DNA conformation and base number simultaneously determined in a nanopore.

When dsDNA polymers containing 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, Fologea, D., Gershow, M., Ledden, B., McNabb, D. S. et al.., Nano Lett. 2005, 5, 1905-1909) 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 among 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.