The Nanoscale and Quantum Phenomena Institute (NQPI) Seminar Series is pleased to welcome Srijana Pandey, Ohio University, as our featured speaker on Thursday, April 23 at 4:10 p.m. All seminars take place in CLIPPINGER 194 and are also accessible virtually via Teams.

Title: Study of binding kinetics and diffusion dynamics of fluorescent probes on surface-immobilized lambda DNA

Abstract: In dilute solutions, molecules move randomly through diffusion, a fundamental process in biology, chemistry, and physics. Advances in fluorescence microscopy now enable the study of diffusion and binding events at the single-molecule level, providing insights into reaction kinetics that are essential for fields such as biosensing, drug delivery, and industrial chemistry. For example, drug-target binding kinetics, often quantified by parameters such as the half-maximum inhibitory concentration (IC50), are crucial for evaluating drug efficacy. Similarly, studying dye-DNA adsorption and diffusion helps reveal mechanisms relevant to cellular transport, receptor interaction, and reaction kinetics in weak solutions. The probe-DNA binding kinetics in single-molecule studies offer detailed insights into DNA molecules and provide valuable information for both scientific research and practical applications in biotechnology and medicine. To study single molecules of dye DNA diffusion kinetics, various kinds of DNA staining probes(dyes) are available, and among them, YOYO-1(bis-intercalator) and YO-PRO-1(mono intercalator) are most widely used. Intercalation is a binding mechanism in which small molecules insert their flat aromatic structures between adjacent base pairs of DNA. In this work, we are trying to study and compare the binding dynamics of probes (YOYO-1 and YO-PRO-1) dye to an immobilized lambda DNA on the functionalized surface using fluorescence microscopy at the single-molecule level and the bulk measurement using the fluorimeter. Also, probe DNA-binding kinetics depend on changes in pH and ionic strength, which can affect DNA conformation and stability. Changes in pH alter the charge of both DNA and the surface, thereby modulating electrostatic interactions that govern DNA binding kinetics and dye diffusion. Likewise, variations in ionic strength influence DNA stability and competitive dye binding, impacting diffusion-controlled interactions. In this study, we investigate the binding dynamics of different probes to DNA across a range of ionic strengths to determine how ionic strength affects dye-DNA interactions in our system. Future work will focus on exploring the role of buffer pH and diverse salt conditions. Overall, these single-molecule probes provide precise insights into DNA interactions, with important implications for both fundamental research and biotechnology and medical applications.