Insights into DNA helical transmons found in protein-DNA complexes

Many proteins essential for the viability of the cell induce large-scale deformations in the DNA double helix. Some of these deformations include transitions of regular B DNA to alternate helical forms, such as A DNA, where base pairs are unwound, displaced, and inclined with respect to the helical axis. Here we examine structural features of the A-like DNA base-pair steps found in a diverse set of high-resolution protein-DNA complexes. The protein-bound DNA is more deformable than the A DNA crystallized in the absence of protein, and the protein microenvironment surrounding A DNA differs in subtle ways from that associated with other types of DNA The kinds of amino-acid atoms in immediate contact with the sugars, phosphates, and bases hint of ways in which small molecules may cluster around A DNA in solution and how changes in solvent may contribute to alterations of helical structure.