(Q41138427)

English

Probing the role of a secondary structure element at the 5'- and 3'-splice sites in group I intron self-splicing: the tetrahymena L-16 ScaI ribozyme reveals a new role of the G.U pair in self-splicing

scientific article published on 27 March 2007

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scholarly article

1 reference

Europe PubMed Central

27 September 2017

Probing the role of a secondary structure element at the 5'- and 3'-splice sites in group I intron self-splicing: the tetrahymena L-16 ScaI ribozyme reveals a new role of the G.U pair in self-splicing (English)

1 reference

Europe PubMed Central

27 September 2017

0 references

Katrin Karbstein

1

object named as

Katrin Karbstein

1 reference

Europe PubMed Central

27 September 2017

author name string

Jihee Lee

2

1 reference

Europe PubMed Central

27 September 2017

Daniel Herschlag

3

1 reference

Europe PubMed Central

27 September 2017

language of work or name

0 references

publication date

27 March 2007

1 reference

Europe PubMed Central

27 September 2017

1 reference

Europe PubMed Central

27 September 2017

46

1 reference

Europe PubMed Central

27 September 2017

16

1 reference

Europe PubMed Central

27 September 2017

4861-4875

1 reference

Europe PubMed Central

27 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Crystal structure of a self-splicing group I intron with both exons

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Extraordinarily slow binding of guanosine to the Tetrahymena group I ribozyme: implications for RNA preorganization and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Dissection of a metal-ion-mediated conformational change in Tetrahymena ribozyme catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

In vivo selection of better self-splicing introns in Escherichia coli: the role of the P1 extension helix of the Tetrahymena intron

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

An unconventional origin of metal-ion rescue and inhibition in the Tetrahymena group I ribozyme reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Use of duplex rigidity for stability and specificity in RNA tertiary structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

On the wobble GoU and related pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

A sulfate pocket formed by three GoU pairs in the 0.97 A resolution X-ray structure of a nonameric RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Characterization of a local folding event of the Tetrahymena group I ribozyme: effects of oligonucleotide substrate length, pH, and temperature on the two substrate binding steps

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

New pathways in folding of the Tetrahymena group I RNA enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Protonated 2'-aminoguanosine as a probe of the electrostatic environment of the active site of the Tetrahymena group I ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Probing the role of metal ions in RNA catalysis: kinetic and thermodynamic characterization of a metal ion interaction with the 2'-moiety of the guanosine nucleophile in the Tetrahymena group I ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Energetics and cooperativity of tertiary hydrogen bonds in RNA structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Crystal structure of an RNA duplex r(G GCGC CC)2 with non-adjacent G*U base pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Specificity from steric restrictions in the guanosine binding pocket of a group I ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

A minor groove RNA triple helix within the catalytic core of a group I intron

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

A preorganized active site in the crystal structure 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=2597287

27 September 2017

Direct demonstration of the catalytic role of binding interactions in an enzymatic reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Quantitating tertiary binding energies of 2' OH groups on the P1 duplex of the Tetrahymena ribozyme: intrinsic binding energy in an RNA enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

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=2597287

27 September 2017

Isolation of a local tertiary folding transition in the context of a globally folded RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Conformational switches involved in orchestrating the successive steps of group I RNA splicing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

The P9.1-P9.2 peripheral extension helps guide folding 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=2597287

27 September 2017

Exocyclic amine of the conserved G.U pair at the cleavage site of the Tetrahymena ribozyme contributes to 5'-splice site selection and transition state stabilization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Metal ion catalysis in the Tetrahymena ribozyme reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Cooperative and anticooperative binding to a ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Guanosine binding to the Tetrahymena ribozyme: thermodynamic coupling with oligonucleotide binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Self-splicing of the group I intron from Anabaena pre-tRNA: requirement for base-pairing of the exons in the anticodon stem

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Dissection of the role of the conserved G.U pair in group I RNA self-splicing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Minor groove recognition of the conserved G.U pair at the Tetrahymena ribozyme reaction site

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Use of binding energy by an RNA enzyme for catalysis by positioning and substrate destabilization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Structure of an RNA double helix including uracil-uracil base pairs in an internal loop

