(Q42418767)

30 October 2017

The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK a (English)

1 reference

30 October 2017

0 references

M Duane Smith

1

1 reference

30 October 2017

Reza Mehdizadeh

series ordinal

2

1 reference

30 October 2017

Joan E Olive

series ordinal

3

1 reference

30 October 2017

Richard A Collins

series ordinal

4

1 reference

30 October 2017

language of work or name

English

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publication date

12 August 2008

1 reference

30 October 2017

1 reference

30 October 2017

14

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30 October 2017

9

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30 October 2017

1942-1949

1 reference

An important role of G638 in the cis-cleavage reaction of the Neurospora VS ribozyme revealed by a novel nucleotide analog incorporation method

30 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Essential role of an active-site guanine in glmS ribozyme catalysis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Structure-function relationships in RNA and RNP enzymes: recent advances

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

A guanine nucleobase important for catalysis by the VS ribozyme

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Evidence for proton transfer in the rate-limiting step of a fast-cleaving Varkud satellite ribozyme

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Extraordinary rates of transition metal ion-mediated ribozyme catalysis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Nucleobase catalysis in the hairpin ribozyme

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Chemical models for ribozyme action

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Structural evidence for a two-metal-ion mechanism of group I intron splicing

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Linkage between proton binding and folding in RNA: a thermodynamic framework and its experimental application for investigating pKa shifting

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

28 May 2018

Ribozyme speed limits

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Challenges in enzyme mechanism and energetics

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Ionization of a Critical Adenosine Residue in theNeurosporaVarkud Satellite Ribozyme Active Site†

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

4-thio-U cross-linking identifies the active site of the VS ribozyme

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

The role of metal ions in RNA catalysis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Structural insights into group II intron catalysis and branch-site selection

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Functional involvement of G8 in the hairpin ribozyme cleavage mechanism

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

The hammerhead cleavage reaction in monovalent cations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Three metal ions at the active site of the Tetrahymena group I ribozyme

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

The role of the metal ion in the p21ras catalysed GTP-hydrolysis: Mn2+ versus Mg2+

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Interactions of polynucleotides and thier components. I. Dissociation constants of the bases and their derivatives.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Salt effects on beta-glucosidase: pH-profile narrowing.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Identification of separate structural features that affect rate and cation concentration dependence of self-cleavage by the Neurospora VS ribozyme.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

General acid catalysis by the hepatitis delta virus ribozyme

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Ligand requirements for glmS ribozyme self-cleavage

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Acid-base and metal ion binding properties of guanylyl(3'-->5')guanosine (GpG-) and 2'-deoxyguanylyl(3'-->5')-2'-deoxyguanosine [d(GpG)-] in aqueous solution

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Local conformational changes in the catalytic core of the trans-acting hepatitis delta virus ribozyme accompany catalysis

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Specific Anion Effects on Glass Electrode pH Measurements of Buffer Solutions: Bulk and Surface Phenomena

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2525962

Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis

1 December 2018

1 reference

12 December 2020

1 reference

12 December 2020

Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage

1 reference

12 December 2020

A second divalent metal ion in the group II intron reaction center

1 reference

12 December 2020

HDV ribozyme activity in monovalent cations

1 reference

12 December 2020

Identifiers

DOI

10.1261/RNA.1102308

1 reference

30 October 2017

1 reference

30 October 2017

PubMed publication ID

18697921

1 reference