Thioflavin T fluorescence and NMR spectroscopy suggesting a non-G-quadruplex structure for a sodium binding aptamer embedded in DNAzymes

Recently, a Na + -binding aptamer was reported to be embedded in few RNA-cleaving DNAzymes, including NaA43, Ce13d, and NaH1. The consists of multiple GG stretches, which is prerequisite for the formation G-quadruplex (G4) structures. These DNAzymes require activity but show no presence K or other metal ions. Given that DNA can selectively bind by forming G4 structure, this work aims answer whether also uses . Through comparative ThT fluorescence spectrometry studies, while control exhibited notable enhancement up 5 mM with d 0.28 ± 0.06 mM, Ce13d DNAzyme negligibly perturbed similar concentrations Opposed this, displayed specific remarkable decrease low millimolar NMR experiments at two different pH values suggest adopts significantly conformation equilibrium conformations versus has more stable structure Additionally, absence characteristic peaks one-dimensional 1 H not responsible binding. This hypothesis confirmed CD spectra sequence. Therefore, we concluded must selective it binds using structural element does contain G4.