Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms.

ABSTRACT: The structural and physical properties of DNA are closely related to its geometry and topology. The classical mathematical treatment of DNA geometry and topology in terms of ideal smooth space curves was not designed to characterize the spatial arrangements of atoms found in high-resolution and simulated double-helical structures. We present here new and rigorous numerical methods for the rapid and accurate assessment of the geometry and topology of double-helical DNA structures in terms of the constituent atoms. These methods are well designed for large DNA datasets obtained in detailed numerical simulations or determined experimentally at high-resolution. We illustrate the usefulness of our methodology by applying it to the analysis of three canonical double-helical DNA chains, a 65-bp m

SUBMITTER: Clauvelin N 

PROVIDER: S-EPMC4004093 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature