Mechanically controlled DNA extrusion from a palindromic sequence by single molecule micromanipulation

Publication Type:

Journal Article

Source:

PHYSICAL REVIEW LETTERS, AMERICAN PHYSICAL SOC, Volume 96, Number 18, ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA (2006)

DOI:

10.1103/PhysRevLett.96.188102

Keywords:

BRANCH MIGRATION; CHAINS; CRUCIFORM STRUCTURES; ELASTICITY; GENETIC-RECOMBINATION; HELICAL REPEAT; LENGTH; SUPERCOILED DNA

Abstract:

A magnetic tweezers setup is used to control both the stretching force and the relative linking number Delta Lk of a palindromic DNA molecule. We show here, in absence of divalent ions, that twisting negatively the molecule while stretching it at similar to 1 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 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 Lk. We use then this experiment to obtain a precise measurement of the pitch of B-DNA in solution : 3.61 +/- 0.03 nm/turn.