Drug binding disrupts chiral water structures in the DNA first hydration shell

Abstract

Knowledge of how intermolecular interactions change hydration structures surrounding DNA will heighten understanding of DNA biology and advance drug development. However, probing changes in DNA hydration structures in response to molecular interactions and drug binding in situ under ambient conditions has remained challenging. Here, we apply a combined experimental and computational approach of chiral-selective vibrational sum frequency generation spectroscopy (chiral SFG) to probe changes of DNA hydration structures when a small-molecule drug, netropsin, binds the minor groove of DNA. Our results show that chiral SFG can detect water being displaced from the minor groove of DNA due to netropsin binding. Additionally, we observe that chiral SFG distinguishes between weakly and strongly hydrogen-bonded water hydrating DNA. Chiral SFG spectra show that netropsin binding, instead of displacing weakly hydrogen-bonded water, preferentially displaces water molecules strongly hydrogen-bonded to thymine carbonyl groups in the DNA minor groove, revealing the roles of water in modulating site-specificity of netropsin binding to duplex DNA rich in adenine–thymine sequences. The results convey the promise of chiral SFG to offer mechanistic insights into roles of water in drug development targeting DNA.