Spontaneous base flipping in DNA and its possible role in methyltransferase binding

Recent crystallographic studies showed that HhaI and other methyltransferas es flip their target DNA base completely out of a DNA helix. This base flip ping is also a key feature in a number of other enzyme-catalyzed processes involving DNA. The mechanism of base flipping by these enzymes remains elus ive. Based on a full atonic level description of bond rotational motions we have studied the energetics of flipping a base in a B-DNA duplex in the ab sence of the enzyme. We have also investigated the effect of the restraints from enzyme-distorted DNA backbone on the movement of a flipped base in se veral methytransferase bound DNA crystal structures. Our study on crystal B -DNA helices showed that a base could be flipped at an energy cost close to the enthalpy observed for base pair opening in premelting thermal fluctuat ions. This suggests that spontaneous base flipping in DNA due to thermal fl uctuation may be achieved. Analysis of several crystal HhaI and HaeIII meth yltransferase DNA duplex structures showed that the enzyme induced DNA back bone distortion severely restricts the movement of the flipped base, which indicates that during base flipping the backbone needs to adopt a substanti ally different conformation than that observed in the x-ray (enzyme-bound) structures. Our results suggest the possible role of thermally induced tran sient base opening in facilitating recognition and binding of methyltransfe rases and other enzymes.