(689h) Thermodynamics of Reversible DNA-Ligand Associations on Solid Supports

A variety of solution methods exist for analysis of interactions between small molecule ligands and nucleic acids, but accomplishing this task economically for hundreds to thousands of sequences remains challenging. Surface assays offer a prospective solution through array-based multiplexing capable of mapping out the full sequence context of a DNA/ligand interaction in a single experiment. In this feasibility study, the binding thermodynamics of a model oligopeptide drug to DNA were analyzed via DNA melting transitions at solid-liquid interfaces. Monolayers of single-stranded DNA “probe” molecules were immersed in a medium containing complementary “target” strands labeled with an electroactive tag. Hybridization between the probes and targets was monitored as a function of temperature with electrochemical methods, leading to generation of a hybridization-melting curve. In the presence of the minor groove binding drug netropsin the DNA helix-coil transition was shifted to higher temperature, indicating stabilization of the double-stranded DNA state by the ligand. Analysis of these shifts allowed determination of the ligand binding thermodynamics. Comparison with solution-derived calorimetric data showed good agreement in free energies, but accurate separation into the enthalpic and entropic contributions was more difficult due to uncertainties in baseline corrections. Analysis of drug-DNA interactions on solid supports with electrochemical techniques can pave the way to multiplexed screening on microelectronic biochips.