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Nucleic Acids Research, 1982, Vol. 10, No. 18 5673-5679
© 1982

MOLECULAR BIOLOGY

Sequence homologies of diverse length tandem repetitions near ends of vaccinia virus genome suggest unequal crossing over

Bahige M. Baroudy and Bernard Moss{dagger}

Laboratory of Biology of Viruses, National Institute of Allergy and Infectious Diseases, National Institute of Health Bethesda, MD 20205, USA

{dagger}To whom reprint should be addressed

Received May 25, 1982. Revised July 25, 1982. Accepted July 25, 1982.

The 180,000 base pair (bp), covalently closed, linear duplex DKA genome of vaccinia virus contains a 10,000 bp inverted terminal repetition within which are one set of 13 and one set of 18 tandem 70 bp repeating units. A 967 bp segment containing the innermost 70 bp repeat and an adjacent region notable for a scarcity of restriction endonuclease sites has been sequenced. This was facilitated by the cloning of TagI and partial TagI fragments in pBR322. We found that the innermost 70 bp repeat overlaps one of two adjacent 125 bp repeats, following which are eight repeats of 54 bp, parts of 54 bp and 70 bp repeats, and four consecutive 6 to 7 bp repeats. The 70, 125, and 54 bp repeating units have extensive sequence homologies and redundancies that suggest evolution by unegual crossing over. Schemes whereby unequal crossovers of 54 bp repeats lead to a recombinant segment 86% homologous to the 125 bp repeat and unequal crossovers of 125 bp repeats lead to a recombinant segment 94% homologous to the 70 bp repeat were considered. This propensity for sequence divergence should provide a useful marker for comparing the relatedness of poxviruses.

*Present address: Division of Molecular Genetics, Vincent T.Lombardi Cancer Center and Department of Biochemistry, Georgetown University Medical Center Washington, DC 20007, USA


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