Atomic description of the reciprocal action between supercoils and melting bubbles on linear DNA

Abstract

Although the response of DNA to physiological torsion and tension is well characterized, the detailed structures are not known yet. By using molecular dynamics simulations on linear DNA with 300 bp, we provide, for the first time, the conformational phase diagram at atomic resolution. Our simulations reveal a novel state in negative supercoiling, where denaturation bubbles form in AT-rich regions independently of the underlying DNA topology, focusing at the tip of plectonemes only when tension is applied. We propose these sequence-dependent bubbles could position plectonemes in longer DNA.