Measurement of Salt Dependence of Single DNA Translocation through Si Nanopores with Ultraviolet Excitation

Abstract

Recently, nanopore-based technologies have shown a great promise for developing single-molecule DNA sequencing. Among these technologies, optical detection with a parallel nanopore array has been proposed as replace of ionic current detection which has challenge to improve its throughout. Optical detection requires to control DNA dynamics near solid-state nanopore. And currently there is no report about DNA dynamics near a nanopore. In this presentation, We report measurement of salt dependence of single-molecule DNA translocation through silicon nanopores by using ultraviolet light. For this study, we used 15nm thickness porous silicon membrane with 15∼25nm diameter, ultraviolet laser diode(λ=375nm) as the excitation light, 10kbp DNA sample stained with DAPI(excitation:λ=360nm,emission: λ=460nm) and 0.5M,1.0M,2.0M KCl with 10mM Tris-HCl. By applying voltage across the silicon membrane, DNA samples pass through a light spot and emit fluorescence immediately after the translocation. As the result of measurement, we found that DNA translocation time through silicon nanopores increased and dwell time in light spot decreased as salt concentration increased. These time shift are explained that counterions bind to negatively charged DNA molecules and change their electrophoretic mobility and conformation. Additionally, we demonstrated similar experiment with NaCl and LiCl. For this experiment, we obtained a great deal of understanding which counterions affect DNA sample. Result of these salt conditions is accordance with previous studies by using ion current detection. Further analytical results will give an absolute proof at the presentation to investigate DNA dynamics.