TY - JOUR

T1 - 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

AU - Gil, Adrià

AU - Melle-Franco, Manuel

AU - Branchadell, Vicenç

AU - Calhorda, Maria José

PY - 2015/6/9

Y1 - 2015/6/9

N2 - © 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, ΔEdisp, is the most important contribution to the interaction energy, ΔEint. However, it is not enough to compensate the Pauli repulsion term, ΔEPauli, and the roles of the orbital contribution, ΔEorb, and, in particular, the electrostatic contribution, ΔEelstat, 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.

AB - © 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, ΔEdisp, is the most important contribution to the interaction energy, ΔEint. However, it is not enough to compensate the Pauli repulsion term, ΔEPauli, and the roles of the orbital contribution, ΔEorb, and, in particular, the electrostatic contribution, ΔEelstat, 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.

U2 - 10.1021/ct5006104

DO - 10.1021/ct5006104

M3 - Article

SN - 1549-9618

VL - 11

SP - 2714

EP - 2728

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

IS - 6

ER -