Reducing a DNA molecule's translocation speed in a solid-state nanopore is a key step toward rapid single molecule identification. Here we demonstrate that DNA translocation speeds can be reduced by an order of magnitude over previous results. By controlling the electrolyte temperature, salt concentration, viscosity, and the electrical bias voltage across the nanopore, we obtain a 3 base/micros translocation speed for 3 kbp double-stranded DNA in a 4-8 nm diameter silicon nitride pore. Our results also indicate that the ionic conductivity inside such a nanopore is smaller than it is in bulk.

When dsDNA polymers containing the identical number of base pairs were electrophoresed through a nanopore in a voltage biased silicon nitride membrane, the measured time integral of blocked ionic current (the event charge deficit, ecd [1]) for each translocation event was the same regardless of whether the molecules were in a linear, circular relaxed, or supercoiled form. Conversely, when DNA polymers containing different numbers of base pairs were electrophoresed through a nanopore, the ecd depended strongly on, and predicted the value of, the molecule's number of base pairs. Measurements showed that the magnitude of the current blockages was strongly affected by a molecule's form. The current blockages exhibited characteristic differences that distinguished between single stranded linear, double stranded linear, circular relaxed, and supercoiled forms. Because the data that establish ecd are usually determined concomitantly with current blockade measurements, our results show that a single nanopore assay can simultaneously determine both DNA conformation and base number.

In this work we report on how salt concentration and cation species affect DNA translocation in voltage-biased silicon nitride nanopores. The translocation of double-stranded DNA (dsDNA) in linear, circular, and supercoiled forms was measured in salt solutions containing KCl, NaCl, and MgCl2. As the KCl concentrations were decreased from 1M to 0.1M, the time taken by a DNA molecule to pass through a nanopore was shorter and the frequency of the translocation in a folded configuration was reduced, suggesting an increase in DNA electrophoretic mobility and DNA persistence length. When the salt concentration was kept at 1M, but replacing K+ with Na+, longer DNA translocation times (td) were observed. The addition of low concentrations of MgCl2 with 1.6M KCl resulted in longer td and an increased frequency of supercoiled DNA molecules in a branched form. These observations were consistent with the greater counterion charge screening ability of Na+ and Mg2+ as compared to K+. In addition, we demonstrated that dsDNA molecules indeed translocated through a ~10 nm nanopore by PCR amplification and gel electrophoresis. We also compared the dependence of DNA mobility and conformation on KCl concentration and cation species measured at single molecule level by silicon nitride nanopores with existing bulk-based experimental results and theoretical predictions.

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