An in silico study of the protonated DNA triplex: In vivo stability of C+GC in a DNA triple helix

Protonated DNA base pairs, particularly the Cytosine–Guanine–Cytosine (CGC) triple pairs, were investigated its relative energetics by theoretical calculations. The energetic stabilities of C+GC and CG+C are almost the same in the gas phase, although the C+G pair is more stable than CG+ by ca. 1150 cm−1 (3.34 kcal/mol). It is to be noted, however, that only C+GC was found in vivo, which seems to indicate different chemical environments for the triple pairs in vivo.