge Transfer Dynamics in Fluctuating DNA

“…are variables as nuclear configuration evolves with time while the reorganization energy λ is pre-prepared parameter in our model. Refer to previous theoretical study, 16,23,26,31,41,42 their definitions and calculations are as follows.…”

“…18 Renaud et al included the interactions with molecular vibrational modes in the Hamiltonian and obtained CT rates quantitatively consistent with experimental data. 17 On the other hand, a cross-scale method combining the MD, QM, Marcus electron transfer theory and kinetic Monte Carlo (MC) simulations was also employed to study DNA CT. 21,23 In comparison with the former, the latter is less used and needs more exploration.…”