DNA size in confined environments

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