Fluorescence Enhancement From Single DNA Molecules Confined In Si/SiO2 Nanochannels

Conference poster, 2010

A large challenge in biophysics when studying single molecules using fluorescence microscopy is to obtain a signal that is clearly detectable above the background noise. Ways to improve or optimize the fluorescence signal is therefore of great interest. We here study DNA extended in 320 nm deep funnel-shaped SiO2 nanochannels with a width ranging from 40nm to 600nm. The DNA is stained with a fluorescent dye (YOYO-1) and we show that the total emission from the DNA varies significantly with the dimensions of the channels (Figure) and has a peak intensity at half the wavelength of the emitted light. Measurements at varying salt concentrations, where the same confinement leads to different extension of the DNA, confirm that it is solely the geometry of the channel that governs the enhancement effect, ruling out alternative explanations, such as self-quenching. By using polarizers on the emission side we can investigate the light polarized parallel and perpendicular to the channel separately and we see that they show vastly different behavior with the peak in emission only detected in the light polarized parallel to the channels. We will discuss how our data may be explained by cavity-resonance effects when the lateral dimensions of the channels coincide with half the wavelength of the emitted light. Our results suggest that it is possible to fine-tune the size and shape of the nanochannels to maximize the number of photons collected from the molecule under study, for example when studying DNA interacting with single DNA-binding proteins where maximizing the photon budget is paramount.