Tuning the Stability of DNA Nanotubes with Salt

Abstract

We report the enhancement of the structural stability of a DNA nanotube (DNT) by changing the salt concentrations for three different salt species, namely, NaCl, KCl, and MgCl2. Using fully atomistic molecular dynamics simulations, we find that, with the gradual increment in the NaCl salt concentration, the DNT becomes compact and rigid. The significant reduction in the average root-mean-square deviation, root-mean-square fluctuation, and effective radius of the DNT with an increase in the NaCl concentration quantifies our observation. We explain how the DNT–ion interactions play a vital role in the conformational fluctuation of the DNT. To understand the salt dependence of the mechanical properties of the DNTs, we have calculated the stretch modulus (γ) and persistence length (LP) as a function of salt concentration. The calculated stretch moduli of the DNTs change from 8.3 to 13 nN, and the persistence length of the DNT varies from 6 to 10 μm when the NaCl salt concentration is varied from 0 to 1 M. Both the stretch modulus and the persistence length calculations reaffirm the structural stability of the DNT at higher salt concentrations. We find similar trends for another monovalent salt (KCl). However, for a divalent salt (MgCl2), we find minimal variation in the structural properties with an increase in the salt concentration.