(Q41840082)

English

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

scientific article published on December 1998

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

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

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Marc Boudvillain

1

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

author name string

Pyle AM

2

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

language of work or name

0 references

publication date

1 December 1998

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

The EMBO Journal

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

17

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

23

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

7091-7104

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

Influence of substrate structure on in vitro ribozyme activity of a group II intron

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Sequence specificity of a group II intron ribozyme: multiple mechanisms for promoting unusually high discrimination against mismatched targets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: comparison with in vivo evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Mismatch base pairs in RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

A general purpose RNA-cleaving DNA enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Mutagenesis of a stacking contact in the MS2 coat protein-RNA complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

A network of heterogeneous hydrogen bonds in GNRA tetraloops

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Rp-deoxy-phosphorothioate modification interference experiments identify 2'-OH groups in RNase P RNA that are crucial to tRNA binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Metal-binding sites in the major groove of a large ribozyme domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

A simple method for 3'-labeling of RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Mutations of the two-nucleotide bulge of D5 of a group II intron block splicing in vitro and in vivo: phenotypes and suppressor mutations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Length changes in the joining segment between domains 5 and 6 of a group II intron inhibit self-splicing and alter 3' splice site selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

RNA tertiary structure mediation by adenosine platforms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Domain 5 interacts with domain 6 and influences the second transesterification reaction of group II intron self-splicing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Interaction of intronic boundaries is required for the second splicing step efficiency of a group II intron.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

A major family of motifs involving G.A mismatches in ribosomal RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

A simplified procedure for synthesizing nucleoside 1-thiotriphosphates: dATP alpha S, dGTP alpha S, UTP alpha S, and dTTP alpha S.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Structure and activities of group II introns

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

A mutant T7 RNA polymerase as a DNA polymerase.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Enzymatic synthesis of 2'-modified nucleic acids: identification of important phosphate and ribose moieties in RNase P substrates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Catalytically critical nucleotide in domain 5 of a group II intron

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

The stereochemical course of group II intron self-splicing.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Stability constants of magnesium and cadmium complexes of adenine nucleotides and thionucleotides and rate constants for formation and dissociation of magnesium-ATP and magnesium-ADP

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Phosphorothioates in molecular biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

DNA and RNA sequence determination based on phosphorothioate chemistry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Improved free-energy parameters for predictions of RNA duplex stability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Integration of group II intron bI1 into a foreign RNA by reversal of the self-splicing reaction in vitro

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Efficient site-directed mutagenesis using uracil-containing DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Synthesis of RNA containing inosine: analysis of the sequence requirements for the 5′ splice site of theTetrahymenagroup I intron

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Reverse self-splicing of group II intron RNAs in vitro

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Analysis of the role of phosphate oxygens in the group I intron from Tetrahymena

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

6 June 2018

Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

18 August 2018

Functional group substitutions of the branchpoint adenosine in a nuclear pre-mRNA and a group II intron.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

18 August 2018

Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

18 August 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

18 August 2018

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

1 reference

https://api.crossref.org/works/10.1093%2FEMBOJ%2F17.23.7091

21 January 2018

A self-splicing RNA excises an intron lariat

1 reference

https://api.crossref.org/works/10.1093%2FEMBOJ%2F17.23.7091

21 January 2018

The two steps of group II intron self-splicing are mechanistically distinguishable.

1 reference

https://api.crossref.org/works/10.1093%2FEMBOJ%2F17.23.7091

21 January 2018

Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site

1 reference

https://api.crossref.org/works/10.1093%2FEMBOJ%2F17.23.7091

21 January 2018

RNA tectonics: towards RNA design

1 reference

https://api.crossref.org/works/10.1093%2FEMBOJ%2F17.23.7091

21 January 2018

Group II intron splicing in vivo by first-step hydrolysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1171056

3 November 2018

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

1 reference

https://api.crossref.org/works/10.1093%2FEMBOJ%2F17.23.7091

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1093%2FEMBOJ%2F17.23.7091

21 January 2018

An engineered ribonuclease preferring phosphorothioate RNA

1 reference

https://api.crossref.org/works/10.1093%2FEMBOJ%2F17.23.7091

21 January 2018

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9843513

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Effect of environment, conformation, sequence and base substituents on the imino proton exchange rates in guanine and inosine-containing DNA, RNA and DNA-RNA duplexes

1 reference

https://pubmed.ncbi.nlm.nih.gov/9843513

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Self-splicing of group II introns in vitro: mapping of the branch point and mutational inhibition of lariat formation

1 reference

https://pubmed.ncbi.nlm.nih.gov/9843513

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and steric exclusion of non-adenine functionalities

1 reference

https://pubmed.ncbi.nlm.nih.gov/9843513

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The detailed structure of tandem G.A mismatched base-pair motifs in RNA duplexes is context dependent

1 reference

https://pubmed.ncbi.nlm.nih.gov/9843513

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif

1 reference

https://pubmed.ncbi.nlm.nih.gov/9843513

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Structural Analysis of a Group II Intron by Chemical Modifications and Minimal Energy Calculations

1 reference

https://pubmed.ncbi.nlm.nih.gov/9843513

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/9843513

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/EMBOJ/17.23.7091

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

13 October 2017

ResearchGate publication ID

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