Interaction of the E. coli DNA G:T-mismatch Endonuclease (vsr Protein) with Oligonucleotides Containing its Target Sequence

The Escherichia coli vsr endonuclease recognises G:T base-pair mismatches in double-stranded DNA and initiates a repair pathway by hydrolysing the phosphate group 5′ to the incorrectly paired T. The enzyme shows a preference for G:T mismatches within a particular sequence context, derived from the recognition site of the E. coli dcm DNA-methyltransferase (CC[A/T]GG). Thus, the preferred substrate for the vsr protein is (CT[A/T]GG), where the underlined T is opposed by a dG base. This paper provides quantitative data for the interaction of the vsr protein with a number of oligonucleotides containing G:T mismatches. Evaluation of specificity constant (kst/KD; kst=rate constant for single turnover, KD=equilibrium dissociation constant) confirms vsrʹs preference for a G:T mismatch within a hemi-methylated dcm sequence, i.e. the best substrate is a duplex (both strands written in the 5′-3′ orientation) composed of CT[A/T]GG and C5MeC[T/A]GG. Conversion of the mispaired T (underlined) to dU or the d5MeC to dC gave poorer substrates. No interaction was observed with oligonucleotides that lacked a G:T mismatch or did not possess a dcm sequence. An analysis of the fraction of active protein, by “reverse-titration” (i.e. adding increasing amounts of DNA to a fixed amount of protein followed by gel-mobility shift analysis) showed that less than 1 % of the vsr endonuclease was able to bind to the substrate. This was confirmed using “competitive titrations” (where competitor oligonucleotides are used to displace a 32P-labelled nucleic acid from the vsr protein) and burst kinetic analysis. This result is discussed in the light of previous in vitro and in vivo data which indicate that the MutL protein may be needed for full vsr activity.