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. Crown Copyright (C) 2010 Published by Elsevier B.V. All rights reserved.