A structural snapshot of base-pair opening in DNA

The response of double-helical DNA to torsional stress may be a driving for ce for many processes acting on DNA, The 1.55-Angstrom crystal structure of a duplex DNA oligonucleotide d(CCAGCCCTGG)(2) with an engineered crosslink in the minor groove between the central guanine bases depicts how the dupl ex can accommodate such torsional stress. We have captured in the same crys tal two rather different conformational states. One duplex contains a strai ned crosslink that is stabilized by calcium ion binding in the major groove , directly opposite the crosslink. For the other duplex, the strain in the crosslink is relieved through partial rupture of a base pair and partial ex trusion of a cytosine accompanied by helix bending. The sequence used is th e target sequence for the HaeIII methylase, and this partially flipped cyto sine is the same nucleotide targeted for extrusion by the enzyme. Molecular dynamics simulations of these structures show an increased mobility for th e partially flipped-out cytosine.