Sequence dependency of canonical base pair opening in the DNA double helix.

ABSTRACT: The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free e

SUBMITTER: Lindahl V 

PROVIDER: S-EPMC5393899 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature