DNA Abasic Lesions in a Different Light:  Solution Structure of an Endogenous Topoisomerase II Poison

Abstract

Topoisomerase II is the target for several anticancer drugs that "poison" the enzyme and convert it to a cellular toxin by increasing topoisomerase II-mediated DNA cleavage. In addition to these "exogenous topoisomerase II poisons," DNA lesions such as abasic sites act as "endogenous poisons" of the enzyme. Drugs and lesions are believed to stimulate DNA scission by altering the structure of the double helix within the cleavage site of the enzyme. However, the structural alterations that enhance cleavage are unknown. Since abasic sites are an intrinsic part of the genetic material, they represent an attractive model to assess DNA distortions that lead to altered topoisomerase II function. Therefore, the structure of a double-stranded dodecamer containing a tetrahydrofuran apurinic lesion at the +2 position of a topoisomerase II DNA cleavage site was determined by NMR spectroscopy. Three major features distinguished the apurinic structure ( = 0.095) from that of wild-type ( = 0.077). First, loss of base stacking at the lesion collapsed the major groove and reduced the distance between the two scissile phosphodiester bonds. Second, the apurinic lesion induced a bend that was centered about the topoisomerase II cleavage site. Third, the base immediately 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.

DNA topoisomerase II, genotoxicity, and cancer

“…The position of the DNA damage relative to the scissile bond cleaved by the type II enzyme is critical to the actions of lesions as topoisomerase II poisons [173][174][175][176][177][178][179]. As discussed earlier, the two scissile bonds on the opposite strands of the double helix are separated by 4 base pairs.…”

“…In this regard, a number of naturally occurring DNA lesions that result from endogenous or environmental stress increase levels of topoisomerase II-DNA cleavage complexes [173][174][175][176][177][178][179]. Both the α and β isoforms of the enzyme are affected similarly in vitro [177,179].…”

“…The ability to distort the double helix appears to be a common feature among lesions that act as topoisomerase II poisons [174,[176][177][178][179]. Abasic sites, which are the most common lesions in the cell, are among the strongest of poisons [173,174,176,177,179].…”

“…Abasic sites, which are the most common lesions in the cell, are among the strongest of poisons [173,174,176,177,179]. Abasic sites are generated by a variety of methods, including spontaneous hydrolysis, DNA reactive chemicals, ionizing radiation, and base excision repair pathways [180][181][182].…”

Acidic pH induces topoisomerase II-mediated DNA damage

“…Our studies using purified hTOP2␣ have demonstrated that acidic pH in the range of 5.0 to 7.0 can induce TOP2-mediated DNA cleavage. The possibility that DNA depurination may contribute to acidic pH-induced DNA cleavage (40,41) was ruled out because acidic pH-treated DNA (under our assay conditions) did not induce DNA cleavage in a subsequent incubation with TOP2 at neutral pH (data not shown). The result from our reversal experiment in which pH-induced DNA cleavage was completely abolished on neutralization also supports this conclusion.…”