DNA elasticity from coarse-grained simulations: The effect of groove asymmetry

Abstract

It is well-established that many physical properties of DNA at sufficiently long length scales can be understood by means of simple polymer models. One of the most widely used elasticity models for DNA is the twistable wormlike chain (TWLC), which describes the double helix as a continuous elastic rod with bending and torsional stiffness. An extension of the TWLC, which has recently received some attention, is the model by Marko and Siggia, who introduced an additional twist-bend coupling, expected to arise from the groove asymmetry. By performing computer simulations of two available versions of oxDNA, a coarsegrained model of nucleic acids, we investigate the microscopic origin of twist-bend coupling. We show that this interaction is negligible in the oxDNA version with symmetric grooves, while it appears in the oxDNA version with asymmetric grooves. Our analysis is based on the calculation of the covariance matrix of equilibrium deformations, from which the stiffness parameters are obtained. The estimated twist-bend coupling coefficient from oxDNA simulations is G = 30 ± 1 nm. The groove asymmetry induces a novel twist length scale and an associated renormalized twist stiffness κ t ≈ 80 nm, which is different from the intrinsic torsional stiffness C ≈ 110 nm. This naturally explains the large variations on experimental estimates of the intrinsic stiffness performed in the past.

Coarse-Grained Modelling of DNA Plectoneme Pinning in the Presence of Base-Pair Mismatches

“…To calculate the twist between two consecutive bps, we use the method defined by Skoruppa et al 55 ; specifically the definition of Triad II, as defined by Skoruppa et al, is used for all calculations.…”

“…Twist can then be defined as the angle between the two for each base pair in the base pair step along the . A more detailed description can be found in Skoruppa et al 55 .…”

Twist-bend coupling and the statistical mechanics of DNA: perturbation theory and beyond

“…(28), plotted with solid lines. The differences are within 5%, and are probably due to higher order corrections in 1/f (recall that all analytical results are based on [15]. oxDNA1, which has symmetric grooves, is characterized by a negligible twist-bend coupling constant, while G = 25 nm for oxDNA2, which has asymmetric grooves.…”

“…oxDNA is a coarse-grained model describing DNA as two intertwined strings of rigid nucleotides [29]. It has been used for the study of a variety of DNA properties, ranging from single molecules to large-scale complexes [15,16,29,[31][32][33]. To date, two versions of oxDNA exist: one with symmetric grooves (oxDNA1) [29] and one with asymmetric grooves (oxDNA2) [32].…”

“…Only a limited number of studies have considered the effect of twistbend coupling on DNA mechanics [13][14][15][16]. A systematic analysis of coarse-grained models with and without groove asymmetry have highlighted several effects associated with twist-bend coupling at long [15] and short [16] length scales. Here, we aim to clarify the role of G in the statistical mechanics of long DNA molecules, as analyzed in optical and magnetic tweezers.…”