Binding of a non-ionic pyrenylisoxazolidine derivative to double-stranded polynucleotides: spectroscopic and molecular modelling studies

Abstract

The binding of [(3RS,5SR)-2-methyl-3-pyren-1-ylisoxazolidin-5-yl]methanol (MPIM), a non-ionic pyrene derivative with potential anticancer activity, to calf-thymus DNA (ct-DNA) and the synthetic double-strand polynucleotides poly-d(AT)₂ and poly-d(GC)₂ was investigated at neutral pH through the combination of UV-Vis absorption and emission spectroscopy, fluorescence quenching experiments and molecular modelling studies. Hypochromic effects accompanied by the formation of tight isosbestic points were observed upon binding of MPIM to polynucleotides. The related binding constants, evaluated by the half-reciprocal plots of the absorbance data, were 6.8 × 10³ M⁻¹, 6.0 × 10³ M⁻¹ and 1.5 × 10³ M⁻¹ for ct-DNA, poly-d(AT)₂ and poly-d(GC)₂, respectively. The fluorescence emission intensity of MPIM was slightly quenched by ct-DNA, basically unaffected by poly-d(AT)₂ and efficiently suppressed by poly-d(GC)₂. The overall results support an intercalative binding mode of the pyrene derivative in the case of ct-DNA and poly-d(AT)₂, whereas a shallow intercalation seems to be involved with poly-d(GC)₂. Docking studies agree with the experimentally observed complex stability order and reveal a common binding mode implying that the chromophore intercalates between the staked base pairs and the isoxazolidine ring lying along the major groove. In any case a stabilizing hydrogen bond is formed between the hydroxyl group of the MPIM methanol moiety and the oxygen of a phosphate group. The preferential binding selectivity of MPIM for intercalation in AT-rich regions is probably attributable to steric hindrance between the N-methyl group of MPIM and the 4-amino one of the cytosine in the GC sites.