title: Comparative study of the interaction of meso-tetrakis (N-para-trimethyl-anilium) porphyrin (TMAP) in its free base and Fe derivative form with oligo(dA.dT)15 and oligo(dG.dC)15.
abstract: Interaction between a cationic porphyrin and its ferric derivative with oligo(dA.dT)15 and oligo(dG.dC)15 was studied by UV-vis spectroscopy, resonance light scattering (RLS), and circular dichroism (CD) at different ionic strengths; molecular docking and molecular dynamics simulation were also used for completion. Followings are the observed changes in the spectral properties of meso-tetrakis (N-para-trimethyl-anilium) porphyrin (TMAP), as a free-base porphyrin with no axial ligand, and its Fe derivative (FeTMAP) upon interaction with oligo(dA.dT)15 and oligo(dG.dC)15: (1) the substantial red shift and hypochromicity at the Soret maximum in the UV-vis spectra; (2) the increased RLS intensity by increasing the ionic strength; and (3) an intense bisignate excitonic CD signal. All of them are the reasons for TMAP and FeTMAP binding to oligo(dA.dT)15 and oligo(dG.dC)15 with the outside binding mode, accompanied by the self-stacking of the ligands along the oligonucleotide helix. The CD results demonstrated a drastic change from excitonic in monomeric behavior at higher ionic strengths, which indicates the groove binding of the ligands with oligonucleotides. Molecular docking also confirmed the groove binding mode of the ligands and estimated the binding constants and energies of the interactions. Their interaction trend was further confirmed by molecular dynamics technique and structure parameters obtained from simulation. It showed that TMAP reduced the number of intermolecular hydrogen bonds and increased the solvent accessible surface area in the oligonucleotide. The self-aggregation of ligands at lower concentrations was also confirmed.
authors.affiliation: a Faculty of Medical Sciences, Department of Clinical Biochemistry , Tarbiat Modares University , P.O.Box: 14115-111, Tehran , Iran.
authors.forename: S Zahra
authors.initials: SZ
authors.lastname: Bathaie
authors.forename: Davood
authors.initials: D
authors.lastname: Ajloo
authors.forename: Marzieh
authors.initials: M
authors.lastname: Daraie
authors.forename: Maryam
authors.initials: M
authors.lastname: Ghadamgahi
mesh_terms: D002942:Circular Dichroism; D007501:Iron / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D009994:Osmolar Concentration; D011166:Porphyrins / Q000737:chemistry*
chemical_list: D009838:Oligodeoxyribonucleotides; D011166:Porphyrins; D007501:Iron
keywords: DNA; binding; docking; molecular dynamics simulation; porphyrin; resonance light scattering