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Nucleic Acids Research, 2003, Vol. 31, No. 20 5868-5876
© 2003 Oxford University Press

The positive and negative regulation of Tn10 transposition by IHF is mediated by structurally asymmetric transposon arms

Sven Sewitz, Paul Crellin and Ronald Chalmers*

Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK

*To whom correspondence should be addressed. Tel: +44 1865 275307; Fax: +44 1865 275297; Email: pcna{at}bioch.ox.ac.uk
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

The Tn10 transpososome has symmetrical components on either side: there are two transposon ends each of which has binding sites for a monomer of transposase and an IHF heterodimer. The DNA bending activity of IHF stimulates assembly of an intermediate with tightly folded transposon ends in which transposase has additional ‘subterminal’ DNA contacts, located distal to the IHF site. These subterminal contacts are required to activate later steps in the reaction. Quantitative hydroxyl radical footprinting and gel retardation unfolding experiments show that the transpososome is fundamentally asymmetric, despite having identical components on either side. Major differences between the transposon ends define {alpha} and ß sides of the complex. IHF can dissociate from the transposon arm on the ß side of the complex in the absence of metal ion. However, IHF is locked onto the {alpha} side of the complex, probably by the subterminal transposase contacts, until released by a metal ion-dependent conformational change. Later in the reaction, IHF inhibits target interactions. Using a very short transposon arm, target interactions are demonstrated at a saturating IHF concentration. This suggests that inhibition of target interactions is due to steric hindrance of the target binding site by a single IHF-folded transposon arm.


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