A Comparable Study of Single Stranded DNA Sensing Using Track-Etched Nanopore Sensors

Abstract

Detection of single-stranded DNA (ss-DNA) has great importance not only for decoding genetic information but understanding its role in DNA replication, recombination, and repair. Recently, its detection in body fluids and the development of its library brought new perspectives to diagnose cancer. Track-etched nanopores are synthetic pores that can be used in several applications to sense and distinguish molecules. Biomolecules such as DNA have special importance due to their usage and applications. Even if most of the studies focus on double-stranded DNA (ds-DNA), nanopore sensing and discriminating single-stranded DNA (ss-DNA) is still of great interest. However, sensing ss-DNA is relatively more challenging than ds-DNA since it is more prone to ionic interactions which changes its translocation dynamics. In this study, single-tracked poly(ethylene terephthalate) (PET) membranes were used to generate conical nanopores. Due to its chemical stability, ease of fabrication at various geometries, and tunable pore size with respect to other polymer nanopores, PET nanopores were preferred. By chemical etching, single nanopores were fabricated, surface modified, and used for ss- and ds-DNA sensing. We presented our results in a comparative way relative to ds-DNA. We observed shorter current-pulse amplitude (for ss-DNA) with similar duration with respect to ds-DNA. Such behavior may indicate the conformational changes of single and double-strand forms during translocation. We also report the effect of electrolyte concentration on the frequency of ss-DNA translocation. Our results demonstrated the feasibility and performance of track-etched PET nanopore for ss-DNA sensing. It provided insight into the electrophoretic transport dynamics of ss-DNA in solution such as linear current-pulse frequency against concentration and applied potential. Additionally, the current-pulse amplitude of ss-DNA was relatively smaller than ds-DNA which enabled to differentiate the DNA strands. Moreover, the results showed the capability and potential use of the track-etched PET nanopore and the limits as a sensor. Finally, the results on electrolyte concentration and its effect on the translocation frequency provided additional insight into the possible non-uniform DNA-ion interactions. Nanopore sensing is a growing research area and powerful as a non-labeling technique. The detection and sensing of ss-DNA has a special importance for various applications.In this study, we showed the nanopore sensing of ss-DNA (100 bases) using track-etched PET nanopores and gave a insight on how the ss-DNA would behave in solution under different conditions.image