It was established that the cytosine·thymine (C·T) mismatched DNA base pair with cis-oriented N1H glycosidic bonds has propeller-like structure (|N3C4C4N3| = 38.4°), which is stabilized by three specific intermolecular interactions–two antiparallel N4H…O4 (5.19 kcal mol−1) and N3H…N3 (6.33 kcal mol−1) H-bonds and a van der Waals (vdW) contact O2…O2 (0.32 kcal mol−1). The C·T base mispair is thermodynamically stable structure (ΔGint = −1.54 kcal mol−1) and even slightly more stable than the A·T Watson–Crick DNA base pair (ΔGint = −1.43 kcal mol−1) at the room temperature. It was shown that the C·T ↔ C*·T* tautomerization via the double proton transfer (DPT) is assisted by the O2…O2 vdW contact along the entire range of the intrinsic reaction coordinate (IRC). The positive value of the Grunenberg's compliance constants (31.186, 30.265, and 22.166 Å/mdyn for the C·T, C*·T*, and TSC·T ↔ C*·T*, respectively) proves that the O2…O2 vdW contact is a stabilizing interaction. Based on the sweeps of the H-bond energies, it was found that the N4H…O4/O4H…N4, and N3H…N3 H-bonds in the C·T and C*·T* base pairs are anticooperative and weaken each other, whereas the middle N3H…N3 H-bond and the O2…O2 vdW contact are cooperative and mutually reinforce each other. It was found that the tautomerization of the C·T base mispair through the DPT is concerted and asynchronous reaction that proceeds via the TSC·T ↔ C*·T* stabilized by the loosened N4HO4 covalent bridge, N3H…N3 H-bond (9.67 kcal mol−1) and O2…O2 vdW contact (0.41 kcal mol−1). The nine key points, describing the evolution of the C·T ↔ C*·T* tautomerization via the DPT, were detected and completely investigated along the IRC. The C*·T* mispair was revealed to be the dynamically unstable structure with a lifetime 2.13·× 10−13 s. In this case, as for the A·T Watson–Crick DNA base pair, activates the mechanism of the quantum protection of the C·T DNA base mispair from its spontaneous mutagenic tautomerization through the DPT. © 2013 Wiley Periodicals, Inc.