Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.

ABSTRACT: A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexible in DNA looping. In this work, we investigate mechanical properties of symmetric AnTn and asymmetric A2n tracts for n = 3, 4, 5 using two types of coarse-grained models. The first model represents DNA as an ensemble of interacting rigid bases with non-local quadratic deformation energy, the second one treats DNA as an anisotropically bendable and twistable elastic rod. Parameters for both models are inferred from microsecond long, atomic-resolution molecular dynamics simulati

SUBMITTER: Drsata T 

PROVIDER: S-EPMC4066768 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature