Apping on their surface would be conserved in the nicked circular and linear forms. Thus after the repair of all breaks, the religated circular form would recover the negative superhelicity of the original circular minichromosome DNA. Our finding that the conversion of linear to supercoiled minichromosome DNA continues at the normal rate when topoisomerases I and II are inhibited by catalytic inhibitors is consistent with this scenario. It appeared paradoxical at first view that repair of double strand breaks in the minichromosome was arrested completely by inhibition of NHEJ, while 20�C30 of the breaks appeared to be repaired by HR as deduced from the effects of inhibiting activation or activity of ATM kinase or depleting Rad51. These findings can be interpreted plausibly by the mechanism which has been proposed to ABT-869 understand similar observations on repair of double strand breaks in genomic DNA, which is reported to be completely inhibited when NHEJ is arrested by the DNA-PKcs inhibitor wortmannin ; trapping of factors involved in NHEJ at DNA extremities is suggested to prevent the access of factors required for HR. We underline, however, that the particular pathway of double strand break repair which is arrested when DNA-PKcs is inhibited does not influence the quantitative outcomes of our model of repair kinetics. In genomic DNA the fraction of double strand breaks repaired by HR varies in different cell types and is predominant in lower eukaryotes, whose smaller purchase NS-398 genome may allow homologous chromosomes to find each other more easily than those in higher eukaryotes. Similarly, HR may be favoured in the minichromosome due to the proximity of numerous replicating and daughter DNA molecules in replication compartments whose limited volume would facilitate finding a region of sequence homology in a neighbouring molecule. Linear oligomers of minichromosome DNA were not detected during repair, as also observed during repair of a 3 Mb double-minute chromosome and transfected plasmids, reflecting juxtaposition of the extremities of the broken DNA by Ku and the RMX complex ; we propose that a further important factor is the crowded macromolecular environment in the nucleus because crowding strongly favours DNA circularisation and ligation by ligases IIIb and IV-XRCC4
