Identification of Four-Nucleotide Single-Stranded DNA Homopolymers with a Solid-State Nanopore Using Alkaline CsCl Solution

DNA sequencing with a solid-state nanopore is promising technology which has the potential to overcome the performance of conventional sequencers. However, identification of four nucleotides with a typical SiN nanopore has yet to be clearly demonstrated because a guanine homopolymer rapidly forms to G-quadruplex under a typical KCl aqueous solution. To overcome this issue, we introduced an alkaline CsCl aqueous solution which induces denaturation of G-quadruplex to single-stranded structure due to disruption of the hydrogen-bonding network between guanines. Using this alkaline CsCl solution, we demonstrated proof-of-principle that four nucleotide single-stranded DNA homopolymers were statistically identified according to the blockade currents with the same single nanopore. Additionally, we also confirmed that a triblock DNA copolymer including three nucleotides exhibited a trimodal gaussian distribution whose peaks correspond to those of DNA homopolymers. Our findings will open the door for actualizing solid-state nanopore sequencing.