Grandivittin as a natural minor groove binder extracted from Ferulago macrocarpa to ct-DNA, experimental and in silico analysis

•Grandivittin was extracted from Ferulago macrocarpa (Fenzl) Boiss.•Interaction of GRA with ct-DNA, was evaluated by experimental and molecular modeling methods.•The minor groove binding between GRA and ct-DNA was obtained.•The polymerase extension study was performed using real-time PCR.

Ferulago macrocarpa (Fenzl) Boiss., is an endemic medicinal herb of Iran. In this study a dihydrofuranocoumarin called grandivittin (GRA) was separate and purified from Ferulago macrocarpa (Fenzl) Boiss, and characterized by 1H NMR and Mass spectroscopic methods. The electrochemical behavior of GRA was evaluated by cyclic voltammetry (CV). The interaction of GRA with calf thymus double strand deoxyribonucleic acid (ct-DNA), was evaluated by CV, differential pulse voltammetry (DPV), fluorescence, UV–Vis, FT-IR and molecular modeling methods. The thermodynamic parameters of GRA-DNA complex were measured and reported as: ΔH = 15.04 kJ mol−1, ΔS = 105.54 J mol−1 and ΔG = −15.62 kJ mol−1. Docking simulation was performed to investigate the probable binding mode of GRA to various DNA, too. The polymerase extension study was performed using real-time PCR to confirm the inhibitory effect of GRA on polymerase extension activity as a mirror of binding to ct-DNA. However, all data showed that the grooves binding especially minor groove between GRA and ct-DNA is more predominant rather than other binding modes.

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