© 2015 American Chemical Society. The effects of phenanthroline (phen) intercalation on the structure, energetics, and bonding of adenine-thymine and guanine-cytosine tetramers (A-T/T-A and G-C/C-G) were studied through density functional theory (DFT) using functionals that were recently improved to consider the effect of dispersion forces. Our results given by energy decomposition analysis show that the dispersion contribution, ΔE<inf>disp</inf>, is the most important contribution to the interaction energy, ΔE<inf>int</inf>. However, it is not enough to compensate the Pauli repulsion term, ΔE<inf>Pauli</inf>, and the roles of the orbital contribution, ΔE<inf>orb</inf>, and, in particular, the electrostatic contribution, ΔE<inf>elstat</inf>, become crucial for the stabilization of the structures in the intercalation process. On the other hand, for G-C/C-G systems, hydrogen-bonding (HB) interactions are more important than stacking (S) interactions, whereas for A-T/T-A systems, HB and S become competitive. Moreover, intercalation produces important changes not only in the hydrogen bonds of base pairs, because S and HB are deeply connected, but also in other characteristic geometric parameters of the base pairs.