Linear plasmids are common genetic elements in both prokaryotes and eu-karyotes. Most linear plasmids found in eukaryotes are double-stranded DNA molecules, with proteins covalently linked to their 5' terminus (reviewed by Meinhardt and Rohe 1993; Griffiths 1995; Gunge et al. 1995; Kempken 1995; Meinhardt et al. 1997). Almost all linear plasmids sequenced to date have long, inverted terminal repeats and include a putative DNA polymerase gene. A different type of linear plasmid, the so-called hairpin plasmid with co-valently closed ends, has been described in a wide variety of organisms, including the vaccinia virus genome (Baroudy et al. 1982), poxvirus (DeLange et al. 1986), African swine fever virus (Gonzalez et al. 1986), Chlorella viruses (Rohozinski et al. 1989), Escherichia coli N15 prophage (Rybchin and Svarchevsky 1984), and the linear plasmids of bacteria in the genus Borrelia burgdorferi (Barbour and Garon 1987; Hinnebusch and Barbour 1991; Cas-jens 1999). The Borrelia linear plasmid consists of a polynucleotide chain that is fully base-paired except for short, single-strand hairpin loops at each end (Hinnenbusch and Barbour 1991). The vaccinia virus genome is incompletely base-paired, with hairpin-loop structures that exist in isomeric forms that are inverted and complementary in sequence ("flip-flopped" structures) (Baroudy et al. 1982).

Hairpin plasmids have been found in a limited number of eukaryotes. The fungal plant pathogen Rhizoctonia solani linear plasmid is single-stranded with hairpin loops at each end (Hashiba et al. 1984; Miyashita et al. 1990). They do not undergo flip-flop inversion, unlike the vaccinia virus DNA. The pFOXC2 and pFOXC3 of the fungal plant pathogen Fusarium oxysporum, however, have a "clothespin" genomic structure, which includes a terminal hairpin and noncovalently linked ends at the other terminus (Walter and Kennel 1999; Simpson et al. 2004). This review focuses on the biology of linear DNA plasmids of the pathogenic fungi R. solani and F. oxysporum, which have unique terminal structures.

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