Aside from a double helix, DNA folds into non-canonical structures, one of which is the guanine quadruplex. Cationic porphyrins bind guanine quadruplexes, but the effects of ligand binding on the structure of guanine quadruplexes with more than four contiguous guanine quartets remains to be fully elucidated. Double electron electron resonance (DEER) spectroscopy conducted at 9.5 GHz (X-band) using shaped broadband excitation pulses was used to measure the distances between cationic copper porphyrins bound to parallel-stranded guanine quadruplexes with increasing numbers of guanine quartets. A monotonic increase in the average Cu2+-Cu2+ distance was found as the poly-guanine tract increased within the oligonucleotide sequence, indicative of tetramolecular quadruplexes. A single Gaussian component was found to best model the time domain datasets, characteristic of a 2:1 binding stoichiometry between the porphyrins and each quadruplex, which is consistent with our previous work. Rather unexpectedly, the measured increase in Cu2+-Cu2+ distances was not linear with oligonucleotide the number of guanine tracts, suggesting a conformational change in the quadruplex secondary structure on changing from four to eight successive guanine quartets.
Physical Chemistry Chemical Physics
Guanine quadruplexes, Double electron electron resonance, arbitrary waveform generator