Coupled nucleotide covariations reveal dynamic RNA interaction patterns (Q34098396)

31 July 2017

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title

Coupled nucleotide covariations reveal dynamic RNA interaction patterns (English)

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31 July 2017

Gultyaev AP

1

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31 July 2017

Franch T

series ordinal

2

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31 July 2017

Gerdes K

series ordinal

3

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31 July 2017

language of work or name

English

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publication date

1 November 2000

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31 July 2017

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31 July 2017

volume

6

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31 July 2017

issue

11

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31 July 2017

page(s)

1483-1491

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Metastable structures and refolding kinetics in hok mRNA of plasmid R1

31 July 2017

cites work

1 reference

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New pathways in folding of the Tetrahymena group I RNA enzyme

5 July 2018

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A conformational switch at the 3' end of a plant virus RNA regulates viral replication.

5 July 2018

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Base pairing between U3 small nucleolar RNA and the 5' end of 18S rRNA is required for pre-rRNA processing

5 July 2018

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Sequential Folding of the Genomic Ribozyme of the Hepatitis Delta Virus: Structural Analysis of RNA Transcription Intermediates

5 July 2018

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Multiple hok genes on the chromosome of Escherichia coli

5 July 2018

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Destabilizing effect of an rRNA stem-loop on an attenuator hairpin in the 5' exon of the Tetrahymena pre-rRNA.

5 July 2018

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Genomic structure of three phenotypically different isolates of peach latent mosaic viroid: implications of the existence of constraints limiting the heterogeneity of viroid quasispecies

5 July 2018

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U2 and U6 snRNA genes in the microsporidian Nosema locustae: evidence for a functional spliceosome

5 July 2018

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

5 July 2018

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Ironing out the kinks: splicing and translation in bacteria

5 July 2018

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High apparent rate of simultaneous compensatory base-pair substitutions in ribosomal RNA.

5 July 2018

1 reference

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Dynamic competition between alternative structures in viroid RNAs simulated by an RNA folding algorithm.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Mechanical Devices of the Spliceosome: Motors, Clocks, Springs, and Things

5 July 2018

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Antisense RNA-regulated programmed cell death

5 July 2018

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Programmed cell death by hok/sok of plasmid R1: Processing at the hok mRNA 3′-end triggers structural rearrangements that allow translation and antisense RNA binding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Programmed cell death by hok/sok of plasmid R1: Coupled nucleotide covariations reveal a phylogenetically conserved folding pathway in the hok family of mRNAs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

An in vivo and in vitro structure-function analysis of the Saccharomyces cerevisiae U3A snoRNP: protein-RNA contacts and base-pair interaction with the pre-ribosomal RNA 1 1Edited by M. Yaniv

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

RNA folding kinetics regulates translation of phage MS2 maturation gene.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

A 451-nucleotide circular RNA from cherry with hammerhead ribozymes in its strands of both polarities.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Hierarchy and dynamics of RNA folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Multiple tertiary interactions involving domain II of group II self-splicing introns.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Inferring the conformation of RNA base pairs and triples from patterns of sequence variation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Phylogenetic analysis of tmRNA secondary structure.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

The rate of compensatory evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Slow folding kinetics of RNase P RNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Multiple pathways of reversion in viroids for conservation of structural elements

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

An alternative helix in the 26S rRNA promotes excision and integration of the Tetrahymena intervening sequence

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Mechanism of post-segregational killing: translation of Hok, SrnB and Pnd mRNAs of plasmids R1, F and R483 is activated by 3'-end processing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

An infectious viroid RNA replicon evolved from an in vitro-generated non-infectious viroid deletion mutant via a complementary deletion in vivo

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Frequent use of the same tertiary motif by self-folding RNAs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Mechanism of post-segregational killing: secondary structure analysis of the entire Hok mRNA from plasmid R1 suggests a fold-back structure that prevents translation and antisense RNA binding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Control of translation by mRNA secondary structure: the importance of the kinetics of structure formation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

The influence of a metastable structure in plasmid primer RNA on antisense RNA binding kinetics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

The guanosine binding site of the Tetrahymena ribozyme

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

pT181 plasmid replication is regulated by a countertranscript-driven transcriptional attenuator

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

A proposal for the secondary structure of a variable area of eukaryotic small ribosomal subunit RNA involving the existence of a pseudoknot

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

The hok killer gene family in gram-negative bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Formation of a thermodynamically metastable structure containing hairpin II is critical for infectivity of potato spindle tuber viroid RNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Alternative secondary structures in the 5' exon affect both forward and reverse self-splicing of the Tetrahymena intervening sequence RNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

In vitro recombination and terminal elongation of RNA by Q beta replicase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Formation of metastable RNA structures by sequential folding during transcription: time-resolved structural analysis of potato spindle tuber viroid (-)-stranded RNA by temperature-gradient gel electrophoresis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Compensatory neutral mutations and the evolution of RNA.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

A functional ribosomal RNA tertiary structure involves a base triple interaction

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

A Conformational Switch in Escherichia coli 16 S Ribosomal RNA During Decoding of Messenger RNA

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Functional base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

The computer simulation of RNA folding pathways using a genetic algorithm.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Folding of RNA involves parallel pathways

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370018

Control of replication of the Lactobacillus pentosus plasmid p353-2: evidence for a mechanism involving transcriptional attenuation of the gene coding for the replication protein

28 October 2018

1 reference

12 December 2020

Mechanism of post-segregational killing by hok-homologue pnd of plasmid R483: two translational control elements in the pnd mRNA

1 reference

12 December 2020

The kinetic folding pathway of the Tetrahymena ribozyme reveals possible similarities between RNA and protein folding

1 reference

12 December 2020

Programmed cell death in bacteria: translational repression by mRNA end-pairing

1 reference

12 December 2020

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

1 reference

12 December 2020

Kinetic intermediates trapped by native interactions in RNA folding

1 reference

12 December 2020

10.1017/S1355838200990708

Identifiers

DOI

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31 July 2017

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31 July 2017

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