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We introduce a coarse-grained model of DNA with bases modeled as rigid-bodyellipsoids to capture their anisotropic stereochemistry. Interaction potentialsare all physicochemical and generated from all-atom simulation/parameterizationwith minimal phenomenology. Persistence length, degree of stacking, and twistare studied by molecular dynamics simulation as functions of temperature, saltconcentration, sequence, interaction potential strength, and local positionalong the chain, for both single- and double-stranded DNA where appropriate.The model of DNA shows several phase transitions and crossover regimes inaddition to dehybridization, including unstacking, untwisting, and collapsewhich affect mechanical properties such as rigidity and persistence length. Themodel also exhibits chirality with a stable right-handed and metastableleft-handed helix.

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