Purification of the Tn3 transposase and analysis of its binding to DNA

The transposase encoded by the tnpA gene of Tn3 is a protein specifically required for Tn3 transposition. We have purified it to homogeneity from an Escherichia coli strain containing a mutant Tn3 that overproduces transposase. About a 10-fold additional increase in transposase resulted from growth into stationary phase. The initial purification was guided by the presence of a protein band with the electrophoretic mobility of the tnpA gene product. The identity of the purified protein was proven by the agreement of five NH2-terminal amino acids with the nucleotide sequence of the A gene; this, in turn, fixed the initiation codon. Transposase formed large aggregates in the absence of Mg2+ at salt concentrations of 0.1 M or less. In nonaggregating conditions, it had 1 or 2 copies of 113,000-dalton protomers. Subsequent purifications exploited the rapid and simple assay of transposase-mediated retention of labeled DNA to a nitrocellulose filter. Transposase bound tightly to single-stranded DNA but weakly to intact duplex DNA. DNA binding did not require Mg2+ and was highly salt-resistant. Binding did not require specific sequences, because poly(dT) was as good a substrate as phi X174 viral DNA. The high DNA binding constant of 4 X 10(9) M-1 is about the same as for some single-stranded DNA binding proteins.