Synthesis of a novel 4H-pyran analog as minor groove binder to DNA using ethidium bromide as fluorescence probe.

In the present work, isopropyl-6-amino-4-(3,5-bis(trifluoromethyl)phenyl)-5-cyano-2-methyl-4H-pyran-3-carboxylate (4H-pyran analog) has been synthesized by a three component reaction catalyzed by CsOH/γ-Al2O3 and characterized. The interaction of 4H-pyran analog with herring sperm DNA (hs DNA) under physiological conditions (phosphate buffer of pH 7.2) was investigated by UV absorption, FT-IR, fluorescence, (31)P NMR and circular dichroism (CD) spectroscopy. Fluorescence quenching results reveal that static quenching mechanism is involved in binding between 4H-pyran analog and hs DNA. The calculated thermodynamic parameters (ΔH° and ΔS°) indicate that hydrogen bonding plays a major role in binding between them. UV absorption and fluorescence shows the binding mode of 4H-pyran analog with hs DNA as non-intercalative. According to the IR spectroscopy, 4H-pyran analog binds to guanine, thymine, adenine bases of hs DNA but not to phosphate backbone of hs DNA which is also in good agreement with (31)P NMR results. CD and competitive binding experiment results confirms the minor groove binding of 4H-pyran analog to hs DNA.

In vitro DNA binding studies of antiretroviral drug nelfinavir using ethidium bromide as fluorescence probe.

Understanding the interaction of small molecules with DNA has become an active research area at the interface between biology and chemistry. In the present work, we investigated the mode of interaction of nelfinavir (NFV) with herring sperm DNA (hs DNA) under physiological conditions using various biophysical techniques. Analysis of UV-absorption and fluorescence spectra indicates the formation of complex between NFV and hs DNA. According to the fluorescence results, the binding constant (K) between NFV and hs DNA was found to be 3.30 × 10(4)LM(-1). The calculated thermodynamic parameters (ΔH° and ΔS°) suggested that hydrogen bonding plays a major role in binding between them. Phosphate group binding studies revealed that there was no electrostatic interactions occurred between NFV and hs DNA. Circular dichroism (CD) and DNA melting curve were employed to measure the conformational change of hs DNA in the presence of NFV, which verified the minor groove binding mode. These results were further supported by viscosity measurements and competitive displacement assay study using Hoechst 33258. According to the sequence specificity experiments, NFV binds to A-T rich region of hs DNA.