Structure of the genome termini of varicella-zoster virus.

The DNA molecule of varicella-zoster virus (VZV) is represented structurally as L-S, where L is a unique sequence and S is a unique sequence flanked by an inverted repeat. S may be present in either orientation in virion DNA molecules, but, to date, L has been found in only one orientation. DNA sequences were determined at the L-S joint and genome termini, which were cloned using methods designed to conserve either the 3' or 5' terminal nucleotide. Molecular hybridization experiments and analysis of the sequences showed that: the genome is not terminally redundant; the unique sequence in L is flanked by an inverted repeat of 88.5 base pairs; a single unpaired nucleotide is located at each 3' terminus of the genome, such that fusion of the termini would produce a sequence identical to that at the L-S joint; approx. 5% of virions contain genomes with L inverted. The implications of these results in possible mechanisms for VZV DNA replication are discussed.