Transposon-encoded site-specific recombination: nature of the Tn3 DNA sequences which constitute the recombination site res.

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Abstract
The tnpR gene of transposon Tn3 encodes a site‐specific recombination enzyme that acts at res, a DNA region adjacent to tnpR, to convert co‐integrate intermediates of interreplicon transposition to the normal transposition end‐products. We have used two complementary approaches to study the nature of the Tn3 recombination region, res. Firstly, the DNA‐binding sites for tnpR protein were determined in DNase I protection experiments. These identified a 120‐bp region between the tnpA and tnpR genes that can be subdivided into three separate protein‐binding sites. Genetic dissection experiments indicate that few, if any, other sequences in addition to this 120‐bp region are required for res function. Moreover, we have shown that the two directly repeated res regions within a molecule are unequal partners in the recombination reaction: a truncated res region, which is unable to recombine with a second identical res region, can recombine efficiently with an intact res region. This demonstration, along with the observation that tnpR/res recombination acts efficiently on directly repeated res regions within a molecule but inefficiently both on inverted res regions in the same molecule and in the fusion reaction between res regions in different molecules, leads us to propose that one‐dimensional diffusion (tracking) of tnpR protein along DNA is used to locate an initial res region, and then to bring a second directly repeated res region into a position that allows recombination between the res regions.