Visualizing the solvent-inaccessible core of a group II intron ribozyme (Q39645080)

13 September 2017

Visualizing the solvent-inaccessible core of a group II intron ribozyme (English)

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13 September 2017

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J Swisher

1

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13 September 2017

C M Duarte

series ordinal

2

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13 September 2017

L J Su

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3

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13 September 2017

A M Pyle

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4

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13 September 2017

language of work or name

English

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publication date

1 April 2001

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13 September 2017

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13 September 2017

20

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8

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13 September 2017

2051-2061

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describes a project that uses

13 September 2017

ImageQuant

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11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC125427/fullTextXML

inferred from PubMed Central ID database lookup

cites work

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

1 reference

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A tertiary interaction that links active-site domains to the 5' splice site of a group II intron

14 September 2017

1 reference

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Stability and cooperativity of individual tertiary contacts in RNA revealed through chemical denaturation.

14 September 2017

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The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution

14 September 2017

1 reference

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Metal ion catalysis during group II intron self-splicing: parallels with the spliceosome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

A map of the binding site for catalytic domain 5 in the core of a group II intron ribozyme

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Domain 5 binds near a highly conserved dinucleotide in the joiner linking domains 2 and 3 of a group II intron

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Sequence Specificity of a Group II Intron Ribozyme: Multiple Mechanisms for Promoting Unusually High Discrimination against Mismatched Targets

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2′-hydroxyl groups

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Stopped-flow fluorescence spectroscopy of a group II intron ribozyme reveals that domain 1 is an independent folding unit with a requirement for specific Mg2 ions in the tertiary structure

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

A simple method for 3'-labeling of RNA.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Crystal structure of a group I ribozyme domain: principles of RNA packing

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Catalytic role of 2'-hydroxyl groups within a group II intron active site

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Characterization of a "kissing" hairpin complex derived from the human immunodeficiency virus genome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Three-dimensional structure of a hammerhead ribozyme

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: elucidation of reaction mechanism and structure/function relationships

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Higher order folding and domain analysis of the ribozyme from Bacillus subtilis ribonuclease P.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Frequent use of the same tertiary motif by self-folding RNAs

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Structure and activities of group II introns

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Catalytically critical nucleotide in domain 5 of a group II intron

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

The phylogenetically predicted base-pairing interaction between alpha and alpha' is required for group II splicing in vitro

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proofreading mechanism for 5'-splice site selection.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Group II intron domain 5 facilitates a trans-splicing reaction

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Conserved sequences and structures of group I introns: building an active site for RNA catalysis--a review

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Comparative and functional anatomy of group II catalytic introns—a review

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Defining the inside and outside of a catalytic RNA molecule

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

A detailed model of the three-dimensional structure of Escherichia coli 16 S ribosomal RNA in situ in the 30 S subunit

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Apparent hydroxyl radical production by peroxynitrite: implications for endothelial injury from nitric oxide and superoxide

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Visualizing the higher order folding of a catalytic RNA molecule

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Group II introns deleted for multiple substructures retain self-splicing activity

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

A three-dimensional perspective on exon binding by a group II self-splicing intron

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Stereochemical selectivity of group II intron splicing, reverse splicing, and hydrolysis reactions

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

An RNA conformational change between the two chemical steps of group II self-splicing.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Restoration of the self-splicing activity of a defective group II intron by a small trans-acting RNA.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

A novel U2-U6 snRNA structure is necessary for mammalian mRNA splicing

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Ribozyme catalysis from the major groove of group II intron domain 5.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. fitting the RNA to a 3D electron microscopic map at 20 Å 1 1Edited by D. E. Drapper

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Rules for RNA recognition of GNRA tetraloops deduced by invitro selection: comparison with invivo evolution

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Identification of structural elements critical for inter-domain interactions in a group II self-splicing intron

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Multiple tertiary interactions involving domain II of group II self-splicing introns.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Efficient trans-splicing of a yeast mitochondrial RNA group II intron implicates a strong 5' exon-intron interaction.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Base-pairing interactions involving the 5' and 3'-terminal nucleotides of group II self-splicing introns

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

Time-resolved synchrotron X-ray "footprinting", a new approach to the study of nucleic acid structure and function: application to protein-DNA interactions and RNA folding.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

A UV-induced, Mg(2 )-dependent crosslink traps an active form of domain 3 of a self-splicing group II intron.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=125427

A group II self-splicing intron from the brown alga Pylaiella littoralis is active at unusually low magnesium concentrations and forms populations of molecules with a uniform conformation

21 August 2018

1 reference

12 December 2020

Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding

1 reference

12 December 2020

A thermodynamic framework and cooperativity in the tertiary folding of a Mg2 -dependent ribozyme

1 reference

12 December 2020

Characterization of the Tetrahymena ribozyme folding pathway using the kinetic footprinting reagent peroxynitrous acid

1 reference

12 December 2020

Erratum: Retrotransposition of a bacterial group II intron

1 reference

12 December 2020

Metal ion binding sites in a group II intron core

1 reference

12 December 2020

Multiple exon-binding sites in class II self-splicing introns

1 reference

12 December 2020

Hydroxyl radical footprinting

1 reference

12 December 2020

How the structure of an adenine tract depends on sequence context: a new model for the structure of TnAn DNA sequences

1 reference

12 December 2020

The architectural organization and mechanistic function of group II intron structural elements

1 reference

12 December 2020

Building a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate

1 reference

12 December 2020

Catalytic site components common to both splicing steps of a group II intron

1 reference

12 December 2020

Probing the higher order structure of RNA with peroxonitrous acid

1 reference

12 December 2020

The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core

1 reference

12 December 2020

Identifiers

DOI

10.1093/EMBOJ/20.8.2051

1 reference

13 September 2017

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13 September 2017

PubMed publication ID

11296237

1 reference