DNA twist at high alkali ion concentrations: evidence against C-form DNA in solution

Abstract

DNA is highly negatively charged, making its structure strongly dependent on the ionic environment. DNA twist—a central DNA property—varies with ion concentration and identity. Prior studies have focused on salt concentrations below 1 M, and it is unclear whether twist trends persist at higher concentrations. It has been proposed that at high salt, DNA transitions from its canonical B-form to C-form, originally observed by fiber diffraction. Here, we use single-molecule magnetic tweezers to measure DNA twist in high concentrations of LiCl, NaCl, KCl, and CsCl. For all salts, twist initially increases approximately as ∼[salt]1/2, but plateaus and even decreases above 3 M. LiCl causes the largest twist increase, by ≤ 0.9° bp−1, compared with physiological salt, still far below the suggested C-form values of 2–3° bp−1. We perform extensive all-atom molecular dynamics simulations for DNA in LiCl solutions with different force fields. For parmbsc1, we observe good agreement with experiments when ion activities are taken into account. We find that simulations initiated in the C-form rapidly convert to the B-form, while the B-form remains stable.