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Chemistry and Biology of Self-Cleaving Ribozymes
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PubMed
title
Chemistry and Biology of Self-Cleaving Ribozymes
(English)
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stated in
PubMed
main subject
ribozyme
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author name string
Randi M. Jimenez
series ordinal
1
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Crossref
Julio A. Polanco
series ordinal
2
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stated in
Crossref
Andrej Lupták
series ordinal
3
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Crossref
language of work or name
English
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stated in
PubMed
publication date
November 2015
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stated in
PubMed
published in
Trends in Biochemical Sciences
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PubMed
volume
40
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PubMed
issue
11
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PubMed
page(s)
648-61
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PubMed
cites work
Crystal structure and mechanistic investigation of the twister ribozyme
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20 March 2017
Structural Insights Into Substrate Recognition by the Neurospora Varkud Satellite Ribozyme: Importance of U-Turns at the Kissing-Loop Junction
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PubMed Central
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20 March 2017
Active-Site Monovalent Cations Revealed in a 1.55-Å-Resolution Hammerhead Ribozyme Structure
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20 March 2017
The ubiquitous hammerhead ribozyme
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PubMed Central
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20 March 2017
Identification of an hepatitis delta virus-like ribozyme at the mRNA 5'-end of the L1Tc retrotransposon from Trypanosoma cruzi
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20 March 2017
Identification of hammerhead ribozymes in all domains of life reveals novel structural variations
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20 March 2017
Structure-based search reveals hammerhead ribozymes in the human microbiome
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20 March 2017
From alpaca to zebrafish: hammerhead ribozymes wherever you look
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20 March 2017
Ubiquitous presence of the hammerhead ribozyme motif along the tree of life
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PubMed Central
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20 March 2017
A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage
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PubMed Central
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20 March 2017
Intronic hammerhead ribozymes are ultraconserved in the human genome
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PubMed Central
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20 March 2017
R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript
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PubMed Central
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20 March 2017
Widespread occurrence of self-cleaving ribozymes
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PubMed Central
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20 March 2017
Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme
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PubMed Central
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20 March 2017
Capturing Hammerhead Ribozyme Structures in Action by Modulating General Base Catalysis
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PubMed Central
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20 March 2017
A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA
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PubMed Central
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20 March 2017
Solvent Structure and Hammerhead Ribozyme Catalysis
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PubMed Central
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20 March 2017
Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor
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PubMed Central
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20 March 2017
Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity
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PubMed Central
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20 March 2017
NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site
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PubMed Central
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20 March 2017
Transition state stabilization by a catalytic RNA
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PubMed Central
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20 March 2017
In vitro evolution suggests multiple origins for the hammerhead ribozyme
1 reference
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PubMed Central
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20 March 2017
A pH controlled conformational switch in the cleavage site of the VS ribozyme substrate RNA
1 reference
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PubMed Central
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20 March 2017
Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
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PubMed Central
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20 March 2017
Structure of the ribozyme substrate hairpin of Neurospora VS RNA: a close look at the cleavage site
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20 March 2017
Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets
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20 March 2017
Structural diversity of self-cleaving ribozymes
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PubMed Central
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20 March 2017
Crystal structure of a hepatitis delta virus ribozyme
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PubMed Central
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20 March 2017
Schistosome satellite DNA encodes active hammerhead ribozymes
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PubMed Central
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20 March 2017
Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme
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PubMed Central
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20 March 2017
A long-range pseudoknot is required for activity of the Neurospora VS ribozyme
1 reference
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PubMed Central
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20 March 2017
Three-dimensional structure of a hammerhead ribozyme
1 reference
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PubMed Central
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20 March 2017
Human hepatitis delta virus RNA subfragments contain an autocleavage activity
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PubMed Central
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20 March 2017
Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity
1 reference
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PubMed Central
reference URL
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20 March 2017
New classes of self-cleaving ribozymes revealed by comparative genomics analysis
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PubMed Central
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20 March 2017
The glmS ribozyme cofactor is a general acid-base catalyst
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PubMed Central
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20 March 2017
Intronic hammerhead ribozymes in mRNA biogenesis
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20 March 2017
Autolytic processing of dimeric plant virus satellite RNA
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20 March 2017
A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene
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PubMed Central
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20 March 2017
Structural basis of glmS ribozyme activation by glucosamine-6-phosphate
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PubMed Central
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20 March 2017
Tertiary contacts distant from the active site prime a ribozyme for catalysis
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PubMed Central
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20 March 2017
Control of gene expression by a natural metabolite-responsive ribozyme
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20 March 2017
Functional involvement of G8 in the hairpin ribozyme cleavage mechanism
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20 March 2017
Self-cleavage of virusoid RNA is performed by the proposed 55-nucleotide active site
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20 March 2017
Nucleotide sequence predicts circularity and self-cleavage of 300-ribonucleotide satellite of arabis mosaic virus
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20 March 2017
Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites
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20 March 2017
Nucleotide sequence and structural analysis of two satellite RNAs associated with chicory yellow mottle virus
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20 March 2017
Small self-cleaving ribozymes
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20 March 2017
Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density
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29 September 2017
In-line alignment and Mg²⁺ coordination at the cleavage site of the env22 twister ribozyme
1 reference
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PubMed Central
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29 September 2017
Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme
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PubMed Central
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29 September 2017
A widespread self-cleaving ribozyme class is revealed by bioinformatics.
