Importance of Base-pair Probing for Mismatch Recognition
|Fakulta / Pracoviště MU
|Stability of canonical base pairs is essential for the integrity of double-stranded DNA (dsDNA) and fidelity of genetic information inheritance, yet many other non-canonical pairs (mismatches) can appear due to replication error. Because mismatches within dsDNA are pathological to various extent, several proteins continuously search for such lesions. One of them is MutS from mismatch repair pathway. Despite many suggestions, mechanism of mismatch detection is not well understood. Thus, we evaluated thermodynamic stability of base pairs composed of 26 unique combinations of A, G, T, and C nucleobases in anti-anti, anti-syn and syn-anti conformations in the central part of 13-nt long palindromic dsDNA by biased molecular dynamics simulations. The bias was introduced through two base-pair parameters, Opening, and Shear, which cover all possible arrangements of nucleobases in the base pair plane. In total, we identified and characterized almost one hundred different free-energy minima. We found excellent agreement between calculated free energy minima and experimental structures of mismatches in both free DNA and DNA complexed with the MutS enzyme. The latter suggests that MutS evolved in such a way that the mismatch recognition is achieved by probing a mismatch towards the minor groove, where mismatches exhibit stable albeit energetically less favorable structures already in the free form while the canonical base pairs do not. We also found that opening of mismatch towards minor groove provides better discrimination from the canonical base pairs than previously suggested bending of DNA. This finding can be helpful in better understanding of sequence-dependent mutability or designing chemical substances targeting damaged DNA.