Published online 11 May 2004
Nucleic Acids Research, 2004, Vol. 32, No. 8 2607-2617
© 2004 Oxford University Press
Synapsis and DNA cleavage in 
C31 integrase-mediated site-specific recombination
Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK and 1 Centre of Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
*To whom correspondence should be addressed at Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK. Tel: +44 1224 555739; Fax: +44 1224 555844; Email: maggie.smith{at}abdn.ac.uk
Received January 9, 2004; Revised and Accepted March 22, 2004
The Streptomyces phage 
C31 encodes an integrase belonging to the serine recombinase family of site-specific recombinases. The well studied serine recombinases, the resolvase/invertases, bring two recombination sites together in a synapse, and then catalyse a concerted four-strand staggered break in the DNA substrates whilst forming transient covalent attachments with the recessed 5' ends. Rotation of one pair of half sites by 180° relative to the other pair occurs, to form the recombinant configuration followed by ligation of the DNA backbone. Here we address the nature of the recombination intermediates formed by C31 integrase when acting on its substrates attP and attB. We have identified intermediates containing integrase covalently attached to cleaved DNA substrates, attB or attP, by analysis of complexes in gels and after treatment of these complexes with proteinases. Using a catalytically inactive integrase mutant, S12A, the synaptic complexes containing integrase, attP and attB were identified. Furthermore, we have shown that attB mutants containing insertions or deletions are blocked in recombination at the stage of strand cleavage. Thus, there is a strict spacing requirement within attB, possibly for correct positioning of the catalytic serine relative to the scissile phosphate in the active site. Finally, using integrase S12A we confirmed the inability of attL and attR or other combinations of sites to form a stable synapse, indicating that the directionality of integrative recombination is determined at synapsis.
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