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Nanopore-based technologies have attracted much attention recently for their promising use in low-cost and high-throughput genome sequencing. To achieve single-base resolution of DNA sequencing, it is critical to slow and control the translocation of DNA, which has been achieved in a protein nanopore but not yet in a solid-state nanopore. Using all-atom molecular dynamics simulations, we investigated the dynamics of a single-stranded DNA (ssDNA) molecule in an aqueous glycerol solution confined in a SiO(2) nanopore. The friction coefficient ξ of the ssDNA molecule is found to be approximately 18 times larger in glycerol than in water, which can dramatically slow the motion of ssDNA. The electrophoretic mobility μ of ssDNA in glycerol, however, decreases by almost the same factor, yielding the effective charge (ξμ) of ssDNA being roughly the same as in water. This is counterintuitive since the ssDNA effective charge predicted from the counterion condensation theory varies with the dielectric constant of a solvent. Due to the larger friction coefficient of ssDNA in glycerol, we further show that glycerol can improve trapping of ssDNA in the DNA transistor, a nanodevice that can be used to control the motion of ssDNA in a solid-state nanopore. Simulation results of slowing ssDNA translocation were confirmed in our nanopore experiment.

Solid state nanopores are a core element of next-generation single molecule tools in the field of nano-biotechnology. Thin film electrodes integrated into a pore can interact with charges and fields within the pore. In order to keep the nanopore open and thus functional electrochemically induced surface alteration of electrode surfaces and bubble formation inside the pore have to be eliminated. This paper provides electrochemical analyses of nanopores drilled into TiN membranes which in turn were employed as thin film electrodes. We studied physical pore integrity and the occurrence of water decomposition yielding bubble formation inside pores by applying voltages between -4.5 and +4.5 V to membranes in various protection stages continuously for up to 24 h. During potential application pores were exposed to selected electrolyte-solvent systems. We have investigated and successfully eliminated electrochemical pore oxidation and reduction as well as water decomposition inside nanopores of various diameters ranging from 3.5 to 25 nm in 50 nm thick TiN membranes by passivating the nanopores with a plasma-oxidized layer and using a 90% solution of glycerol in water as KCl solvent. Nanopore ionic conductances were measured before and after voltage application in order to test for changes in pore diameter due to electrochemical oxidation or reduction. TEM imaging was used to confirm these observations. While non-passivated pores were electrochemically oxidized, neither electrochemical oxidation nor reduction was observed for passivated pores. Bubble formation through water decomposition could be detected in non-passivated pores in KCl/water solutions but was not observed in 90% glycerol solutions. The use of a protective self-assembled monolayer of hexadecylphosphonic acid (HDPA) was also investigated.