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 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 Torin 1 environment in the nucleus because crowding strongly favours DNA circularisation and ligation by ligases IIIb and IV-XRCC4 which participate in NHEJ. Kinetic models of strand break repair can be constructed with different degrees of complexity, but theory shows that the least complex model is preferable to provide concrete predictions. Our data were fitted well by using first-order kinetics, and we consider that this strategy was justified since other datasets for DNA repair have been fitted satisfactorily by first-order kinetics, which only deviate significantly from higherorder models after two half-times ; further, theoretical arguments show that “multiple processes may combine to produce kinetic behavior indistinguishable from firstorder and. are more likely to exist when reactions occur in a complex environment”. A number of conclusions which were not directly apparent from the experimental data LY2157299 illustrated the usefullness of modeling. First, when repair of double strand breaks was arrested, the single strand breaks in linear molecules were still repaired and circular molecules containing single strand breaks were converted to supercoiled molecules at close to the normal rate showing that the systems which repair single and double strand breaks operate independently, which has not been demonstrated previously as far as we are aware. Second, the calculated rate constants show that in an average linearised minichromosome the double strand break was repaired three to four times faster than all the single strand breaks, so that the ratelimiting step for complete repair of minichromosomes was the repair of single strand breaks. These repair rates cannot be compaired directly with those reported for genomic DNA where the methods used could not quantitate breaks directly, but comparisons can be made in terms of the half-time for repair which is independent of the radiation dose and of the length of the region considered. In the minichromosome the calculated half-time for repair of the double strand break in each molecule was,40 min, which is within the range of 20 to 110 min reported for genomic DNA. For repair of single strand breaks the half-time of,140 min for repairing 8 to 9 breaks per molecule was equivalent to an average of,16 min/break, which is within the range reported for genomic DNA. This minichromosome offers an simple experimental system for quantitative testing of potential inhibitors of repair of strand breaks, and since the sequence and structural features of its DNA and its transcription pattern have been studied extensively.