Anatomy of herpes simplex virus DNA: evidence for four populations of molecules that differ in the relative orientations of their long and short components

Intact DNA molecules extracted from HSV 1 (herpes simplex virus 1, human herpes virus 1) strain MP virions have a molecular weight of approximately 97 x 10⁶, but cleavage with the HinIII restriction enzyme yields fourteen fragments with summed molecular weights of 160 x 10⁶. Six 'major' fragments occur once in every molecule in the population and account for 60% of the genetic information. Four 'minor' fragments are present in amounts equivalent to one copy for every two genomes (0.5 molar ratio) and the other four occur only once in every four molecules (0.25 molar ratio). The minor fragments can be arranged into four equimolar sets, each with summed molecular weights that account for the remaining 40% of the genome. Treatment with lambda 5' exonuclease revealed that all molecules contain 0.5 molar ratio fragments at both termini. These observations and the results of similar analyses of the EcoRI and double HinIII/EcoRI digests indicate that there are four distinct structural forms of HSV DNA which differ only in the relative orientations of two subregions, designated L and S. The L and S segments consist of 82 and 18% of the sequences, respectively, and each has inverted terminally redundant regions that correspond to the internal duplications observed by electron microscopy. The DNA from other strains of HSV 1 and 2 also consists of equal proportions of all four possible permutations of the L and S segments. These unusual features of HSV DNA molecules have novel implications with regard to the genetic map and the model of replication and evolution of herpes simplex viruses.