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dc.contributor.authorSaran, Runjhun
dc.contributor.authorPiccolo, Kyle A.
dc.contributor.authorHe, Yanping
dc.contributor.authorKang, Yongqiang
dc.contributor.authorHuang, Po-Jung Jimmy
dc.contributor.authorWei, Chunying
dc.contributor.authorChen, Da
dc.contributor.authorDieckmann, Thorsten
dc.contributor.authorLiu, Juewen 17:48:33 (GMT) 17:48:33 (GMT)
dc.description.abstractRecently, a Na+-binding aptamer was reported to be embedded in a few RNA-cleaving DNAzymes including NaA43, Ce13d and NaH1. These DNAzymes require Na+ for activity but show no activity in the presence of K+ or other metal ions. Given that DNA can selectively bind K+ by forming a G-quadruplex structure, this work aims to answer whether this Na+ aptamer also uses a G-quadruplex to bind Na+. The Na+ aptamer embedded in Ce13d consists of multiple GG sequences, which is also a pre-requisite for the formation of G4 structures. To delineate the structural differences and similarities between Ce13d and G-quadruplex in terms of metal binding, thioflavin T (ThT) fluorescence spectroscopy, NMR spectroscopy and CD spectroscopy were used. Through comparative ThT fluorescence spectrometry studies, we deciphered that while a control G-quadruplex DNA exhibited notable fluorescence enhancement up to 5 mM K+ with a Kd of 0.52 mM, the Ce13d DNAzyme fluorescence was negligibly perturbed with similar concentrations of K+. Opposed to this, Ce13d displayed specific remarkable fluorescence decrease with low millimolar concentrations of Na+. NMR experiments at two different pH values suggest that Ce13d adopts a significantly different conformation or equilibrium of conformations in the presence of Na+ versus K+ and has a more stable structure in the presence of Na+. Additionally, absence of characteristic peaks expected for a G-quadruplex structure in 1D 1H NMR suggest that G4 is not responsible for the Na+ binding. This theory is confirmed by absence of characteristic peaks in the CD spectra of this sequence. Therefore, we concluded that the aptamer must be selective for Na+ and binds using a structural element that does not contain G4.en
dc.description.sponsorshipNatural Sciences and Engineering Research Council of Canada, Discovery Grant 303454.en
dc.publisherCanadian Science Publishingen
dc.relation.ispartofseriesCanadian Journal of Chemistry;
dc.subjectNMR spectroscopyen
dc.titleThioflavin T fluorescence and NMR spectroscopy 1 suggesting a non-G-quadruplex structure for a 2 sodium binding aptamer embedded in DNAzymesen
dcterms.bibliographicCitationSaran, R., Piccolo, K. A., He, Y., Kang, Y., Huang, P.-J. J., Wei, C., Chen, D., Dieckmann, T., & Liu, J. (2021). Thioflavin T fluorescence and NMR spectroscopy suggesting a non-G-quadruplex structure for a sodium binding aptamer embedded in DNAzymes. Canadian Journal of Chemistry, 99(11), 860–866.
uws.contributor.affiliation1Faculty of Scienceen

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