A study of conformational response of DNA to nanoconfinement by Monte Carlo simulation

The Monte Carlo simulations were carried out to explore how the restriction of the configurational degrees of freedom by a cylindrical potential, which mimics the nanochannel, alters certain structural properties of the supercoil. The simulation results were interpreted with the wormlike chain model. The simulation model was further employed to simulate a supercoil in a dense solution where the simulated form factors were then interpreted with the results of small-angle neutron scattering experiment in zero-average contrast condition. Finally, confined isolated hairpin formations along a linear DNA chain in a nanochannel was explored by using the cooperativity model. The two-parameter cooperativity model was applied to describe the hairpin formations in term of S-loop formations and its growth along the chain. The cooperativity model was then compared with Monte Carlo simulation in order to study the isolated hairpins in a quantitative and systematic way.

Author dc:creator

• NG SIOW YEE

• Monte Carlo Simulation, Nanochannel, Supercoil, Hairpin, Cooperativity Model, Form Factor