DNA binding and phasing analyses of Tn5 transposase and a monomeric variant

Both full-length Tn5 transposase and a COOH-terminal truncated monomeric form of the protein, Delta 369, have been shown to specifically bind end sequences at comparable affinities. In addition, both proteins distort the target sequence in a similar manner, as determined by a circular permutation assay. In this study, Delta EK54, a derivative of Delta 369 with a single amino acid substitution that significantly enhances binding activity, is used in further binding and bending studies along with full-length transposase. Phasing analysis has shown that distortion of the end sequences upon binding of full-length transposase and Delta EK54 protein is due in part to a protein-induced bend oriented towards the major groove. Because the center of transposase-induced bending maps to the extreme leftward end of the 19 bp consensus sequence, we examined the possibility that optimal protein binding requires additional upstream nucleotide contacts. Experiments presented here show that 9-10 nucleotides are needed upstream of +1 of the 19 bp sequence for efficient binding and this requirement can be met by either single-stranded or double-stranded DNA.