Figure 1.
SS-nanopore detection of DNA depurination.
(a) Schematic of the measurement system. A voltage applied across a membrane containing a single nanopore drives dsDNA from the cis- side to the trans- side. Inset: typical conductance blockade event shape with depth (ΔG) and duration (Δt) indicated. (b) Cartoon representation of pH-induced DNA depurination. Acidic conditions preferentially remove purine bases (G and A), which cause progressive loss of structure.
Figure 2.
Conductance blockade depth across the pH range.
Mean conductance change measured for 61-10. No significant variation is observed. Error bars represent the width of a Gaussian fit to the data and the dashed line represents the average value from all data sets.
Figure 3.
Event durations across the pH range.
(a) Event duration histograms for 61 bp DNA translocation events from pH 10 (top) to pH 2 (bottom). Total numbers of events considered are n = 714 (pH 10), 662 (pH 8), 552 (pH 6), 423 (pH 4) and 1852 (pH 2). The black lines represent Gaussian fits to the data (pH 10 & 8: single peak; pH 6 & 4: two peaks; pH 2: three peaks). (b) Example traces of typical events measured at the adjacent pH level. Black traces represent undamaged (low Δt) events. For pH 6, 4 and 2, the blue traces are typical events derived from the long duration (i.e. depurinated) population, indicated by a blue arrow on the histograms. For each event trace shown, the label indicates a coarse approximation of the relative amount of depurination. Note that the final event at pH 2 (marked with *) may be indicative of DNA fragmentation (see text). (c) Fraction of translocation events in the undamaged population and (d) intensity of the DNA band on a gel (see also Supplementary Information), each measured over the entire range of pH investigated. Dashed lines are logarithmic fits to the data.
Figure 4.
Isolating structural factors from solvent effects.
Dwell time histograms for two different SS-nanopore measurements of dsDNA incubated at pH 4. (a) Incubation and measurement in 1 M KCl at pH 4 (same data as pH 4 histogram in Fig. 3) and (b) incubation in 1 M KCl at pH 4 and measurement in 1 M KCl at pH 8 (n = 408).