Mechanically Controlled DNA Extrusion from a Palindromic Sequence by Single Molecule Micromanipulation

Abstract

A magnetic tweezers setup is used to control both the stretching force and the relative linking number $\Delta \mathrm{Lk}$ of a palindromic DNA molecule. We show here, in absence of divalent ions, that twisting negatively the molecule while stretching it at $\sim 1\mathrm{pN}$ induces the formation of a cruciform DNA structure. Furthermore, once the cruciform DNA structure is formed, the extrusion of several kilo-base pairs of palindromic DNA sequence is directly and reversibly controlled by varying $\Delta \mathrm{Lk}$. Indeed the branch point behaves as a nanomechanical gear that links rotation with translation, a feature related to the helicity of DNA. We obtain experimentally a very good linear relationship between the extension of the molecule and $\Delta \mathrm{Lk}$. We use then this experiment to obtain a precise measurement of the pitch of B-DNA in solution : $3.61\pm 0.03$ nm/turn.