Nascent Pieces of ϕ X174 Viral-strand DNA Are Shorter Than Unit-length and Are Derived from All Regions of the Genome

Abstract

There is good evidence that the synthesis of the two strands of ϕ X174 replicative-form (RF) DNA is asymmetric—i.e., that in each “round” of replication the viral strand is synthesized continuously and the complementary strand is synthesized discontinuously (Denhardt 1977). It is also commonly believed that once viral-strand synthesis is initiated, the DNA polymerase then simply moves around the complementary-strand ring indefinitely (Dressler 1970; Watson 1976). This was first promulgated as the rolling-circle model (Gilbert and Dressler 1969). According to this concept, the viral strand is elongated “endlessly” from the 3′-OH primer created by the insertion of a nick into the viral strand by the ϕ X gene-A protein; the circular complementary strand serves repeatedly as the template, in the fashion of a “stamping machine.” This simple mechanism produces, as an intermediate, a viral strand longer than unit length, and evidence for the existence of such strands under certain conditions has been reported (Dressler and Wolfson 1970; Eisenberg et al. 1977; Baas and Jansz, this volume).

However, little by little, data have been accumulating that bring this model into question. First, it was shown that a gap exists at a specific location in the viral strand of newly synthesized RF molecules produced during RF DNA replication (Eisenberg and Denhardt 1974; Eisenberg et al. 1975) and during progeny viral-strand DNA synthesis (Johnson and Sinsheimer 1974). Second, the dnaG protein of Escherichia coli, which is thought to produce primers for initiating DNA synthesis, is required for viral-strand synthesis as well as...