Strategies for RNA folding and assembly (Q28291162)

Nature Reviews Molecular Cell Biology

Europe PubMed Central

title

Strategies for RNA folding and assembly (English)

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Andrea Barta

2

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author name string

Renée Schroeder

series ordinal

1

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Katharina Semrad

series ordinal

3

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language of work or name

English

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publication date

November 2004

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published in

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volume

5

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page(s)

908-19

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issue

11

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cites work

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Ribosome structure and the mechanism of translation

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Hierarchy and dynamics of RNA folding

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Geometric nomenclature and classification of RNA base pairs

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Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity

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FinO is an RNA chaperone that facilitates sense-antisense RNA interactions

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Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA.

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Conformational flexibility in RNA: the role of dihydrouridine

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Locking and unlocking of ribosomal motions

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Crystal structure of the two RNA binding domains of human hnRNP A1 at 1.75 A resolution

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Sorting out the complexity of SR protein functions

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Spliceosomal UsnRNP biogenesis, structure and function

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A doughnut-shaped heteromer of human Sm-like proteins binds to the 3'-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro

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Mechanical devices of the spliceosome: motors, clocks, springs, and things

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Control of gene expression by a natural metabolite-responsive ribozyme

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A preorganized active site in the crystal structure of the Tetrahymena ribozyme

21 April 2017

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Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs

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

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Gene regulation by riboswitches

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Allosteric cascade of spliceosome activation

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DEAD-box proteins: the driving forces behind RNA metabolism

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hnRNP complexes: composition, structure, and function

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RNA chaperones and the RNA folding problem

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mRNA-mediated detection of environmental conditions.

21 January 2018

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The Structural Basis of Large Ribosomal Subunit Function

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Tertiary Motifs in RNA Structure and Folding

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A guide to ions and RNA structure

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Metal ions in ribozyme folding and catalysis

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Metal ions in the structure and function of RNA.

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Structure, folding and catalysis of the small nucleolytic ribozymes

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Conformational flexibility of four-way junctions in RNA.

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Beyond kinetic traps in RNA folding

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Recent insights on RNA folding mechanisms from catalytic RNA.

21 January 2018

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

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Folding of RNA involves parallel pathways

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New pathways in folding of the Tetrahymena group I RNA enzyme

21 January 2018

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Fast folding of a ribozyme by stabilizing core interactions: evidence for multiple folding pathways in RNA.

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Rapid compaction during RNA folding

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RNA Folding at Millisecond Intervals by Synchrotron Hydroxyl Radical Footprinting

21 January 2018

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

21 January 2018

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The Fastest Global Events in RNA Folding: Electrostatic Relaxation and Tertiary Collapse of the Tetrahymena Ribozyme

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

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A Single-Molecule Study of RNA Catalysis and Folding

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Reversible unfolding of single RNA molecules by mechanical force

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Force as a useful variable in reactions: unfolding RNA

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Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme

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A DEAD-box protein functions as an ATP-dependent RNA chaperone in group I intron splicing

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RNA chaperones exist and DEAD box proteins get a life

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A novel mechanism for protein-assisted group I intron splicing.

21 January 2018

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Induced fit in RNA-protein recognition

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Coupling of rRNA transcription and ribosomal assembly in vivo. Formation of active ribosomal subunits in Escherichia coli requires transcription of rRNA genes by host RNA polymerase which cannot be replaced by bacteriophage T7 RNA polymerase.

21 January 2018

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Neomycin B inhibits splicing of the td intron indirectly by interfering with translation and enhances missplicing in vivo

21 January 2018

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Folding problems of the 5' splice site containing the P1 stem of the group I thymidylate synthase intron: substrate binding inhibition in vitro and mis-splicing in vivo

21 January 2018

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Assaying RNA chaperone activity in vivo using a novel RNA folding trap

21 January 2018

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Monitoring intermediate folding states of the td group I intron in vivo

21 January 2018

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RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo

21 January 2018

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Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon

21 January 2018

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A La protein requirement for efficient pre-tRNA folding.

21 January 2018

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A role for the yeast La protein in U6 snRNP assembly: evidence that the La protein is a molecular chaperone for RNA polymerase III transcripts

21 January 2018

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An expanding universe of noncoding RNAs

21 January 2018

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Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator

21 January 2018

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Nucleic acid binding properties of the nucleic acid chaperone domain of hepatitis delta antigen

21 January 2018

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The fragile X mental retardation protein has nucleic acid chaperone properties

21 January 2018

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The prion protein has RNA binding and chaperoning properties characteristic of nucleocapsid protein NCP7 of HIV-1.

21 January 2018

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PrPC has nucleic acid chaperoning properties similar to the nucleocapsid protein of HIV-1.

21 January 2018

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RNA molecules stimulate prion protein conversion

21 January 2018

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CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone.

21 January 2018

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A hierarchy of RNA subdomains in assembly of the central domain of the 30 S ribosomal subunit

21 January 2018

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In vitro assembly of a ribonucleoprotein particle corresponding to the platform domain of the 30S ribosomal subunit

21 January 2018

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Ribosome assembly in eukaryotes

21 January 2018

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The DnaK chaperone system facilitates 30S ribosomal subunit assembly.

21 January 2018

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The DEAD-box RNA helicase SrmB is involved in the assembly of 50S ribosomal subunits in Escherichia coli.

21 January 2018

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Osmolytes stimulate the reconstitution of functional 50S ribosomes from in vitro transcripts of Escherichia coli 23S rRNA.

