How the Intercalation of Phenanthroline Affects the Structure, Energetics, and Bond Properties of DNA Base Pairs: Theoretical Study Applied to Adenine-Thymine and Guanine-Cytosine Tetramers

Adrià Gil, Manuel Melle-Franco, Vicenç Branchadell, Maria José Calhorda

Research output: Contribution to journalArticleResearchpeer-review

15 Citations (Scopus)

Abstract

© 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.
Original languageEnglish
Pages (from-to)2714-2728
JournalJournal of Chemical Theory and Computation
Volume11
Issue number6
DOIs
Publication statusPublished - 9 Jun 2015

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