Download MendeleyA pH-Responsive Topological Switch Based on a DNA Quadruplex-Duplex Hybrid.
Vianney, Y.M., Jana, J., Weisz, K.(2024) Chemistry 30: e202400722-e202400722
- PubMed: 38497675
- DOI: https://doi.org/10.1002/chem.202400722
- Primary Citation of Related Structures:
8RW2, 8S1W - PubMed Abstract:
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.
Organizational Affiliation:
Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489, Greifswald, Germany.
