The DNA Dynamics Near Nanopores at Sub-Millisecond and Sub-Micrometer Levels by the Ultraviolet Light Spot

Abstract

Phenomenon of deoxyribonucleic acid (DNA) translocation through a nanopore is a significant interest in the field of biophysics. In the condition of applied voltage, coiled DNA molecules in the electrolyte approach to the mouth of a nanopore and thread into a nanopore by uncoiling its structure. Then DNA molecules recoil and diffuse outward from a nanopore after DNA translocation. Because DNA molecules uncoil to thread into a nanopore and recoil after DNA translocation, DNA dynamics near a nanopore strongly correlate with DNA translocation. Here, we propose an optical method for investigating DNA dynamics near nanopores at sub-millisecond and sub-micrometer levels by using ultraviolet light and silicon nanopores. Silicon nanopores, which have high refractive index and extinction coefficient at ultraviolet light, induces the light spot, whose size is 100nm, upon nanopores due to low transmitted light condition. By threading into nanopores, DAPI-stained DNA molecules pass through the ultraviolet light spot and emit fluorescence. We use the fluorescence intensity trace as the information of DNA translocation through nanopores. As the results of our measurement, the fluorescence intensity traces were in accordance with previous investigation of the voltage dependence of DNA electrophoresis mobility. Furthermore, our analytical results of fluorescence intensity traces showed the correlation between DNA conformations during DNA translocation through nanopores, which are unfolded or folded DNA translocation, and DNA dynamics after DNA translocation through nanopores, which reveal the usefulness of our optical method for investigating DNA dynamics near nanopores.