Abstract
Base pair mismatches in DNA can have many adverse consequences, yet the exact mechanism by which mismatches are repaired is unknown. Both matched and mismatched DNA sequences were studied using molecular dynamics in biased and unbiased simulation. Significant differences were found between matched and mismatched pairs in structure, hydrogen bonding, and base flip work profiles. Mismatched pairs show greater movement perpendicular to the DNA strand and a lower free energy barrier for base flip than matched pairs. This supports experimental findings that the primary mechanism utilized by mismatch repair enzymes is to fully flip the base into the active site.
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