A DNAzyme requiring two different metal ions at two distinct sites
dc.contributor.author | Zhou, Wenhu | |
dc.contributor.author | Zhang, Yupei | |
dc.contributor.author | Huang, Po-Jung Jimmy | |
dc.contributor.author | Ding, Jinsong | |
dc.contributor.author | Liu, Juewen | |
dc.date.accessioned | 2017-04-28T16:12:01Z | |
dc.date.available | 2017-04-28T16:12:01Z | |
dc.date.issued | 2015-12-10 | |
dc.description.abstract | Most previously reported RNA-cleaving DNAzymes require only a single divalent metal ion for catalysis. We recently reported a general trivalent lanthanide-dependent DNAzyme named Ce13d. This work shows that Ce13d requires both Na+ and a trivalent lanthanide (e.g. Ce3+), simultaneously. This discovery is facilitated by the sequence similarity between Ce13d and a recently reported Na+-specific DNAzyme, NaA43. The Ce13d cleavage rate linearly depends on the concentration of both metal ions. Sensitized Tb3+ luminescence and DMS footprinting experiments indicate that the guanines in the enzyme loop are important for Na+-binding. The Na+ dissociation constants of Ce13d measured from the cleavage activity assay, Tb3+ luminescence and DMS footprinting are 24.6, 16.3 and 47 mM, respectively. Mutation studies indicate that the role of Ce3+ might be replaced by G(23) in NaA43. Ce3+ functions by stabilizing the transition state phosphorane, thus promoting cleavage. G(23) competes favorably with low concentration Ce3+ (below 1 mu M). The G(23)-to-hypoxanthine mutation suggests the N1 position of the guanine as a hydrogen bond donor. Together, Ce13d has two distinct metal binding sites, each fulfilling a different role. DNAzymes can be quite sophisticated in utilizing metal ions for catalysis and molecular recognition, similar to protein metalloenzymes. | en |
dc.description.sponsorship | Natural Sciences and Engineering Research Council of Canada (NSERC); Foundation for Shenghua Scholar of Central South University; National Natural Science Foundation of China [ 21301195]; Fellowship from the China Scholarship Council (CSC) [ 201406370116 to W.Z.]. Funding for open access charge: NSERC. | en |
dc.identifier.uri | http://dx.doi.org/10.1093/nar/gkv1346 | |
dc.identifier.uri | http://hdl.handle.net/10012/11800 | |
dc.language.iso | en | en |
dc.publisher | Oxford University Press | en |
dc.rights | Attribution-NonCommercial 4.0 International | * |
dc.rights.uri | https://creativecommons.org/licenses/by-nc/4.0/ | * |
dc.subject | Lanthanide-Dependent Dnazyme | en |
dc.subject | In-Vitro Selection | en |
dc.subject | Cleaving DNA Enzyme | en |
dc.subject | Hammerhead Ribozyme | en |
dc.subject | Cleavage Reaction | en |
dc.subject | RNA | en |
dc.subject | Acid | en |
dc.subject | Evolution | en |
dc.subject | Catalysis | en |
dc.subject | Aptamers | en |
dc.title | A DNAzyme requiring two different metal ions at two distinct sites | en |
dc.type | Article | en |
dcterms.bibliographicCitation | Zhou, W., Zhang, Y., Huang, P.-J. J., Ding, J., & Liu, J. (2016). A DNAzyme requiring two different metal ions at two distinct sites. Nucleic Acids Research, 44(1), 354–363. https://doi.org/10.1093/nar/gkv1346 | en |
uws.contributor.affiliation1 | Faculty of Science | en |
uws.contributor.affiliation2 | Chemistry | en |
uws.contributor.affiliation3 | Waterloo Institute for Nanotechnology (WIN) | en |
uws.peerReviewStatus | Reviewed | en |
uws.scholarLevel | Faculty | en |
uws.typeOfResource | Text | en |