Friction and Interactions between Bare DNA Molecules: The Role of DNA Handedness

Abstract

Cellular DNA is packaged through a range of re-modeling proteins. As a result, disparate regions of the genome may find themselves in close contact with one another. Here, we address an important and emerging issue resulting from this fact: what happens when DNA becomes entangled? Is it possible that the mechanical properties of DNA can influence interactions of the genome even in the absence of proteins? Recent experiments have suggested that the handedness of DNA may affect the stability of DNA-DNA pairs.Using a single-molecule approach, we employ a unique 4-way optical trap to wrap two separate DNA molecules around one another. By displacing optically trapped beads, it is possible to slide one DNA molecule along the other. Using triangulation, we are then able to track the location at which the DNA molecules are entwined. This analysis reveals that a small but clear friction is present only when sliding the DNA molecule through a right-handed wrap. Moreover, when sliding the DNA further, tension is built up and then released, giving rise to an abrupt stick-release force pattern. Strikingly, the latter is once again found predominantly in the case of a right-handed wrap. By staining the DNA molecules with the force-sensitive fluorescent dye Sytox, we are able to both visualize and measure this build-up and release of force. The stick-release behavior occurs only after a force of ∼65 pN has been applied. This suggests that the DNA molecules interact at their point of contact via melting of base-pairs, possibly creating a 3- or 4-stranded complex.The existence of chiral and force dependent interactions between bare DNA molecules has strong implications for the study of DNA in confined environments and raises interesting questions as to their potential importance in vivo.