Force-dependent elasticity of nucleic acids

Abstract

The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort...

Systematic Comparison of Atomistic Force Fields for the Mechanical Properties of Double-Stranded DNA

“…47 θ of the molecule as a whole are defined starting from atomistic data, and the elastic constants S, C, and g are determined from stress-vs-strain curves 48,49 or by analyzing the thermal fluctuations of L and θ. 50,51 The parm99 force field 52 in combination with the bsc0 modification 53 has been shown to predict elastic constants in good quantitative agreement with the experimental estimations. 46,48,49,54,55 More recently, further force-field modifications have been proposed�OL15 56 and bsc1 57 �mainly to improve on the prediction of the helical twist, which was slightly underestimated in bsc0.…”

“…Following the theory presented in ref , the elastic parameters in eq can be computed at each value of F by analyzing the fluctuations involving L and θ, thus unveiling the presence of force dependence in the elastic response. For completeness, we report here the formulas employed in this work and derived in ref true{ .25ex2ex S = L 0 k B T false⟨ Δ θ 2 false⟩ F − F ( ⟨ normalΔ L normalΔ θ ⟩ F ⟨ normalΔ θ ⟩ F − ⟨ normalΔ θ 2 ⟩ F ⟨ normalΔ L ⟩ F ) false⟨ Δ L 2 false⟩ F false⟨ Δ θ 2 false⟩ F − false⟨ Δ L Δ θ false⟩ F 2 C = L 0 k B T false⟨ Δ L 2 false⟩ F false⟨ Δ L 2 false⟩ F false⟨ Δ θ 2 false⟩ F −...…”

“…All in all, the present analysis fully extends to the bsc1 and OL15 force fields our previous findings on the force-induced stiffening of dsDNA. 51 3.4. Twist Modulus Ranking Depends on Sequence.…”

“…It is worth mentioning that this duplex is the most crooked molecule, for which the force-induced straightening of the spontaneous curvature is likely to induce a softer twist response. 51 3.5. Force Fields Qualitatively Capture the Twist-Stretch Coupling.…”

Influence of temperature on bend, twist and twist–bend coupling of dsDNA

“…36 These force-dependent twist elasticities were corroborated by all-atom MD simulations employing short dsDNA sequences. 37,38 Subsequently, the twistable wormlike chain (TWLC) model and an elastic model proposed by Marko and Siggia (MS) 39 were employed to reconcile these experimental findings, yielding excellent agreement. 40 MD simulation data further suggested that the twist persistence length is influenced by groove asymmetry in dsDNA.…”