We used adaptive umbrella sampling on a modified version of the roll angle to simulate the bending of DNA dodecamers. Simulations were carried out with the AMBER and CHARMM force fields for 10 sequences in which the central base pair step was varied. On long length scales, the DNA behavior was found to be consistent with the worm-like chain model. Persistence lengths calculated directly from the simulated structures and indirectly through the use of sequence-independent coarse-grained models based on simulation data were similar to literature values. On short length scales, the free energy cost of bending DNA was found to be consistent with the worm-like chain model for small and intermediate bending angles. At large angles, the bending free energy as a function of the roll angle became linear, suggesting a relative increase in flexibility at larger roll angles. Counterions congregated on the concave side of the highly bent DNA and screened the repulsion of the phosphate groups, facilitating the bending.
ASJC Scopus subject areas
- Computer Science Applications
- Physical and Theoretical Chemistry