Molecular recognition of double-stranded DNA by a synthetic, homoaromatic tripeptide (YYY): The spectroscopic and calorimetric study.

The intermolecular interactions of a homoaromatic tripeptide, H-Tyr-Tyr-Tyr-OH (YYY) with model double-stranded (ds) DNA (ct-DNA) have been investigated by isothermal titration calorimetric (ITC) method along with various biophysical techniques such as fluorescence, time correlated single photon counting (TCSPC) and circular dichroism (CD) spectroscopy. The binding affinity [log (K) at 25 °C] of the YYY to ct-DNA is calculated as ≈4.3. The binding mode of the YYY to ds-DNA is elucidated by fluorescence intercalator displacement (FID) assay, melting temperature analysis, viscosity measurement and salt-induced fluorescence quenching study. The studies establish that the YYY recognizes the groove of the ct-DNA. The temperature dependent ITC studies show that the binding interaction is thermodynamically favourable. The compensation between enthalpy and entropy leads to the overall Gibbs free energy change almost invariant. Finally, the generality of the YYY to recognize ds-DNA has been analyzed with other model ds-DNA, ds26, which reveals almost similar binding affinity of the YYY as ct-DNA. The studies elucidate both the spectroscopic and calorimetric insight of the interactions of a homoaromatic tripeptide with ds-DNA and hold the promise of future applications as DNA targeting drug.