(Q37300652)

19 August 2017

1 reference

title

Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs (English)

1 reference

19 August 2017

Alain Laederach

3

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author name string

Inna Shcherbakova

series ordinal

1

1 reference

19 August 2017

Somdeb Mitra

series ordinal

2

1 reference

19 August 2017

Michael Brenowitz

series ordinal

4

1 reference

19 August 2017

14 October 2008

1 reference

Current Opinion in Chemical Biology

19 August 2017

1 reference

19 August 2017

12

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19 August 2017

6

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19 August 2017

655-666

1 reference

Hinge stiffness is a barrier to RNA folding

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Crystal Structure of a Self-Spliced Group II Intron

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Folding of a universal ribozyme: the ribonuclease P RNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Structural metals in the group I intron: a ribozyme with a multiple metal ion core

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Deletion of the P5abc peripheral element accelerates early and late folding steps of the Tetrahymena group I ribozyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Coplanar and coaxial orientations of RNA bases and helices

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Small-angle X-ray scattering from RNA, proteins, and protein complexes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Analytical ultracentrifugation for the study of protein association and assembly

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

An obligate intermediate along the slow folding pathway of a group II intron ribozyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Crystal structure of a phage Twort group I ribozyme-product complex

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

The accuracy of ribosomal RNA comparative structure models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

The rate-limiting step in the folding of a large ribozyme without kinetic traps

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Rapid compaction during RNA folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Exploring the folding landscape of a structured RNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Concerted kinetic folding of a multidomain ribozyme with a disrupted loop-receptor interaction

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

The crystal structure of yeast phenylalanine tRNA at 2.0 A resolution: cleavage by Mg(2+) in 15-year old crystals

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Charge density of divalent metal cations determines RNA stability

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Small angle X-ray scattering reveals a compact intermediate in RNA folding

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

A large collapsed-state RNA can exhibit simple exponential single-molecule dynamics

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Tertiary interactions determine the accuracy of RNA folding

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

A kinetic intermediate that regulates proper folding of a group II intron RNA.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

The paradoxical behavior of a highly structured misfolded intermediate in RNA folding.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Concordant exploration of the kinetics of RNA folding from global and local perspectives.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Perturbation of the hierarchical folding of a large RNA by the destabilization of its Scaffold's tertiary structure

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

An alternative route for the folding of large RNAs: apparent two-state folding by a group II intron ribozyme

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

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.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Counterion Charge Density Determines the Position and Plasticity of RNA Folding Transition States

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Protein-independent Folding Pathway of the 16S rRNA 5′ Domain

3 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Principles of RNA Compaction: Insights from the Equilibrium Folding Pathway of the P4-P6 RNA Domain in Monovalent Cations

3 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2739931

Mg2+-dependent folding of a large ribozyme without kinetic traps

3 December 2018

1 reference

12 December 2020

Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding

1 reference

12 December 2020

Folding Mechanism of theTetrahymenaRibozyme P4−P6 Domain†

1 reference

12 December 2020

Mg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering

1 reference

12 December 2020

Kinetic analysis of the M1 RNA folding pathway

1 reference

12 December 2020

Multiple Monovalent Ion-dependent Pathways for the Folding of the L-21 Tetrahymena thermophila Ribozyme

1 reference

12 December 2020

A folding control element for tertiary collapse of a group II intron ribozyme

1 reference

12 December 2020

Kinetic intermediates in RNA folding

1 reference

12 December 2020

A magnesium ion core at the heart of a ribozyme domain

1 reference

12 December 2020

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

1 reference

12 December 2020

RNA Folding at Millisecond Intervals by Synchrotron Hydroxyl Radical Footprinting

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Pathway modulation, circular permutation and rapid RNA folding under kinetic control

1 reference

12 December 2020

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

1 reference

12 December 2020

10.1016/J.CBPA.2008.09.017

Identifiers

DOI

1 reference

19 August 2017

1 reference

19 August 2017

PubMed publication ID

18926923

1 reference