21 January 2018

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Major rearrangements in the 70S ribosomal 3D structure caused by a conformational switch in 16S ribosomal RNA

21 January 2018

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Ribosomal Proteins S12 and S13 Function as Control Elements for Translocation of the mRNA:tRNA Complex

21 January 2018

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Pre-mRNA splicing: awash in a sea of proteins

21 January 2018

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The U1 snRNP base pairs with the 5' splice site within a penta-snRNP complex

21 January 2018

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Mutagenesis Suggests Several Roles of Snu114p in Pre-mRNA Splicing

21 January 2018

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New insights into the auxiliary domains of eukaryotic RNA binding proteins.

21 January 2018

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RNA recognition by RNP proteins during RNA processing.

21 January 2018

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Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction

21 January 2018

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A biochemical function for the Sm complex.

21 January 2018

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Characterization of Sm-like proteins in yeast and their association with U6 snRNA

21 January 2018

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Assembly of the U1 snRNP involves interactions with the backbone of the terminal stem of U1 snRNA

21 January 2018

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Molecular biology. RNP remodeling with DExH/D boxes

21 January 2018

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The DEAD box protein eIF4A. 2. A cycle of nucleotide and RNA-dependent conformational changes.

21 January 2018

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An RNA switch at the 5' splice site requires ATP and the DEAD box protein Prp28p

21 January 2018

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Deletion of MUD2, the yeast homolog of U2AF65, can bypass the requirement for sub2, an essential spliceosomal ATPase

21 January 2018

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Active disruption of an RNA-protein interaction by a DExH/D RNA helicase

21 January 2018

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Kinetic analysis of ribozyme-substrate complex formation in yeast

21 January 2018

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Selective strand annealing and selective strand exchange promoted by the N-terminal domain of hepatitis delta antigen

21 January 2018

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Splicing double: insights from the second spliceosome

21 January 2018

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Representation of the secondary and tertiary structure of group I introns

21 January 2018

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One sequence, two ribozymes: implications for the emergence of new ribozyme folds

21 January 2018

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

31 March 2020

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An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme

31 March 2020

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31 March 2020

Dissecting RNA function

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Kinetic intermediates trapped by native interactions in RNA folding

31 March 2020

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The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA

31 March 2020

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New roles for structure in biology and drug discovery

31 March 2020

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A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core

31 March 2020

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A collapsed non-native RNA folding state

31 March 2020

1 reference

Near native structure in an RNA collapsed state

31 March 2020

1 reference

A collapsed state functions to self-chaperone RNA folding into a native ribonucleoprotein complex

31 March 2020

1 reference

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

31 March 2020

1 reference

A ribosomal function is necessary for efficient splicing of the T4 phage thymidylate synthase intron in vivo

31 March 2020

1 reference

Escherichia coli protein analogs StpA and H-NS: regulatory loops, similar and disparate effects on nucleic acid dynamics

31 March 2020

1 reference

Nucleic-acid-chaperone activity of retroviral nucleocapsid proteins: significance for viral replication

31 March 2020

1 reference

Protein enhancement of hammerhead ribozyme catalysis

31 March 2020

1 reference

The GAG-like protein of the yeast Ty1 retrotransposon contains a nucleic acid chaperone domain analogous to retroviral nucleocapsid proteins

31 March 2020

1 reference

Factor Fraction required for the Synthesis of Bacteriophage Qβ-RNA

31 March 2020

1 reference

Mechanistic studies of ribonucleic acid renaturation by a helix-destabilizing protein

31 March 2020

1 reference

Escherichia coli proteins, including ribosomal protein S12, facilitate in vitro splicing of phage T4 introns by acting as RNA chaperones

31 March 2020

1 reference

Multifunctional proteins suggest connections between transcriptional and post-transcriptional processes

31 March 2020

1 reference

Total reconstitution of functionally active 50S ribosomal subunits from Escherichia coli

31 March 2020

1 reference

RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA.

31 March 2020

1 reference

Independent in vitro assembly of a ribonucleoprotein particle containing the 3' domain of 16S rRNA.

31 March 2020

1 reference

Summary: the modified nucleosides of RNA.

31 March 2020

1 reference

Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2'-hydroxyl group

31 March 2020

1 reference

Posttranscriptional modification of tRNA in psychrophilic bacteria

31 March 2020

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hnRNP proteins and the biogenesis of mRNA

31 March 2020

1 reference

Renaturation of complementary DNA strands mediated by purified mammalian heterogeneous nuclear ribonucleoprotein A1 protein: implications for a mechanism for rapid molecular assembly

31 March 2020

1 reference

Heterogeneous nuclear ribonucleoprotein A1 catalyzes RNA.RNA annealing

31 March 2020

1 reference

Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA

31 March 2020

1 reference

Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells

31 March 2020

1 reference

Interaction of U2AF65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA [corrected]

31 March 2020

1 reference

The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs

31 March 2020

1 reference

RNA helicases: modulators of RNA structure

31 March 2020

1 reference

Specific alterations of U1-C protein or U1 small nuclear RNA can eliminate the requirement of Prp28p, an essential DEAD box splicing factor

31 March 2020

1 reference

The kinetic mechanism of the hairpin ribozyme in vivo: influence of RNA helix stability on intracellular cleavage kinetics

31 March 2020

1 reference

RNA annealing activities in HeLa nuclei.

31 March 2020

1 reference

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

31 March 2020

1 reference

RNA chaperone activity of large ribosomal subunit proteins from Escherichia coli

31 March 2020

1 reference

The human immunodeficiency virus type 1 Gag polyprotein has nucleic acid chaperone activity: possible role in dimerization of genomic RNA and placement of tRNA on the primer binding site

31 March 2020

1 reference

inferred from DOI database lookup

7 January 2021

based on heuristic

Posttranscriptional modifications in 16S and 23S rRNAs of the archaeal hyperthermophile Sulfolobus solfataricus

1 reference