DNA repair enzymes are known to distort the damaged DNA upon the formation of the enzyme substrate complex. The DNA in the vicinity of the damage is considerably more bent, more twisted and the damaged base is flipped into an extrahelical position. The distortion energy contributes to the total energy of interaction between the protein and DNA and thus is an important part of the specificity of damage recognition. To study the contribution of DNA flexibility to specific recognition, we have conducted several MD simulations in aqueous solution of various forms of damaged DNA. Using a Potential of Mean Force representation we have constructed the energy surfaces for bending and twisting as well as an energy surface for base flipping. We show that the damaged DNA is considerably more flexible than the undamaged DNA. Furthermore, the bending flexibility correlates with enzymatic activity, indicating that the distortion of the DNA in the process of enzyme substrate interaction affects the efficiency of the enzyme through changing its KM. A similar analysis of a DNA with an abasic site shows that the flexibility properties of the two isomeric forms of deoxyribose in DNA are substantially different. The results indicate that the a-isomer is more similar to the DNA in the complex that the b-isomer. These results are in agreement with the crystallographic structure of the complex of the abasic DNA in complex with its repair enzyme. The energy surface for base flipping was constructed for a G*U mismatch. The barrier for uracil flipping is 11.6 kcal/mole lower than the barrier for flipping a cytosine in the undamaged DNA. The lowering of the barrier results primarily from an increased flexibility of the damaged DNA.  The barrier for base flipping in the damaged DNA predicts that the rate of base flipping is similar to the rate of linear scanning of proteins on DNA. The proposed mechanism for specific recognition depends on the dynamic properties of the damaged DNA reflected in increased flexibility near the damage gives rise to a DNA more susceptible to distortion induced by the enzyme.


Supported by PHS Grant CA 63317.