Kinetically Trapped Ligand Binding in DNA Tandem Repeats

Tandem DNA repeats are ubiquitous in the human genome. They often exist in microsatellite and minisatellite domains, serving as targets for transcription factors and small molecules in gene regulation. Investigation of ligand binding to tandem DNA repeats is rather challenging using traditional methods, such as NMR spectroscopy and X-ray crystallography, whose ensemble-averaging nature prevents deconvolution of individual binding events in a dynamic equilibrium. Harnessing the high sensitivity and temporal resolution of single-molecule techniques such as optical tweezers, we interrogated the binding mechanism between netropsin, a DNA minor groove binder with anticancer properties, and individual recognition sites in the adenine-thymine (A-T) DNA repeats. Surprisingly, we found that the binding between netropsin and the A-T DNA repeats favored kinetically trapped states over thermodynamically stable ones. Although kinetic traps are known in the folding of biomolecules, such kinetically trapped misbinding between ligands and biomolecules, particularly in DNA, has not been directly demonstrated until now. Given the widely occurring tandem repeats of proteins and nucleic acids, our study provides the first direct demonstration in DNA that ligand binding to such repeats can enter kinetically trapped states, which may represent a fundamental aspect of ligand-receptor interactions in cells. Our findings therefore offer insights into new molecular binding mechanisms which may modulate subsequent biological activities.