Inferring DNA Kinkability from Biased MD Simulations.

ABSTRACT: In several biological processes, such as looping, supercoiling, and DNA-protein interactions, DNA is subject to very strong deformations. While coarse-grained models often approximate DNA as a smoothly bendable polymer, experimental and theoretical studies have demonstrated that mechanical stress can induce localized kinks. Here, we employ the Rigid Base Biasing of Nucleic Acids (RBB-NA) algorithm to systematically probe the properties of highly deformed DNA in all-atom simulations of short dodecamers. A simultaneous bias in bending (roll) and twist is applied locally to two consecutive base pairs in the center of the dodecamers. Using umbrella sampling, we construct free energy landscapes that reveal sequence-dependent effects for kink formation and quantify the energetic cost of kinking.

SUBMITTER: Fassino A 

PROVIDER: S-EPMC12854757 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature