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Double-stranded DNA may contain mismatched base pairs beyond the Watson-Crickpairs guanine-cytosine and adenine-thymine. Such mismatches bear adverseconsequences for human health. We utilize molecular dynamics and metadynamicscomputer simulations to study the equilibrium structure and dynamics for bothmatched and mismatched base pairs. We discover significant differences betweenmatched and mismatched pairs in structure, hydrogen bonding, and base flip workprofiles. Mismatched pairs shift further in the plane normal to the DNA strandand are more likely to exhibit non-canonical structures, including the e-motif.We discuss potential implications on mismatch repair enzymes' detection of DNAmismatches.

DNA Base Pair Mismatches Induce Structural Changes and Alter the Free Energy Landscape of Base Flip