ArticleBiochemistry2009
The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme.
Article in Biochemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 25 citations in OpenAlex.
- A hammerhead ribozyme selects mechanically stable conformations for catalysis against viral RNA.Communications biology · 2025Article
- Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations.Biochemistry · 2017Article
- Dynamic nuclear polarization of nucleic acid with endogenously bound manganese.Journal of biomolecular NMR · 2015Article
- Nucleic acid catalysis: metals, nucleobases, and other cofactors.Chemical reviews · 2014Review
- NMR localization of divalent cations at the active site of the Neurospora VS ribozyme provides insights into RNA-metal-ion interactions.Biochemistry · 2014Article
- Site-specific platinum(II) cross-linking in a ribozyme active site.Journal of the American Chemical Society · 2012Article
- Ground-state coordination of a catalytic metal to the scissile phosphate of a tertiary-stabilized Hammerhead ribozyme.RNA (New York, N.Y.) · 2012Article
- Two distinct catalytic strategies in the hepatitis δ virus ribozyme cleavage reaction.Biochemistry · 2011Review
- Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme.Journal of chemical theory and computation · 2011Article
- Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from?Molecules (Basel, Switzerland) · 2010Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Potential metal interactions with the cleavage site of a minimal hammerhead ribozyme (mHHRz) were probed using (31)P NMR-detected Cd(2+) titration studies of HHRz constructs containing a phosphorothioate (PS) modification at the cleavage site. The mHHRz nucleophile position was replaced by either a 2'-F or a 2'-NH(2) in order to block cleavage activity during the study. The 2'-F/PS cleavage site mHHRz construct, in which the 2'-F should closely imitate the atom size and electronegativity of a 2'-OH, demonstrates low levels of metal ion association (<1 ppm (31)P chemical shift changes). This observation indicates that having an atom size and electrostatic properties that are similar to the 2'-OH are not the governing factors in allowing metal interactions with the scissile phosphate of the mHHRz. With a 2'-NH(2) substitution, a large upfield change in (31)P NMR chemical shift of the phosphorothioate peak (Delta approximately 3 ppm with 6 equiv of added Cd(2+)) indicates observable Cd(2+) interactions with the substituted site. Since a 2'-NH(2), but not a 2'-F, can serve as a metal ligand, these data suggest that a metal ion interaction with the HHRz cleavage site may include both the scissile phosphate and the 2' nucleophile. Control samples in which the 2'-NH(2)/PS unit is placed either next to the mHHRz cleavage site (at U16.1), in a duplex, or in a (am)U(PS)U dinucleotide show much weaker interactions with Cd(2+). Results with these control samples indicate that simply the presence of a 2'-NH(2)/PS unit does not create a strong metal binding site, reinforcing the possibility that the 2'-NH(2)-moderated Cd-PS interaction is specific to the mHHRz cleavage site. Upfield chemical shifts of both (31)P and H-2' (1)H resonances in (am)U(PS)U are observed with addition of Cd(2+), consistent with the predicted metal coordination to both 2'-NH(2) and phosphorothioate ligands. These data suggest that metal ion association with the HHRz cleavage site may include an interaction with the 2'-OH nucleophile.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.