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. Author manuscript; available in PMC: 2015 Apr 28.
Published in final edited form as: J Mol Biol. 2004 Sep 3;342(1):57–71. doi: 10.1016/j.jmb.2004.07.012

Figure 6.

Figure 6

Visualization of strand exchange products using substrates with interrupted homology. M13wins dsDNA was linearized with BamHI (A and B), EcoRI (C–E), or PacI (F–H). Strand exchange reactions using these DNAs, ssM13mp18 DNA, UL12 and ICP8, as described in Materials and Methods, were examined. Examples of an alpha structure (A) and gapped circles (A–H) are shown to illustrate how the position of the non-homologous 1.5 kb fragment within the dsDNA substrate affected the resulting strand exchange products. Arrows in F–H point to a 2 kb region of dsDNA followed by ssDNA loops (identified by stars) which are formed by the non-homologous DNA within the gapped circle product. The scale bar represents 700 bp (A and B) and 1000 bp (C–H) of dsDNA.