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

Abstract

Nucleic acids play essential roles in some biological processes and nanotechnology. Understanding their structural elasticity is very important for biological functions. Differences in structural elasticity of RNA and DNA duplexes are investigated by all‐atom molecular dynamics in this work. Two models double‐strand (ds) B‐DNA and A‐RNA short sequences are used. For two typical sequences, bending persistence length, stretch, and twist modulus are analyzed and compared in detail. These results demonstrate that dsDNA has a smaller bending persistence length value than dsRNA, however, the former has about 2.6 times stretch modulus than the latter one and the twist modulus in the former is smaller than the latter. Furthermore, the microstructural parameter analysis indicates that the inclination angle of a single base pair and the dihedral angle between two bases in a base pair, as well as the slide between adjacent base pairs, influences the structural elasticities of these two types of nucleic acids. Results also show that the dsDNA has a positive stretch‐twist coupling parameter while the dsRNA has a negative stretch‐twist coupling parameter. Results offer research comprehensive comparing and understanding about structural elasticity of RNA and DNA and provide novel perspectives for grasping nucleic acids' elastic properties.

RNA multiscale simulations as an interplay of electrostatic, mechanical properties, and structures inside viruses

“…Particularly, it was found that 𝑙 𝑝 = 43−51 nm for parm99+bsc0 [122], 𝑙 𝑝 = 40 − 60 nm for parm99+bsc1 [65,110,123] and 𝑙 𝑝 ≃ 60 nm for parm99+OL15 [110]. In the case of dsRNA, it was estimated that 𝑙 𝑝 = 70 − 80 nm for bsc0 [99] and bsc0+𝜒 OL3 [123]. Hence, all-atom simulations capture the relative bending flexibility of dsDNA and dsRNA, although slightly overestimating the quantitative estimations.…”

“…Atomistic simulations for dsDNA based on AMBER force fields account with good accuracy for the experimental results. Particularly, it was found that 𝑙 𝑝 = 43−51 nm for parm99+bsc0 [122], 𝑙 𝑝 = 40 − 60 nm for parm99+bsc1 [65,110,123] and 𝑙 𝑝 ≃ 60 nm for parm99+OL15 [110]. In the case of dsRNA, it was estimated that 𝑙 𝑝 = 70 − 80 nm for bsc0 [99] and bsc0+𝜒 OL3 [123].…”