A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

摘要

We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids tocapture their anisotropic stereochemistry. Interaction potentials are all physicochemical andgenerated from all-atom simulation/parameterization with minimal phenomenology. Persistencelength, degree of stacking, and twist are studied by molecular dynamics simulation as functions oftemperature, salt concentration, sequence, interaction potential strength, and local position along thechain for both single- and double-stranded DNA where appropriate. The model of DNA showsseveral phase transitions and crossover regimes in addition to dehybridization, including unstacking,untwisting, and collapse, which affect mechanical properties such as rigidity and persistence length.The model also exhibits chirality with a stable right-handed and metastable left-handed helix.