Solid State Nanopore Kit for Real-Time Analysis of DNA and Other Analytes

Abstract

Recent improvements in nanofabrication techniques have greatly increased the reproducibility and stability of nanopores fabricated in ultrathin dielectrics such as silicon nitride or silicon oxide. These nanopores are now suitable for a wide range of accurate and reliable molecular analyses. Here we present a compact, portable and easy to use nanopore kit, intended for laboratory experiments and development of prototype devices. Experiments range from simple nanopore conductance and stability determination, to the more complex analysis of translocations of DNA and other analytes (resistive pulse sensing/nanopore spectroscopy). The kit consists of: -A Teflon flow-cell with two 1.0 ml chambers, hosting a central cassette containing the silicon chip with the nanopore. -A miniaturized low-noise and high bandwidth amplifier. The entire kit is contained within a 16x10x5 cm Faraday cage and connects to a laptop via a USB cable. The real-time analyses are performed using the amplifier control software, enabling a fast characterization of nanopore conductance, production of I/V curves and production of histograms for blockade sizes and dwell times. The kit was tested under different conditions, using nanopores in the range from 5 to 50nm. A 3,000bp fragment of DNA was successfully translocated on a 6 nm nanopore. A 48,500bp phage lambda DNA was successfully translocated on a 11 nm nanopore. Translocations were performed between potentials of 200mV and 380mV in 1M KCl buffer, 10mM HEPES pH 8.0. The versatility of the nanopore kit combined with the real-time analysis feature allows for quick and easy characterizations of nanopores and their interaction with analytes, for both educational and research purposes.