Atomic-scale determination of DNA conformational response to strained furanose: a static mode approach

An original approach of macromolecular ‘induced-fit’ flexibility, namely the static modes, is applied to shed light on some fundamental mechanisms impacting DNA conformations. We first investigate a constrained nucleic acid of the D-CNA family, in which some backbone torsional angles are conformationally restricted by a dioxaphosphorinane ring structure. We take a special interest in α,β-D-CNA, in which α and β angles are restricted to the canonical conformation. We used the static mode method to evaluate the impact of the insertion of modified nucleotides on the stability of DNA/DNA and DNA/RNA duplexes. Although our approach authorizes the design of complex excitation modes on a specific molecule, we here establish with an atomic precision how a DNA south to north transition can be optimally operated through C5′ and O5′ single excitations.