Structure of frog virus 3 genome: size and arrangement of nucleotide sequences as determined by electron microscopy

Abstract

The structural features of frog virus 3 (FV 3) DNA have been analyzed by electron microscopy. The FV 3 genome is a linear duplex molecule of 52.00 ± 5.60 μm in length which corresponds to 98.28 ± 10.58 X 106 daltons. To compare the structure of the genomes of FV 3, vaccinia virus, and herpes simplex virus, the three viral DNAs were denatured, quickly renatured, and examined in the electron microscope. The FV 3 DNA consisted of linear single strands while the vaccinia virus DNA contained reannealed duplexes and the herpesvirus DNA contained single-stranded circles with bushes or molecules in which two single-stranded circles were joined by a duplex region. These data suggest that the FV 3 genome contains neither crosslinked terminii nor inverted repeats. To construct a partial denaturation map of the FV 3 genome, the DNA was denatured with 85% formamide and examined in the electron microscope. The partially denatured molecules failed to match by their denatured regions when lined up end to end, suggesting that the molecules were dissimilar with respect to the arrangement of nucleotide sequences. However, a distinct denaturation map was obtained when the molecules were matched by their denatured regions rather than by the physical ends. The map revealed (1) a continuous stretch of about 40 μm (or 75.60 × 10 6 daltons) of uniquely ordered sequences common to all molecules, and (2) a distribution of the ends within 20 to 28% of the map length. These observations suggest that FV 3 DNA molecules contain various circular permutations of a common overall nucleotide sequence and that the extent of circular permutation is restricted as in bacteriophage P22 ( B. K. Tye, J. A. Huberman, and D. Botstein, 1974, J. Mot Biol. 85, 501–532).