DNA sequencing by the majority of next-generation methods relies on PCR amplification of the original genomic material with consequent loss of all information regarding base modifications that may have arisen due to epigenetic or DNA damaging events. We are particularly interested in locating sites of guanine oxidation due to oxidative stress; such lesions are thought to be particularly common in the guanine-rich G-quadruplex structures of telomeric sequences as well as in certain promoter regions of the genome. In this work, we examine a single-molecule method that involves electrophoretic translocation of single-stranded DNA through the protein ion channel alpha-hemolysin. Specific electrical signatures are observed for various folded states of the human telomeric G-quadruplex, and the kinetics of unfolding are affected by the presence of oxidized Gs. In addition, G oxidation sites can be chemically functionalized with markers that alter the current signature, providing a direct read of the location of a modified base in the sequence.
Figure 1. G-Quadruplexes are electrophoretically drawn into the alpha-hemolysin ion channel and interact with the vestibule before translocating through the nanopore. Sites of G oxidation are tagged with a crown ether to produce characteristic electrical signatures while single molecules containing DNA damage translocate through the 1.4 nm constriction.