DNA abasic lesions in a different light: Solution structure of an endogenous topoisomerase II poison

Topoisomerase II is the target for several anticancer drugs that "poison" t he enzyme and convert it to a cellular toxin by increasing topoisomerase IT -mediated DNA cleavage. In addition to these "exogenous topoisomerase II po isons," DNA lesions such as abasic sites act as "endogenous poisons" of the enzyme. Drugs and lesions are believed to stimulate DNA scission by alteri ng the structure of the double helix within the cleavage site of the enzyme . However, the structural alterations that enhance cleavage are unknown. Si nce abasic sites are an intrinsic part of the genetic material, they repres ent an attractive model to assess DNA distortions that lead to altered topo isomerase II function. Therefore, the structure of a double-stranded dodeca mer containing a tetrahydrofuran apurinic lesion at the +2 position of a to poisomerase II DNA cleavage site was determined by NMR spectroscopy. Three major features distinguished the apurinic structure (R-1(x) = 0.095) from t hat nf wild-type (R-1(x) = 0.077). First, loss of base II stacking at the l esion collapsed the major groove and reduced the distance between the two s cissile phosphodiester bonds. Second, the apurinic lesion induced a bend th at was centered about the topoisomerase II cleavage site. Third, the base i mmediately opposite the lesion was extrahelical and relocated to the minor groove. All of these structural alterations have the potential to influence interactions between topoisomerase II and its DNA substrate.