Mutation Research, 219 (1989) 147-156 147 Elsevier MTR 09025 Hypothesis A double-loop model for the replication of eukaryotic DNA S. Spadari, A. Montecucco, G. Pedrali-Noy and G. Ciarrocchi Istituto di Genetica Biochimica ed Evoluzionistica, CNR, Pavia (Italy) F. Focher * and U. Htibscher Department of Pharmacology and Biochemistry, Ziirich (Switzerland) (Received 3 March 1989) (Accepted 14 March 1989) Keywords: DNA polymerases; DNA ligase; DNA topoisomerases Summary Coordinated DNA synthesis of both strands at the replication fork by a fixed 'replisome' may cause dynamic and topological problems. Based upon known properties of DNA helicase, DNA primase and DNA topoisomerases, and on novel properties of DNA polymerases and DNA ligase, we propose a 'double-loop' model for the replication of eukaryotic DNA that could minimize such problems. A complex network of interacting proteins and enzymes is required for the different types of DNA synthesis in the cell, i.e., DNA replication, DNA repair and special forms of DNA recombi- nation. Among these the most complex appears to be DNA replication. In prokaryotic replication systems, to date, the functions of about 25-30 proteins are understood at an elementary level (Kornberg, 1988; Alberts, 1987; Huber et al., 1988). They work as multisubunit assemblies and represent a guide for the identification and the purification of similar proteins in eukaryotes. In Fig. 1 a scheme for some enzymes operating at the eukaryotic replication fork is presented. It shows the classical replication fork as an asym- Correspondence: Dr. S. Spadari, Istituto di Genetica Bio- chimicaed Evoluzionistica, CNR, Via Abbiategrasso207, 27100 Pavia (Italy). . On leave from: lstituto di Genetica Biochimicaeel Evoluzio- nistica, CNR, Pavia (Italy). metric structure with two distinct modes of DNA synthesis: continuous on the leading and discon- tinuous on the lagging strand. A DNA helicase opens the helix and one DNA polymerase (DNA polymerase 8, see DNA polymerases section) rep- licates the leading strand. On the lagging strand DNA primase provides the RNA primers (4-10 nucleotides each) for initiation of the DNA frag- ments which are then elongated by another DNA polymerase molecule (DNA polymerase a, see DNA polymerases section). The joining of these DNA fragments (Okazaki fragments), whose aver- age size in eukaryotes is about 150 nucleotides (Alberts, 1987), is complicated by the presence of the RNA primers at the 5' end of each fragment. They are removed by RNase H; the remaining gap is filled by DNA polymerase/3 or a and the pieces are finally sealed by DNA ligase. The above view of the replication raised several problems. The most complex was the fact that the DNA polymerase synthesizing the lagging strand 0921-8734/89/$03.50 © 1989 ElsevierSciencePublishers B.V. (BiochemicalDivision)