Research Article: Sequence dependency of canonical base pair opening in the DNA double helix

Date Published: April 3, 2017

Publisher: Public Library of Science

Author(s): Viveca Lindahl, Alessandra Villa, Berk Hess, Alexander MacKerell

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 energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair.

Partial Text: DNA base pair opening, or base breathing, is the process of breaking the hydrogen bonds of a base pair. Opening is the first critical step of base flipping in which either base moves away from the DNA double helix. Fundamental biological processes such as DNA replication, modification and repair [1–3] rely on this mechanism for accessing the functional groups of the bases.