A peptide fragment (p26) generated as a result of limited tryptic proteolysis of methyltransferase MspI retains transient but non-specific DNA binding capability. The transient DNA binding by p26 was characterized with respect to physicochemical factors. Limited proteolysis was performed to probe gross structural deviation from the reported two-domain organization for m5C-MTases, in light of topoisomerase activity shown by MspI, resulted in two peptide fragments; a large fragment p26 and a small fragment p18, consistent with the other reported m5C-MTase structures. The purified large peptide fragment p26, spans between 6 and 251 in the amino acid sequence of M.MspI. The peptide p26 does not bind S-adenosylmethionine, although in the intact protein the AdoMet binding region can be mapped to a region in the protein that is present in this peptide. Such transient DNA binding has not been reported for other protolytic product of any other m5C-DNA methyltransferase.