Surface charges effects on the 2D conformation of supercoiled DNA

We have adsorbed plasmid pUc19 DNA on a supported bilayer. The mobility of the lipids within the bilayer ensured a 2D equilibrium of the DNA molecule. By varying the fraction of cationic lipids in the membrane, we have tuned the surface charge. Plasmids conformations were imaged by Atomic Force Microscopy (AFM).We performed two sets of experiments: deposition from salt free solution on charged bilayers and deposition from salty solutions on neutral bilayers. Plasmids can be seen as rings, completely opened structures, or tightly supercoiled plectonemes, depending on the experimental conditions. The plectonemic conformation is observed either on a highly charged surface in the absence of salt or on a neutral bilayer at 30 mM of salt. We demonstrate the equivalence of surface screening by mobile interfacial charges and bulk screening from salt ions. INTRODUCTION Since its discovery (1), supercoiled DNA has been extensively studied by biologists and by physicists. The former were mostly interested in its implication in biological processes (2-8), the later were amazed by the beauty of its structure and studied its topology and conformation (9,10). Topology and conformation are inter-dependent so that, in order to study the conformation of a supercoiled DNA we need to define a few topological concepts. A supercoiled DNA is a circular double stranded DNA (ds-DNA) molecule that is constrained by a fixed linking number Lk. Lk is a topological invariant. Two other numbers are of great importance: the Twist number TW and the Writhing number Wr. These three quantities are linked by the following equation: r W k W T L + = . Because of the natural twist of the DNA double helix, there is an intrinsic linking number Lk0. Therefore, in practice, linking numbers are always defined with respect to Lk0 via the linking number difference ∆Lk. As Lk0 increases with the DNA length, one usually introduces an intensive parameter σ, the supercoiled density, that enables the comparison of plasmids of different lengths :