DNA size in confined environments

Abstract

For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The ds-DNA is modeled by a mesoscopic Hamiltonian which accounts for the three dimensional helical structure and incorporates fluctuational effects at the level of the base pair. The computational method assumes that the base pair fluctuations are temperature dependent trajectories whose amplitudes can be spatially modulated according to the crowders distribution. We show that the molecular elongation, as measured by the end-to-end distance, varies non-monotonically with the strength of the confinement. Furthermore it is found that, if the crowders mostly confine the DNA mid-chain, the helix over-twists and its end-to-end distance grows in the strong confinement regime. Instead, if the crowders mostly pin one chain end, the helix untwists while the molecule stretches for large confinement strengths. Thus, our results put forward a peculiar relation between stretching and twisting which significantly depends on the crowders profile. The method could be applied to design specific DNA shapes by controlling the environment which constrains the molecule.