The interaction between the GGCC-specific BspRI DNA methyltransferase (M.BspRI) and substrate DNA was studied with footprinting techniques using a DNA fragment that was unmodified on both strands. Footprinting with DNase I revealed an ≃14 bp protected region. Footprinting with dimethylsulfate detected major groove interactions with the guanine bases of the recognition sequence. Reaction with l,l0-phenanthroline-copper did not show protection, suggesting that minor groove interactions play little role in sequence-specific recognition by M.BspRI. Hydroxyl radical footprinting revealed a protected stretch of 6 nt. The hydroxyl radical footprint of M.BspRI differs markedly from the the footprint reported for the HhaI and SssI methyltransferases. The pattern of protection from dimethylsulfate and hydroxyl radicals suggests that the interactions of M.BspRI with DNA are similar to those detected in the co-crystal structure of the HaeIII methyltransferase.
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