Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions (Q36148295)

12 August 2017

Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions (English)

1 reference

12 August 2017

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Durga M Chadalavada

1

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12 August 2017

Andrea L Cerrone-Szakal

series ordinal

2

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12 August 2017

Philip C Bevilacqua

series ordinal

3

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12 August 2017

language of work or name

English

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publication date

23 October 2007

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12 August 2017

13

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inferred from page(s)

published in

RNA

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12 August 2017

13

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12 August 2017

12

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12 August 2017

2189-2201

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RNA folding during transcription

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Satellite tobacco ringspot virus RNA: A subset of the RNA sequence is sufficient for autolytic processing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Informational complexity and functional activity of RNA structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Mfold web server for nucleic acid folding and hybridization prediction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Stimulation of RNA polymerase II elongation by hepatitis delta antigen

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Folding of a large ribozyme during transcription and the effect of the elongation factor NusA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Crystal structure of a hepatitis delta virus ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Promoter escape limits the rate of RNA polymerase II transcription and is enhanced by TFIIE, TFIIH, and ATP on negatively supercoiled DNA

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

RNA virus mutations and fitness for survival

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Autophosphorylation sites participate in the activation of the double-stranded-RNA-activated protein kinase PKR

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

The molecular biology of hepatitis delta virus

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Kinetic characterization of intramolecular and intermolecular hammerhead RNAs with stem II deletions

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

The intervening sequence RNA of Tetrahymena is an enzyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Molecular cloning and sequencing of a human hepatitis delta (delta) virus RNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Information content of binding sites on nucleotide sequences

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Basic local alignment search tool

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Basic mechanisms of transcript elongation and its regulation

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Structural and sequence elements required for the self-cleaving activity of the hepatitis delta virus ribozyme

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

The self-cleaving domain from the genomic RNA of hepatitis delta virus: sequence requirements and the effects of denaturant

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Secondary structure of the self-cleaving RNA of hepatitis delta virus: applications to catalytic RNA design

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Hepatitis delta antigen binds to the clamp of RNA polymerase II and affects transcriptional fidelity

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

A single nucleotide linked to a switch in metal ion reactivity preference in the HDV ribozymes.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

The human RNA polymerase II interacts with the terminal stem-loop regions of the hepatitis delta virus RNA genome

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

A conformational switch controls hepatitis delta virus ribozyme catalysis

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

A mechanistic framework for co-transcriptional folding of the HDV genomic ribozyme in the presence of downstream sequence

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Identification and characterization of the RNA chaperone activity of hepatitis delta antigen peptides

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

A designed heterotrimeric coiled coil

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080589

Characterization and application of the selective strand annealing activity of the N terminal domain of hepatitis delta antigen

23 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17956974

12 December 2020

inferred from PubMed ID database lookup

Thermodynamics of single mismatches in RNA duplexes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17956974

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1261/RNA.778107

1 reference

release_ktkbrwi4evatjn7yeda2hzvwyi

12 August 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ktkbrwi4evatjn7yeda2hzvwyi

24 November 2022

mapped directly with Wikidata item

1 reference

12 August 2017

1 reference