Slowed Down Double-Stranded DNA Transport through Solid-State Nanopores by using a Lithium Chloride Concentration Gradient

Abstract

Nanopore biosensors represent the future of diagnostic devices as they are low-cost, high-throughput engines for single molecule detection. Solid-state nanopores are particularly attractive since their size can be controlled to detect a wide range of analytes in solution. However, progress in the field is impeded by inadequate sensitivity of data acquisition systems in detection of fast DNA translocations through the pore. One way to overcome this is by slowing translocation of DNA through the nanopore by use of various media or by altering experimental parameters. Applying a concentration gradient of KCl in the experimental buffer has been shown to effectively prolong dwell times by creating a free-energy barrier that DNA molecules have to overcome. In addition to this, the concentration gradient enhances the magnitude of the local potential, Vr, increasing the capture rate of DNA and thereby increasing event frequency. Our previous work has demonstrated the ability of LiCl buffer to slow down the transport of dsDNA through the nanopore by up to 10-fold through cation/DNA interactions. However, this drastically reduced the event frequency, which can affect the efficacy of this system as a reliable biosensor downstream. Here, we present the use of a concentration gradient of Lithium Chloride buffer to increase the event frequency of dsDNA translocation and further increase dwell time to enhance detection of single molecules through a solid state nanopore. By using 0.5M/3M LiCl on the cis/trans chambers respectively, average dwell times experienced up to a 3-fold increase when compared to experiments run in symmetric 1M LiCl. Additionally, experiments using the 0.5M/3M displayed a greater than 10-fold increase in event frequency, confirming the capture propensity of the asymmetric conditions.