Twist-diameter coupling drives DNA twist changes with salt and temperature

Abstract

DNA deformations upon environmental changes, e.g., salt and temperature, play crucial roles in many biological processes and material applications. Here, our magnetic tweezers experiments observed that the increase in NaCl, KCl, or RbCl concentration leads to substantial DNA overwinding. Our simulations and theoretical calculation quantitatively explain the salt-induced twist change through the mechanism: More salt enhances the screening of interstrand electrostatic repulsion and hence reduces DNA diameter, which is transduced to twist increase through twist-diameter coupling. We determined that the coupling constant is 4.5 ± 0.8 k B T/(degrees∙nm) for one base pair. The coupling comes from the restraint of the contour length of DNA backbone. On the basis of this coupling constant and diameter-dependent DNA conformational entropy, we predict the temperature dependence of DNA twist Δω bp /Δ T ≈ −0.01 degree/°C, which agrees with our and previous experimental results. Our analysis suggests that twist-diameter coupling is a common driving force for salt- and temperature-induced DNA twist changes.

Understanding the Structural Elasticity of RNA and DNA: All‐Atom Molecular Dynamics

“…Generally, the microscopic structural parameters, that describe the elastic properties, are coupling with each other. [ 27 ] These coupling parameters include the twist‐stretch coupling, [ 46,47,49 ] twist‐diameter coupling, [ 77 ] and so on. Here, we considered stretch‐twist, twist‐inclination, and twist‐roll couplings, as shown in Figures 7 and 8.…”

“…The translation parameters, that is, the Rise D , the H‐rise $$D_{z}$$, and the Slide $$D_{y}$$, as shown in Figure 2b, describe the length relationship between the two adjacent base pairs. Usually, the Groove model was used to describe the conformations of the nucleic acids, [ 11,77 ] in which the $$W_{\min }$$ and the $$D_{\min }$$ denote the width and depth of the minor groove while the $$W_{\text{maj}}$$ and the $$D_{\text{maj}}$$ represent the width and depth of the major groove, as shown in Figure 2b.…”

“…Generally, the microscopic structural parameters, that describe the elastic properties, are coupling with each other. [27] These coupling parameters include the twist-stretch coupling, [46,47,49] twistdiameter coupling, [77] and so on. Here, we considered stretchtwist, twist-inclination, and twist-roll couplings, as shown in In the experiment, the elastic modulus can be measured in the dsRNA and dsDNA chains under external forces, Libel et al concluded that dsDNA and dsRNA had an opposite twist-stretch coupling coefficient under 100 mm NaCl solution.…”

Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions

“…In addition, due to the polyanionic nature of DNAs, metal ions (e.g., Na + and Mg 2+ ) in solutions can play an essential role in DNA folding and dynamics [12][13][14][62][63][64][65]. Although several of the existing models such as 3SPN, oxDNA, TIS, and NARES-2P have taken the electrostatic interactions into account using the Debye-Huckel approximation or mean-field multipole-multipole potentials and reproduced some monovalent salt-dependent structural properties (e.g., persistence length, torsional stiffness or melting temperatures) of DNAs [45,48,50,58], quantitatively predicting the 3D structure and thermodynamic stability for DNA including both ssDNA and dsDNA in ion solutions (especially divalent ions) from the sequence is still an unresolved problem.…”

Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions

“…In addition, due to the polyanionic nature of DNAs, metal ions (e.g., Na + and Mg 2+ ) in solutions can play an essential role in DNA folding and dynamics (12)(13)(14)(61)(62)(63)(64). Although several of the existing models such as 3SPN, oxDNA, TIS, and NARES-2P have taken the electrostatic interactions into account using the Debye-Huckel approximation or mean-field multipole-multipole potentials and reproduced some monovalent salt-dependent structural properties (e.g., persistence length, torsional stiffness or melting temperatures) of DNAs (45,48,50,57), quantitatively predicting the 3D structure and thermodynamic stability for DNA including both ssDNA and dsDNA in ion solutions (especially divalent ions) from the sequence is still an unresolved problem.…”