Structural and mechanical properties of nucleic acid nanotubes: A combined all-atom and coarse-grained molecular dynamics study

Abstract

In this work, we introduce a computational framework to model nucleic acid nanotubes and estimate their mechanical properties using various levels of theory. Using atomistic molecular dynamics (MD) simulations, we report the enhancement of the structural and mechanical stability of DNA nanotube (DNT) by changing the salt concentrations. The calculated persistence length (Lp) of the DNTs is ~1-2 μm which is an order of magnitude higher than that of a single dsDNA. DNTs have stretch modulus (γ) value in the range of ~6-8 nN. We find that, with the gradual increment of salt concentration, an increase in Lp and γ which reaffirms the structural and mechanical stability of the DNT at higher salt concentrations. We also model DNT using two widely used coarse-grain (CG) models – namely Martini and oxDNA. We compare and contrast the all-atom MD and experimental results with the results obtained using these CG models. We also propose a model of hexagonal nanotubes made of dsRNA connected by double crossover at different positions. The calculated γ and Lp of the in silico modeled RNTs are in the same range of values as in the case of DNTs. Using helicoidal parameters of individual base pairs, we explain the relative flexibility and rigidity of the RNTs having different sequences.