(Q34978942)

5 August 2017

title

The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine (English)

1 reference

5 August 2017

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Joseph W Cottrell

1

1 reference

5 August 2017

Lincoln G Scott

series ordinal

2

1 reference

5 August 2017

Martha J Fedor

series ordinal

3

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5 August 2017

language of work or name

English

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publication date

28 March 2011

1 reference

Journal of Biological Chemistry

5 August 2017

published in

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5 August 2017

volume

286

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5 August 2017

issue

20

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5 August 2017

page(s)

17658-17664

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Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme

5 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Catalytic importance of a protonated adenosine in the hairpin ribozyme active site

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Competition between Co(NH(3)(6)3+ and inner sphere Mg2+ ions in the HDV ribozyme

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Comparative enzymology and structural biology of RNA self-cleavage

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Raman crystallography of RNA.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Identification of an Imino Group Indispensable for Cleavage by a Small Ribozyme

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

A catalytic metal ion interacts with the cleavage Site G.U wobble in the HDV ribozyme

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Nucleobase catalysis in ribozyme mechanism

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Linkage between proton binding and folding in RNA: implications for RNA catalysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Role of an active site adenine in hairpin ribozyme catalysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Transition state stabilization by a catalytic RNA

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Catalytic strategies of the hepatitis delta virus ribozymes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Rescue of an abasic hairpin ribozyme by cationic nucleobases: evidence for a novel mechanism of RNA catalysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

2-Aminopurine fluorescence quenching and lifetimes: role of base stacking

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Tertiary structure stabilization promotes hairpin ribozyme ligation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Nucleotide analog interference mapping of the hairpin ribozyme: implications for secondary and tertiary structure formation.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Metal ions play a passive role in the hairpin ribozyme catalysed reaction

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Fluorescence studies of DNA and RNA structure and dynamics

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside, and their derivatives.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Synthesis of small RNAs using T7 RNA polymerase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Equimolar addition of oligoribonucleotides with T4 RNA ligase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3093841

Catalytic roles for proton transfer and protonation in ribozymes

8 July 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M111.234906

Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M111.234906

Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M111.234906

Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M111.234906

Fluorescence emission properties of 8-azapurines and their nucleosides, and application to the kinetics of the reverse synthetic reaction of purine nucleoside phosphorylase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M111.234906

8-Azaguanine reporter of purine ionization states in structured RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M111.234906

Solution conformation of an RNA hairpin loop

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M111.234906

Adenine protonation in domain B of the hairpin ribozyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M111.234906

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M111.234906

First principles calculations of the pKa values and tautomers of isoguanine and xanthine

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M111.234906

Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction

21 January 2018

1 reference

https://api.crossref.org/works/10.1074%2FJBC.M111.234906

Hairpin ribozymes with four-way helical junctions mediate intracellular RNA ligation

21 January 2018

1 reference

12 December 2020

A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage

1 reference

12 December 2020

The internal equilibrium of the hairpin ribozyme: temperature, ion and pH effects

1 reference

12 December 2020

An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis

1 reference

12 December 2020

Analysis of hairpin ribozyme base mutations in loops 2 and 4 and their effects on cis-cleavage in vitro

1 reference

12 December 2020

Structural basis for the guanosine requirement of the hairpin ribozyme

1 reference

12 December 2020

A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion

1 reference

12 December 2020

Identifiers

DOI

10.1074/JBC.M111.234906

1 reference

5 August 2017

1 reference

5 August 2017

1 reference