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Fig. 3 | Mobile DNA

Fig. 3

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

Fig. 3

PCR detection of attS in fractions of genomic DNA. a Restriction map of SE-6945 located on the chromosome 1 of V. alfacsensis strain 04Ya108 (Genbank accession no. AP024168.1). The positions of TfiI sites are indicated by vertical lines. Filled arrowheads indicate the annealing positions of outward-facing primers, 6945_L_out, and 6945_R_out. b Agarose gel electrophoresis of BHY606 genomic DNA with the circular SE analog pHY1603 and M13mp18 single-stranded DNA. A mixture of pHY1603 and genomic DNA was loaded on the 6th to 9th lanes to precisely identify the positions of the SC and OC forms. Gel slices were prepared from the 6th to 9th lanes from left at the positions indicated by 1 to 8. The amounts of DNA loaded are as follows: genomic DNA, 880 ng; M13mp18 ssDNA, 200 ng; pHY1603, 172 ng (SC form for lane 3, linear form for lane 4, mixture of OC and SC forms for lane 5). c Quantitation of PCR products by microtip electrophoresis. Subpanel i, attS products. Subpanel ii, gyrB products. The numbers in the template row indicates the gel slice numbers in (b). PC, positive control (genomic DNA). NTC, no template control. The leftmost lane shows a size marker (bp) and internal standards (UM, LM) used for quantitation of each band. d The effect of restriction enzyme TfiI and single-strand-specific S1 nuclease on attS detection. The results of triplicate experiments are shown in parallel. No nuclease was added to the reactions in lanes labelled rCutSmart

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