The Escherichia coli Uvr(A)BC endonuclease (Uvr(A)BC) initiates nucleotide 
excision repair of a large variety of DNA damages. The damage recognition and 
incision steps by the Uvr(A)BC is a complex process utilizing an ATP-dependent 
DNA helix-tracking activity associated with the UvrA2B1 complex. The latter 
activity leads to the generation of highly positively supercoiled DNA in the 
presence of E. coli topoisomerase I in vitro. Such highly positively supercoiled 
DNA, containing ultraviolet irradiation-induced photoproducts (uvDNA), is 
resistant to the incision by Uvr(A)BC, whereas the negatively supercoiled and 
relaxed forms of the uvDNA are effectively incised. The E. coli gyrase can 
contribute to the above reaction by abolishing the accumulation of highly 
positively supercoiled uvDNA thereby restoring Uvr(A)BC-catalyzed incision. 
Eukaryotic (calf thymus) topoisomerase I is able to substitute for gyrase in 
restoring this Uvr(A)BC-mediated incision reaction. The inability of Uvr(A)BC to 
incise highly positively supercoiled uvDNA results from the failure of the 
formation of UvrAB-dependent obligatory intermediates associated with the DNA 
conformational change. In contrast to Uvr(A)BC, the Micrococcus luteus UV 
endonuclease efficiently incises uvDNA regardless of its topological state. The 
in vitro topodynamic system proposed in this study may provide a simple model 
for studying a topological aspect of nucleotide excision repair and its 
interaction with other DNA topology-related processes in E. coli.