Methods, systems, and compounds for detecting modified nucleic acid bases are disclosed and described. The methods provide for detecting a nucleic acid lesion and can include directing a nucleic acid adduct into a channel, wherein the nucleic acid adduct includes a nucleic acid having a lesion and a current modulating compound coupled to the nucleic acid at the lesion (110), and measuring a change in current through the channel in response to the current modulating compound to detect the lesion (112). The method can optionally include forming the nucleic acid adduct. Also provided is a method for identifying the number of repeat nucleotides in at least a portion of a nucleic acid strand, a method of assigning a registration marker within a nucleic acid, and a method of obtaining sequence information from a nucleic acid comprising assigning a registration marker on the nucleic acid.