MECHANISMS OF DNA TOPOISOMERASES

Abstract

ABSTRACT The apparently disparate abilities of DNA gyrase to reversibly catalyze the supercoiling, catenation and knotting of DNA circles are explained by the “sign inversion” mechanism whose intrinsic feature is the passing of one duplex DNA through a transient double-strand break in another. DNA gyrase negatively supercoils closed duplex DNA by directly inverting a right-handed DNA loop into a left-handed loop, thus reducing the linking of the DNA strands by two twists. Catenation or decatenation results when crossing DNA segments from different DNA molecules are inverted. The transient stage of double-strand DNA discontinuity can be trapped by nalidixic acid, revealing staggered scissions and the covalent attachment of each resulting 5' DNA terminus to the enzyme. The cleavage site is asymmetrically located within an extensive region of DNA bound tightly by gyrase and thereby protected from nuclease attack. A detailed model illustrating how sign inversion might be engineered by gyrase is described. The ability of E. coli omega protein ( E. coli topoisomerase I) to catenate duplex DNA rings suggests a unified mechanism for topoisomerases. In a process analogous to the action of gyrase on double-stranded DNA, omega protein may operate by passing one single DNA strand through a transient break in another, and thus alter linking number by one.