The mechanisms of plastid DNA replication and maintenance will be reflected in the topologies of DNA molecules found in plastids. Plastids are most likely to be descendents of ancient cyanobacteria (Martin et al. 2002), which contain circular double-stranded DNA genomes. Circular DNA overcomes the problems of replicating gaps at the ends of linear DNA molecules following RNA primer removal at the 5' ends of newly synthesized DNA (Cavalier-Smith 1974). The sequence maps of all the plastid genomes that have been characterized are circular (Chapter 3). In the majority of species the genomes can be represented as a single circular double-stranded DNA molecule containing all genes. Dinoflagellates are an exception and contain genes dispersed over a number of DNA mini-circles each with one to three genes (Koumandou et al. 2004). A circular sequence or restriction map does not necessarily imply the physical structure of a DNA species is a circle (Streisinger et al. 1964). Tandemly repeated DNA sequences (Fig. 2a), such as nuclear ribosomal RNA genes, on a linear chromosome or circularly permuted sequences arranged on separate linear DNA molecules of defined (Fig. 2b) or varying lengths (Fig. 2c) will also give rise to circular maps (Fig. 2d). To study the structure of plastid DNA requires the analysis of intact DNA isolated from chloroplasts. Because double-stranded DNA is prone to breakage by shearing, the analysis of plastid DNA topology requires distinguishing breakage products of the extraction process from intact plastid DNA molecules. Most studies have involved chloroplasts, which are easily identified, abundant in leaves and relatively easy to purify. The structure of chloroplast DNA has been studied by microscopic and gel electrophoretic methods.
An early electron microscopic study showed that monomer circles corresponding in size to a single set of plastid genes represented 37% of the DNA extracted from P. sativum chloroplasts (Kolodner and Tewari 1972). The remaining DNA
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