Yoanes M. Vianney, Jagannath Jana, Klaus Weisz

• A guanine‐rich oligonucleotide based on a human telomeric sequence but with the first three‐nucleotide intervening stretch replaced by a putative 15‐nucleotide hairpin‐forming sequence shows a pH‐dependent folding into different quadruplex‐duplex hybrids in a potassium containing buffer. At slightly acidic pH, the quadruplex domain adopts a chair‐type conformation. Upon increasing the pH, a transition with a midpoint close to neutral pH to a major and minor (3+1) hybrid topology with either a coaxially stacked or orthogonally oriented duplex stem‐loop occurs. NMR‐derived high‐resolution structures reveal that an adenine protonation is prerequisite for the formation of a non‐canonical base quartet, capping the outer G‐tetrad at the quadruplex‐duplex interface and stabilizing the antiparallel chair conformation in an acidic environment. Being directly associated with interactions at the quadruplex‐duplex interface, this unique pH‐dependent topological transition is fully reversible. Coupled with a conformation‐sensitive optical readout demonstrated as a proof of concept using the fluorescent dye thiazole orange, the present quadruplex‐duplex hybrid architecture represents a potentially valuable pH‐sensing system responsive in a physiological pH range of 7±1.