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

The importance of being ribose at the cleavage site in the Tetrahymena ribozyme reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Contributions of 2'-hydroxyl groups of the RNA substrate to binding and catalysis by the Tetrahymena ribozyme. An energetic picture of an active site composed of RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Structure of the P1 helix from group I self-splicing introns

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Translocation of an RNA duplex on a ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Catalysis of RNA cleavage by a ribozyme derived from the group I intron of Anabaena pre-tRNA(Leu).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

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=2597287

27 September 2017

Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

A Labile Phosphodiester Bond at the Ligation Junction in a Circular Intervening Sequence RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Autocatalytic cyclization of an excised intervening sequence RNA is a cleavage–ligation reaction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Reactions of the intervening sequence of the Tetrahymena ribosomal ribonucleic acid precursor: pH dependence of cyclization and site-specific hydrolysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Sites of circularization of the Tetrahymena rRNA IVS are determined by sequence and influenced by position and secondary structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

The intervening sequence RNA of Tetrahymena is an enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

The Tetrahymena ribozyme acts like an RNA restriction endonuclease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Determinants of the 3' splice site for self-splicing of the Tetrahymena pre-rRNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Base pairing between the 3' exon and an internal guide sequence increases 3' splice site specificity in the Tetrahymena self-splicing rRNA intron

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 2. Kinetic description of the reaction of an RNA substrate that forms a mismatch at the active site

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Direct measurement of oligonucleotide substrate binding to wild-type and mutant ribozymes from Tetrahymena

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Visualizing the higher order folding of a catalytic RNA molecule

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Evidence for processivity and two-step binding of the RNA substrate from studies of J1/2 mutants 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=2597287

27 September 2017

Ribozyme recognition of RNA by tertiary interactions with specific ribose 2′-OH groups

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

27 September 2017

Tertiary Structure Around the Guanosine-Binding Site 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=2597287

27 September 2017

The guanosine binding site 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=2597287

14 June 2018

Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

19 August 2018

Probing the Tetrahymena group I ribozyme reaction in both directions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

19 August 2018

The tetrahymena ribozyme cleaves a 5'-methylene phosphonate monoester approximately 10(2)-fold faster than a normal phosphate diester: implications for enzyme catalysis of phosphoryl transfer reactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

19 August 2018

pH dependencies of the Tetrahymena ribozyme reveal an unconventional origin of an apparent pKa.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

19 August 2018

Comparison of pH dependencies of the Tetrahymena ribozyme reactions with RNA 2'-substituted and phosphorothioate substrates reveals a rate-limiting conformational step

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2597287

19 August 2018

New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/17385892

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Probing the interplay between the two steps of group I intron splicing: competition of exogenous guanosine with omega G

1 reference

https://pubmed.ncbi.nlm.nih.gov/17385892

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The self-splicing RNA of Tetrahymena is trapped in a less active conformation by gel purification

1 reference

https://pubmed.ncbi.nlm.nih.gov/17385892

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods

1 reference

https://pubmed.ncbi.nlm.nih.gov/17385892

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Binding of guanosine and 3' splice site analogues to a group I ribozyme: interactions with functional groups of guanosine and with additional nucleotides

1 reference

https://pubmed.ncbi.nlm.nih.gov/17385892

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Kinetic intermediates in RNA folding

1 reference

https://pubmed.ncbi.nlm.nih.gov/17385892

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Predicting thermodynamic properties of RNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/17385892

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mechanistic investigations of a ribozyme derived from the Tetrahymena group I intron: insights into catalysis and the second step of self-splicing

1 reference

https://pubmed.ncbi.nlm.nih.gov/17385892

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Thermodynamics of single mismatches in RNA duplexes

1 reference

https://pubmed.ncbi.nlm.nih.gov/17385892

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Characterization of the Azoarcus ribozyme: tight binding to guanosine and substrate by an unusually small group I ribozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/17385892

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Making ends meet: a model for RNA splicing in fungal mitochondria

1 reference

https://pubmed.ncbi.nlm.nih.gov/17385892

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/BI062169G

1 reference

Europe PubMed Central

27 September 2017

1 reference

Europe PubMed Central

27 September 2017

1 reference

Europe PubMed Central

27 September 2017

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