In biological systems, DNA is often found in congested states. The congestion can come from high concentrations of the genome itself, protein, other biomacromolecules (crowding), and/or the presence of quasi-stationary elements such as fiber lattices and membranes (confinement). It is now well established that the congestion has an important effect on molecular structure, transport, reaction rates, and chemical equilibrium. In my presentation, I will discuss a few in vitro and in silico studies showing how crowding and confinement affect the conformation of DNA.
In the first part of my talk, I will discuss the interduplex distance of supercoiled plasmid and how this is controlled by DNA crowding. For this purpose, I will present results from small angle neutron scattering obtained in the condition of zero average scattering length contrast using mixtures of hydrogenated and perdeuterated plasmid. The obtained single molecule scattering form factors are analyzed with the help of Monte Carlo computer simulation. We will show that besides ionic strength, DNA crowding is important in controlling the interwound structure and site juxtaposition of distal segments of supercoiled DNA. I will discuss possible future experiments to elucidate the effect of macromolecular crowding on the conformation of plasmids close to the native state.
In the second part, single DNA molecules will be confined in nanochannels with cross-sectional diameters in the range of 50 to 300 nm. Here, we will investigate the effects of crowding by a neutral nanoparticles (dextran), like-charge protein (bovine serum albumin and hemoglobin), bacterial architectural protein (HFQ, HNS, and HU), as well as collagen-like block copolypeptide. Differences in behavior as observed inside the channels versus the bulk phase show that the effect of crowding is not only related to osmotic pressure and/or DNA protein interaction, but that the interplay with the anisotropic confinement is of paramount importance in controlling the conformation of DNA in a congested state.