Extended Data Fig. 6: Intensity-based smFRET studies of dsDNA containing an AP site in the presence and absence of Endo IV.

The influence of having a PTO modification framed by the 5′-neighboring nucleotide and the AP site is evaluated. a) Example smFRET time traces of the system containing dsDNA with AP site without PTO modification, in the absence (top) and presence (bottom) of Endo IV. On the right, the histograms obtained from the shown traces are depicted. b) FRET efficiency histograms obtained from 75 (dsDNA containing AP, without PTO, in the absence of Endo IV) and 55 traces (dsDNA containing AP, without PTO, in the presence of Endo IV). Here, the FRET efficiencies obtained from every movie frame from all traces are computed together as independent FRET efficiency values. c) and d) Same description as in a) and b), but for systems containing both AP site and PTO modification. 30 traces were analyzed for the population histogram without Endo IV and 66 traces for the case, where Endo IV was added to the solution. Due to the intensity-based measurement protocol, the histograms from b) and d) are weighted by the respective dwell times of each state. This contrasts measurements on graphene, where the fluorescence lifetime of each state is independent of any weighing. As mentioned before, the presented smFRET data are based on the fluorescence intensity and not the fluorescence lifetime as used for GETvNA.