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PubMed Central
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29 September 2017
Two distinct catalytic strategies in the hepatitis δ virus ribozyme cleavage reaction
1 reference
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PubMed Central
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29 September 2017
Processing and translation initiation of non-long terminal repeat retrotransposons by hepatitis delta virus (HDV)-like self-cleaving ribozymes
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29 September 2017
The glmS ribozyme tunes the catalytically critical pK(a) of its coenzyme glucosamine-6-phosphate
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
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29 September 2017
Aptamers for allosteric regulation
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29 September 2017
Computational discovery of folded RNA domains in genomes and in vitro selected libraries
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29 September 2017
Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme
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PubMed Central
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29 September 2017
A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes
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29 September 2017
CPEB3 is associated with human episodic memory.
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PubMed Central
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29 September 2017
The complete VS ribozyme in solution studied by small-angle X-ray scattering
1 reference
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PubMed Central
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29 September 2017
Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography
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PubMed Central
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29 September 2017
Functional aptamers and aptazymes in biotechnology, diagnostics, and therapy
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29 September 2017
Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme
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29 September 2017
In vivo commitment to yeast cotranscriptional splicing is sensitive to transcription elongation mutants
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29 September 2017
Role of an active site adenine in hairpin ribozyme catalysis
1 reference
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PubMed Central
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29 September 2017
A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate
1 reference
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PubMed Central
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29 September 2017
The Neurospora Varkud satellite ribozyme
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PubMed Central
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29 September 2017
4-thio-U cross-linking identifies the active site of the VS ribozyme
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PubMed Central
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29 September 2017
Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
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29 September 2017
Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
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29 September 2017
Hepatitis delta virus
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PubMed Central
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29 September 2017
Rational design of allosteric ribozymes
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PubMed Central
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29 September 2017
Secondary structure content of the HDV ribozyme in 95% formamide
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PubMed Central
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29 September 2017
How many catalytic RNAs? Ions and the Cheshire cat conjecture.
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29 September 2017
A secondary-structure model for the self-cleaving region of Neurospora VS RNA.
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29 September 2017
Ribozymes: a distinct class of metalloenzymes
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29 September 2017
The molecular biology of hepatitis delta virus
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PubMed Central
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retrieved
29 September 2017
Antigenomic Hepatitis delta virus ribozymes self-cleave in 18 M formamide
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
29 September 2017
A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
2 June 2018
Competition between Co(NH(3)(6)3+ and inner sphere Mg2+ ions in the HDV ribozyme
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
2 June 2018
A guanine nucleobase important for catalysis by the VS ribozyme
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
2 June 2018
Nucleobase catalysis in the hairpin ribozyme
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
2 June 2018
The reverse transcriptase of the R2 non-LTR retrotransposon: continuous synthesis of cDNA on non-continuous RNA templates
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
2 June 2018
Eukaryotic penelope-like retroelements encode hammerhead ribozyme motifs.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
27 November 2018
Model-driven engineering of RNA devices to quantitatively program gene expression
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
27 November 2018
Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
27 November 2018
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
27 November 2018
General acid catalysis by the hepatitis delta virus ribozyme
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
27 November 2018
Ligand requirements for glmS ribozyme self-cleavage
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
27 November 2018
Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
27 November 2018
Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
27 November 2018
A conformational switch controls hepatitis delta virus ribozyme catalysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
27 November 2018
Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
27 November 2018
Sjalpha elements, short interspersed element-like retroposons bearing a hammerhead ribozyme motif from the genome of the oriental blood fluke Schistosoma japonicum.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4630146
retrieved
27 November 2018
Observation of internal cleavage and ligation reactions of a ribozyme
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/26481500
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/26481500
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
End-to-end template jumping by the reverse transcriptase encoded by the R2 retrotransposon
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/26481500
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Crystallization and X-ray diffraction analysis of an all-RNA U39C mutant of the minimal hairpin ribozyme
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/26481500
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Transcripts of newt satellite DNA self-cleave in vitro
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/26481500
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Self-cleaving viroid and newt RNAs may only be active as dimers
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/26481500
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
HDV ribozyme activity in monovalent cations
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/26481500
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1016/J.TIBS.2015.09.001
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
525618
Fatcat ID
release_msu3z3ah5vfgxi67ma3deydcny
1 reference
stated in
Fatcat
reference URL
https://api.fatcat.wiki/v0/release/msu3z3ah5vfgxi67ma3deydcny
retrieved
24 November 2022
based on heuristic
mapped directly with Wikidata item
OpenCitations bibliographic resource ID
525618
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
525618
PMCID
4630146
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
525618
PubMed ID
26481500
1 reference
stated in
Consolidated OpenCitations Corpus – April 2017
OpenCitations bibliographic resource ID
525618
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