Cloning of the human parvovirus B19 genome and structural analysis of its palindromic termini

We describe the molecular cloning of the entire 5.6-kb single-stranded DNA genome of the human parvovirus B19 in bacterial plasmids. Stable amplification of the recombinant plasmid DNA was achieved in Escherichia coli JC8111 but not in HB101 cells. Sequence analysis of the cloned DNA shows that the terminal 383 nucleotides at each end of the genome are identical inverted repeats. The distal 365 nucleotides of the repeat represent an imperfect palindrome which presumably folds over to form a hairpin structure. The sequence of the hairpin occurs in two distinct configurations which are related in that one is the inverted complement of the other. Such alternative configurations of the terminal hairpins have been found for all parvoviruses analyzed so far and are referred to as flip and flop.