Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decatenation.

Dusan Racko,Andrzej Stasiak,Fabrizio Benedetti,Julien Dorier,Yannis Burnier

doi:10.1093/nar/gkv683

Abstract

Due to the helical structure of DNA the process of DNA replication is topologically complex. Freshly replicated DNA molecules are catenated with each other and are frequently knotted. For proper functioning of DNA it is necessary to remove all of these entanglements. This is done by DNA topoisomerases that pass DNA segments through each other. However, it has been a riddle how DNA topoisomerases select the sites of their action. In highly crowded DNA in living cells random passages between contacting segments would only increase the extent of entanglement. Using molecular dynamics simulations we observed that in actively supercoiled DNA molecules the entanglements resulting from DNA knotting or catenation spontaneously approach sites of nicks and gaps in the DNA. Type I topoisomerases, that preferentially act at sites of nick and gaps, are thus naturally provided with DNA–DNA juxtapositions where a passage results in an error-free DNA unknotting or DNA decatenation.

Highlights

DNA topoisomerases permit DNA segments to pass through each other
In vitro studies using non-supercoiled DNA molecules have revealed that preferential DNA unknotting and decatenation by type II DNA topoisomerases is only efficient in the case of relatively short DNA molecules [4]
We show that supercoiling generated in freshly replicated DNA molecules has the ability to push and confine DNA knots in the vicinity of single-stranded gaps and nicks where torsional stress is released

Summary

Introduction

DNA topoisomerases permit DNA segments to pass through each other. These passages are necessary to decatenate and unknot newly replicated circular DNA molecules [1,2]. Several studies have shown that in relatively short DNA molecules the DNA–DNA juxtapositions resulting from knotting and/or catenation have, on average, slightly different geometry than other DNA– DNA juxtapositions [6,7]. These differences may be sufficient to target action of DNA topoisomerases to catenated or knotted portions of DNA molecules and cause their selective decatenation or unknotting [2,8,9]. Due to their increased flexibility and reduced electrostatic repulsion, form specific juxtapositions with other portions of the tightened knot Such juxtapositions constitute preferred sites of DNA topoisomerase III action [10]. Passages occurring at such juxtaposition lead to very specific DNA unknotting and decatenation of freshly replicated DNA molecules

Methods

Results

Conclusion