(Q37326624)

English

Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker

scientific article published on March 2006

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scholarly article

1 reference

Europe PubMed Central

19 August 2017

Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker (English)

1 reference

Europe PubMed Central

19 August 2017

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4

object named as

Jose H Hodak

1 reference

Europe PubMed Central

19 August 2017

David J. Nesbitt

5

object named as

David J Nesbitt

1 reference

Europe PubMed Central

19 August 2017

author name string

Christopher D Downey

1

1 reference

Europe PubMed Central

19 August 2017

Julie L Fiore

2

1 reference

Europe PubMed Central

19 August 2017

Colby D Stoddard

3

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Europe PubMed Central

19 August 2017

Arthur Pardi

6

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Europe PubMed Central

19 August 2017

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publication date

1 March 2006

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Europe PubMed Central

19 August 2017

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Europe PubMed Central

19 August 2017

45

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Europe PubMed Central

19 August 2017

11

1 reference

Europe PubMed Central

19 August 2017

3664-3673

1 reference

Europe PubMed Central

19 August 2017

Docking kinetics and equilibrium of a GAAA tetraloop-receptor motif probed by single-molecule FRET.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Site-directed spin labeling studies reveal solution conformational changes in a GAAA tetraloop receptor upon Mg(2+)-dependent docking of a GAAA tetraloop

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Ions and RNA folding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

From genes to machines: DNA nanomechanical devices

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion 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=2735227

6 September 2017

Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Single-molecule transition-state analysis of RNA folding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Crystal structure of the specificity domain of ribonuclease P

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

DNA duplex-quadruplex exchange as the basis for a nanomolecular machine

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Metal ions in the structure and function of RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

The involvement of RNA in ribosome function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

The chemical repertoire of natural ribozymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

In the fluorescent spotlight: global and local conformational changes of small catalytic RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Beyond kinetic traps in RNA folding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Quantitative analysis of the isolated GAAA tetraloop/receptor interaction in solution: a site-directed spin labeling study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

RNA tertiary interactions in the large ribosomal subunit: the A-minor motif

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Monitoring the structure of Escherichia coli RNase P RNA in the presence of various divalent metal ions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

An early transition state for folding of the P4-P6 RNA domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

TectoRNA: modular assembly units for the construction of RNA nano-objects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Multiple folding pathways for the P4-P6 RNA domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Structural biology. The ribosome is a ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Structural motifs in RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Tertiary Motifs in RNA Structure and Folding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

Solution structure of a GAAA tetraloop receptor RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

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=2735227

6 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=2735227

6 September 2017

GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

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=2735227

6 September 2017

Metal ion requirements for sequence-specific endoribonuclease activity 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=2735227

6 September 2017

Structural Features that Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA Loops

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

6 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

14 September 2017

Lead cleavage sites in the core structure of group I intron-RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

14 September 2017

Metal ion binding and the folding of the hairpin ribozyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

26 June 2018

An important RNA tertiary interaction of group I and group II introns is implicated in gram-positive RNase P RNAs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

26 June 2018

Conformation of an RNA pseudoknot

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

26 June 2018

Influence of metal ions on the ribonuclease P reaction. Distinguishing substrate binding from catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

26 June 2018

RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

2 September 2018

The tertiary structure of the hairpin ribozyme is formed through a slow conformational search

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

2 September 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

2 September 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=2735227

2 September 2018

The GAAA tetraloop-receptor interaction contributes differentially to folding thermodynamics and kinetics for the P4-P6 RNA domain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

2 September 2018

The linkage between magnesium binding and RNA folding.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

2 September 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=2735227

2 September 2018

GNRA tetraloops make a U-turn

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

2 September 2018

Role of counterion condensation in folding of the Tetrahymena ribozyme. I. Equilibrium stabilization by cations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2735227

3 December 2018

Observation of internal cleavage and ligation reactions of a ribozyme

1 reference

https://pubmed.ncbi.nlm.nih.gov/16533049

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape

1 reference

https://pubmed.ncbi.nlm.nih.gov/16533049

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes

1 reference

https://pubmed.ncbi.nlm.nih.gov/16533049

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mechanochemical coupling in actomyosin energy transduction studied by in vitro movement assay

1 reference

https://pubmed.ncbi.nlm.nih.gov/16533049

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Tecto-RNA: One-Dimensional Self-Assembly through Tertiary Interactions This work was carried out in Strasbourg with the support of grants to N.B.L. from the NIH (1R15 GM55898) and the NIH Fogarty Institute (1-F06-TW02251-01) and the support of the C

1 reference

https://pubmed.ncbi.nlm.nih.gov/16533049

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor

1 reference

https://pubmed.ncbi.nlm.nih.gov/16533049

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Folding Mechanism of theTetrahymenaRibozyme P4−P6 Domain†

1 reference

https://pubmed.ncbi.nlm.nih.gov/16533049

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A collapsed non-native RNA folding state

1 reference

https://pubmed.ncbi.nlm.nih.gov/16533049

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity

1 reference

https://pubmed.ncbi.nlm.nih.gov/16533049

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A Single-Molecule Study of RNA Catalysis and Folding

1 reference

https://pubmed.ncbi.nlm.nih.gov/16533049

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/BI0520941

1 reference

Europe PubMed Central

19 August 2017

release_ygcknjw54fcjjo7qsnsroqrv4e

1 reference

https://api.fatcat.wiki/v0/release/ygcknjw54fcjjo7qsnsroqrv4e

24 November 2022

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mapped directly with Wikidata item

1 reference

Europe PubMed Central

19 August 2017

1 reference

Europe PubMed Central

19 August 2017

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