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Papers In Press, published online ahead of print December 27, 2001
J. Biol. Chem, 10.1074/jbc.M110342200
Submitted on October 26, 2001
Revised on December 25, 2001
Accepted on December 26, 2001

Sequence and positional requirements for DNA sites in a Mu transpososome

Ilana Goldhaber-Gordon, Michael H. Early, Matthew K. Gray, and Tania A. Baker

Biology, Massachusetts Institute of Technology, Cambridge, MA 02139

Corresponding Author: ilana{at}mit.edu

Transposition of bacteriophage Mu uses two DNA cleavage sites and six transposase recognition sites, with each recognition site divided into two half sites. The recognition sites can activate transposition of non-Mu DNA sequences, if a complete set of Mu sequences is not available. We have analyzed 18 sequences from a non-Mu DNA molecule, selected in a functional assay for the ability to be transposed by MuA transposase. These sequences are remarkably diverse. Nonetheless, when viewed as a group they resemble a Mu DNA end, with a cleavage site and a single recognition site. Analysis of these "pseudo-Mu ends" indicates that most positions in the cleavage and recognition sites contribute sequence-specific information that helps drive transposition, though only the strongest contributors are apparent from mutagenesis data. The sequence analysis also suggests variability in the alignment of recognition half-sites. Transposition assays of specifically designed DNA substrates support the conclusion that the transposition machinery is flexible enough to permit variability in half-site spacing, and also perhaps variability in the placement of the recognition site with respect to the cleavage site. This variability causes only local perturbations in the protein-DNA complex, as indicated by experiments in which altered and unaltered DNA substrates are paired.


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