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Fig. 2 | Mobile DNA

Fig. 2

From: Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria

Fig. 2

Models for the formation of SE circular transposition intermediates. Upper panel: Schematic of SE structure. The intA-proximal border between SE and the insertion location is termed attL, while intA-distal border is termed attR [18]. The triangle in gray, with number 1, 2, 3, or 4, indicates the primer annealing position used for PCR detection of attL, attR, attS, and attB throughout this study. Lower panel: four hypothetical routes to circular transposition intermediate formation. The most likely path suggested by previous studies [18, 19] is indicated by the thicker arrow. Six bases next to C and C′ are shown in distinct colors (cyan/orange) to easily track their fates in the strand exchange processes. The triangle in black indicates nicking at the top strand. Left: the most likely model for SE’s route. A single-stranded DNA bridge is generated by top strand exchange in attL × attR recombination, leaving the host DNA side unjointed. Cleaning of the covalently linked integrase by DNA–protein crosslink (DPC) repair allows replication, resulting in the IS911-like copy-out [21]. Right: Phage/ICE/gene cassette routes (unlikely for SEs). Top strand exchange generates a Holliday junction (HJ). Bottom strand exchange generates circular DNAs with a heteroduplex spacer like Tn916 excision [22]. Replication of the HJ-forming molecule generates a single-strand gene cassette-like circle and a molecule with attB

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