Conformational response of supercoiled DNA to confinement in a nanochannel.

摘要: Monte Carlo simulations were done to study the conformation of supercoiled DNA confined in a nanochannel. The molecule has superhelical density around -0.05 and is bathed monovalent salt solution with an ionic strength 2, 10, or 150 mM. cross-sectional diameter circular shaped nanochannel was varied range 10 80 nm. conformational properties characterized by writhing number distribution distance between two opposing strands superhelix. With increasing confinement, as set smaller tube and/or decreased screening Coulomb interaction, supercoil becomes more tightly interwound long-range structural features such branching formation hairpins are progressively suppressed. Analysis energetics shows concurrent increase electrostatic energy interaction wall, but elastic twisting decreases. Confinement otherwise hence results decrease absolute value twist exerted on duplex. bending remains approximately constant, which means that there no significant deflections from wall. simulation interpreted theory based wormlike chain model, including effects charge, elasticity, configurational entropy. It found reasonably successful predicting response confinement at local level pitch supercoil.