An inverted terminal repetition was observed in DNA molecules extracted from vaccinia virus. The repeated sequence was visualized by (i) nicking the hairpin loops present at the ends of vaccinia virus DNA, (ii) separating the strands of DNA by alkali denaturation, (iii) allowing the single strands to self-anneal, and (iv) examining the DNA with an electron microscope. Single-stranded circular molecules, each of which contained a duplex projection (3.54 i 0.12 M&m) representing the terminal repetition, readily formed. Similar size projections were also seen in heteroduplex structures formed by crosshybridization of the separated strands of the two terminal HindIll restriction fragments. Based on contour length measurements and the electrophoretic mobility of the isolated inverted terminal repetition, a molecular weight of approximately 6.9 X 106, equivalent to about 10,500 nucleotide base pairs, was estimated. Evidence was obtained from DNA*RNA hybridization studies that the terminal repetition is transcribed. The genome of vaccinia virus appears, in the electron microscope, as a typical linear duplex DNA molecule of approximately 122 X 106 daltons (1). Upon complete denaturation, however, single-stranded circles measuring twice the length of the linear duplex are observed (1). The latter finding, together with the failure of the complementary strands to separate upon sedimentation through an alkaline sucrose gradient (1), indicate that the ends of the DNA duplex form a continuous hairpin loop or are crosslinked in some unknown manner. A similar genome structure has been found in molluscum contagiosum virus (2) and may be characteristic of all poxviruses.Partial denaturation mapping of vaccinia virus DNA indicated that the base composition at the two ends of the molecule is similar (1, 2). Observations that restriction fragments from opposite ends of rabbitpox virus DNA crosshybridize (3) and that similar size restriction fragments are generated from both ends of the vaccinia virus genome (R. Wittek, personal communication) suggested the presence of a terminal repetition in poxvirus DNA. By using a single-strand-specific endonuclease (4) to cleave the hairpin loops at the two ends of the vaccinia virus genome (1) and then self-annealing the separated strands of DNA, we now provide direct visual evidence for an inverted terminal repetition approximately 10,500 nucleotide base pairs long. Evidence that at least a portion of the repeated sequence is transcribed will also be presented.MATERIALS AND METHODS Preparation of Vaccinia Virus DNA. HeLa S-3 cells were infected with cloned vaccinia virus (strain WR) and virions were purified without sonication as described (5). DNA was extracted as described (6) except that digestion with 1 mg of proteinase K (EM Laboratories Inc., Elmsford, NY) per ml for 5 hr was followed by repeated phenol extraction and dialysisThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in Lab...