Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme (Q35794693)

10 August 2017

Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme (English)

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10 August 2017

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Manami Roychowdhury-Saha

series ordinal

1

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10 August 2017

Donald H Burke

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2

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10 August 2017

language of work or name

English

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publication date

24 April 2007

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10 August 2017

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10 August 2017

13

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10 August 2017

6

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10 August 2017

841-848

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describes a project that uses

10 August 2017

ImageQuant

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11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC1869042/fullTextXML

inferred from PubMed Central ID database lookup

cites work

Topological rearrangement yields structural stabilization and interhelical distance constraints in the Kin.46 self-phosphorylating ribozyme

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Extraordinary rates of transition metal ion-mediated ribozyme catalysis

12 July 2018

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Tertiary contacts distant from the active site prime a ribozyme for catalysis

12 July 2018

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Cation-specific structural accommodation within a catalytic RNA.

12 July 2018

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Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn

12 July 2018

1 reference

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Separate metal requirements for loop interactions and catalysis in the extended hammerhead ribozyme

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Characterization of a native hammerhead ribozyme derived from schistosomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures

12 July 2018

1 reference

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Exogenous control of mammalian gene expression through modulation of RNA self-cleavage

12 July 2018

1 reference

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Entropy-driven folding of an RNA helical junction: an isothermal titration calorimetric analysis of the hammerhead ribozyme.

12 July 2018

1 reference

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Exceptionally fast self-cleavage by a Neurospora Varkud satellite ribozyme

12 July 2018

1 reference

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Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Folding and activity of the hammerhead ribozyme

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Existence of efficient divalent metal ion-catalyzed and inefficient divalent metal ion-independent channels in reactions catalyzed by a hammerhead ribozyme

12 July 2018

1 reference

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The hammerhead cleavage reaction in monovalent cations

12 July 2018

1 reference

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

12 July 2018

1 reference

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

12 July 2018

1 reference

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Determination of metal ion binding sites within the hairpin ribozyme domains by NMR.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Solution structure of Cobalt(III)hexammine complexed to the GAAA tetraloop, and metal-ion binding to G.A mismatches

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudoknot

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Unusual metal ion catalysis in an acyl-transferase ribozyme.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Crystallographic structures of the hammerhead ribozyme: relationship to ribozyme folding and catalysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Self-cleavage activity of the genomic HDV ribozyme in the presence of various divalent metal ions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Three-dimensional structure of a hammerhead ribozyme

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Role of divalent metal ions in the hammerhead RNA cleavage reaction

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Three conserved guanosines approach the reaction site in native and minimal hammerhead ribozymes.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Hammerheads derived from sTRSV show enhanced cleavage and ligation rate constants.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Photocrosslinking detects a compact, active structure of the hammerhead ribozyme

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Diffusely bound Mg2+ ions slightly reorient stems I and II of the hammerhead ribozyme to increase the probability of formation of the catalytic core.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Solvent Protection of the Hammerhead Ribozyme in the Ground State: Evidence for a Cation-Assisted Conformational Change Leading to Catalysis

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Enhancement in the cleavage activity of a hammerhead ribozyme by cationic comb-type polymers and an RNA helicase in vitro

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Fast Cleavage Kinetics of a Natural Hammerhead Ribozyme

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1869042

Cobalt hexammine inhibition of the hammerhead ribozyme

15 November 2018

1 reference

12 December 2020

Activities and relative affinities of divalent metals in unmodified and phosphorothioate-substituted hammerhead ribozymes

1 reference

12 December 2020

Metal-phosphate interactions in the hammerhead ribozyme observed by 31P NMR and phosphorothioate substitutions

1 reference

12 December 2020

Effects of cobalt hexammine on folding and self-cleavage of the Neurospora VS ribozyme

1 reference

12 December 2020

Analysis on a cooperative pathway involving multiple cations in hammerhead reactions

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

Thermodynamics of stabilization of RNA pseudoknots by cobalt(III) hexaammine

1 reference

12 December 2020

Identifiers

DOI

10.1261/RNA.339207

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10 August 2017

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10 August 2017

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