A model study on the stacking interaction of phenanthroline ligand with nucleic acid base pairs: An ab initio, MP2 and DFT studies

Abstract

The stacking of phenanthroline(phen) ligand within base pair sequences is one of the important factors for the stabilization of metalphen complex within DNA. The stacking ability of this ligand has been assessed to deduce the base pair selectivity as well as to identify the favored region of intercalation. Different level of theories have been used to predict the favorable regions for stacking interaction of phen ligand with base pair, but the results of MP2/6-31+G(d,p) is found to be reasonably good for monitoring such interactions

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

“…This preference of phen for thymine was already observed by Hazarika et al in their recent study. 33 Also, it must be said that in relation to the extrusion of the adenine base, this easy disruption of A-T base pairs was already mentioned in previous gas-phase studies. [87][88][89] On the other hand, for systems with guanine and cytosine, a similar trend is observed and the system without phen has a R parameter of 3.05…”

“…Such intrinsic interactions were studied previously in the seminal works of Bondarev et al 28 and Řeha et al 29 with threebody models (intercalator + one base pair) which continued to be used for more than one decade 28-34 until the recent work of Hazarika et al 33 Nevertheless, as pointed by Hill et al, 37 we need the other base-pair to provide a better description on the role of the intrinsic forces that rule the intercalation. On the other hand, when two base pairs are considered [35][36][37][38][39][40][41] either the no analysis of the intrinsic interactions is carried out or the main conclusion is that dispersion and the electrostatic contributions are more important than charge transfer.…”

Synthesis, CMC determination, and intercalative binding interaction with nucleic acid of a surfactant–copper(II) complex with modified phenanthroline ligand (dpq)

“…These positive shifts are considered as evidences for intercalation of our complex with nucleic acids. Some literature reports on model studies involving interaction between phen ligand and base pair of NDA indicate that the favorable sequence of this intercalation may be GC pair of nucleic acids (Hazarika, Bezbaruah, Das, Medhi, & Medhi, 2011;Hazarika et al, 2009;Shahabadi et al, 2010). Had the surfactant molecule bound electrostatically to the negatively charged deoxyribose-phosphate backbone of DNA, negative peak potential shifts should have been detected.…”

Synthesis, Characterization and Antimicrobial Activities of New Mixed Ligand Complexes of Copper(II) with 1,10-Phenanthroline and Thymine

“…Coordination occurs through the ring nitrogen and carbonyl oxygen atoms. At alkaline pH, the hydrogen N(1) for thymine is removed [5]. Thymine exists in two tautomeric forms: the keto form and the enol form, where the keto form is strongly favored in equilibrium which is important in coordination [6].…”