Photonic-plasmonic hybrid single-molecule nanosensor measures the effect of fluorescent labels on DNA-protein dynamics

Abstract

Current methods to study molecular interactions require labeling the subject molecules with fluorescent reporters. The effect of the fluorescent reporters on molecular dynamics, however, has not been quantified due to lack of alternative methods. We develop a hybrid photonic-plasmonic antenna-in-a-nanovacity single molecule biosensor to study DNA-protein dynamics without using fluorescent labels. Our results indicate that the fluorescein and fluorescent protein labels will decrease the interaction between a single DNA and a protein due to weakened electrostatic interaction. While the study is performed on the DNA-XPA system, the conclusion has a generall implication that the traditional fluorescent labeling methods might be misestimating the molecular interactions.