Linear adenovirus DNA is organized into supercoiled domains in virus particles

Electron microscopic analysis of bis-psoralen crosslinked adenovirus type 5 virion DNA revealed supercoiled domains in an otherwise linear DNA. The existence of supercoiled arrangement in all the virion DNA was demonstrated by the sensitivity of Ad5 DNA in pentonless virus particles to the supercoiling-dependent endonucleolytic activity of Bal31 and S1 nucleases. These nucleases were found to cleave Ad5 virion DNA at specific sites. The observation of stable cleavage sites in the limit digestion of virion DNA by Bal31 suggests that cleavage sites represent boundaries of core proteins which impede the exonuclease activity of Bal31. These data suggest that specific arrangement of core proteins on Ad5 virion DNA. Based on this analysis we determined positions of core proteins in viral genome using indirect end labeling technique. The size of supercoiled domains of virion DNA was estimated by electron microscopy and also by boundaries of mutually exclusive Bal31 cleavage sites at limit digestion condition. Our data suggest each supercoiled domain is equal to about 12% of Ad5 genome length and about 8 loops can be accommodated in Ad5 virion. However sequences at two extreme ends of the viral genome were found to be outside of supercoiled domains. An interesting correlation between supercoiled domains and gene domains of Ad5 genome was noticed.