Sequence arrangement in herpes simplex virus type 1 DNA: identification of terminal fragments in restriction endonuclease digests and evidence for inversions in redundant and unique sequences

Abstract

It was proposed by Sheldrick and Berthelot (1974) that the terminal sequences of herpes simplex virus type 1 (HSV-1) DNA are repeated in an internal inverted form and that the inverted redundant sequences delimit and separate 2 unique sequences, S and L. In this study the sequence arrangement in HSV-1 DNA was investigated with restriction endonuclease cleavage, end-labeling studies and molecular hybridizaiton experiments. The terminal fragments in digests with restriction endonucleases Hind III, Hpa-1, EcoRI and Bum [Brevibacterium umbrii] were identified and were consistent with the Sheldrick and Berthelot model. Inverted fragments which contain unique sequences and redundant sequences, and which the model predicts, were identified by DNA-DNA hybridization studies. Further cleavage of Bum fragments with Hpa-1 also revealed inversions of the terminal sequences that contained unique sequences. The unique sequences S and L are relatively inverted in different DNA molecules in the population, resulting in the presence of 4 related genomes with rearranged sequences in apparently equal amounts. The redundant sequences bounding S do not share complete sequence homology with those bounding L, but hybridization studies are presented which show that the terminal 0.3% of the genome is repeated in every redundant sequence.