Orateur
Description
Uracil can exist in dsDNA by spontaneous cytosine deamination or by misincorporation of dUMP instead of dTMP during the replication process [1]. A highly specific Uracil-DNA glycosylase (UDG) enzyme recognizes and excise the flipped uracil base from the dsDNA helix; this mechanism is part of the base-excision repair (BER) pathway [2]. There remains a lack of complete understanding in the debate over the DNA base flipping mechanism—whether base flip happens due to the DNA helix's distortion or if it is induced by the UDG enzyme during BER. However, the dynamic mechanism of uracil base flipping at an atomic level is still not understood. To gain an insightful understanding, we perform metadynamics (MtD) simulations to generate free energy profiles for uracil base flipping out of its helical stack in the dsDNA in this work. The uracil base causes a slight perturbation (intrahelical) towards the major groove side initially, and the opening angle is ~50º with an energy barrier of ~6 kcal/mol. The energy barrier difference from the intrahelical to extrahelical state is about ~2kcal/mol. We docked intrahelical and extrahelical poses of uracil base in dsDNA with the UDG enzyme using molecular docking tools to understand the UDG enzyme activity in the base flipping mechanism. The obtained docking confirmation indicated that the extrahelical state of uracil in dsDNA fits well into the catalytic pocket of the UDG enzyme. Our simulations suggest that uracil base flipping may be the key step that permits UDG to recognize and excise uracil from the dsDNA.
References:
1. Vassylyev, D. G. & Morikawa, K. Precluding uracil from DNA. Structure 4, 1381–1385 (1996).
2. Hegde, M. L., Hazra, T. K. & Mitra, S. Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells. Cell Res. 18, 27–47 (2008).
