Tuning RNA folding and function through rational design of junction topology (Q49220038)

19 February 2018

title

Tuning RNA folding and function through rational design of junction topology (English)

1 reference

19 February 2018

0 references

1 reference

19 February 2018

author name string

May Daher

1 reference

19 February 2018

Anthony M Mustoe

1 reference

19 February 2018

Alex Morriss-Andrews

1 reference

19 February 2018

Charles L Brooks

1 reference

19 February 2018

language of work or name

English

0 references

publication date

1 September 2017

1 reference

19 February 2018

published in

Nucleic Acids Research

1 reference

19 February 2018

volume

1 reference

19 February 2018

issue

1 reference

19 February 2018

page(s)

9706-9715

1 reference

19 February 2018

Creative Commons Attribution-NonCommercial 4.0 International

start time

17 July 2017

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

describes a project that uses

ImageQuant

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5766210/fullTextXML

inferred from PubMed Central ID database lookup

cites work

Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Molecular crowding accelerates ribozyme docking and catalysis

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Understanding nucleic acid-ion interactions

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

The many faces of the hairpin ribozyme: structural and functional variants of a small catalytic RNA.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

The Small Ribozymes: Common and Diverse Features Observed through the FRET Lens

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Structure of the three-way helical junction of the hepatitis C virus IRES element

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Analysis of complex single-molecule FRET time trajectories

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Do conformational biases of simple helical junctions influence RNA folding stability and specificity?

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Analysis of four-way junctions in RNA structures

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

CHARMM: the biomolecular simulation program

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting".

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

A nomenclature of junctions and branchpoints in nucleic acids

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Building programmable jigsaw puzzles with RNA.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Modifications and deletions of helices within the hairpin ribozyme-substrate complex: an active ribozyme lacking helix 1.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Transition state stabilization by a catalytic RNA

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Correlating structural dynamics and function in single ribozyme molecules

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Structural dynamics of catalytic RNA highlighted by fluorescence resonance energy transfer.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

The folding of the hairpin ribozyme: dependence on the loops and the junction

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

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

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Structural basis for heterogeneous kinetics: reengineering the hairpin ribozyme

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Hierarchy and dynamics of RNA folding

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Catalytically active geometry in the reversible circularization of ‘mini-monomer’ RNAs derived from the complementary strand of tobacco ringspot virus satellite RNA

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Mutually Exclusive Formation of G-Quadruplex and i-Motif Is a General Phenomenon Governed by Steric Hindrance in Duplex DNA.

22 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Topology links RNA secondary structure with global conformation, dynamics, and adaptation

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Topology of three-way junctions in folded RNAs

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

The linkage between magnesium binding and RNA folding.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Probing non-selective cation binding in the hairpin ribozyme with Tb(III).

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5766210

Construction of hairpin ribozymes with a three-way junction

14 August 2018

1 reference

12 December 2020

The hairpin ribozyme: structure, assembly and catalysis

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

An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis

1 reference

12 December 2020

Structure-mapping of the hairpin ribozyme. Magnesium-dependent folding and evidence for tertiary interactions within the ribozyme-substrate complex

1 reference

12 December 2020

RNA self-assembly and RNA nanotechnology

1 reference

12 December 2020

Helical junctions as determinants for RNA folding: origin of tertiary structure stability of the hairpin ribozyme

1 reference

12 December 2020

Bulge-induced bends in RNA: quantification by transient electric birefringence

1 reference

12 December 2020

The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKX614

1 reference

19 February 2018

PMC publication ID

5766210

1 reference

19 February 2018

PubMed publication ID

28934478

1 reference

19 February 2018