Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme (Q34702891)

4 August 2017

title

Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme (English)

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4 August 2017

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Anne T Perrotta

1

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4 August 2017

Timothy S Wadkins

series ordinal

2

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4 August 2017

Michael D Been

series ordinal

3

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4 August 2017

language of work or name

English

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publication date

11 May 2006

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4 August 2017

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4 August 2017

volume

12

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4 August 2017

issue

7

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4 August 2017

page(s)

1282-1291

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Role of an active site adenine in hairpin ribozyme catalysis

4 August 2017

cites work

1 reference

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The hairpin ribozyme: from crystal structure to function

7 July 2018

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Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot

7 July 2018

1 reference

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Catalytic strategies of the hepatitis delta virus ribozymes

7 July 2018

1 reference

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Rescue of an abasic hairpin ribozyme by cationic nucleobases: evidence for a novel mechanism of RNA catalysis

7 July 2018

1 reference

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Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Crystal structure of a hepatitis delta virus ribozyme

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Core-associated non-duplex sequences distinguishing the genomic and antigenomic self-cleaving RNAs of hepatitis delta virus

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Cloning and expression of the gene for bacteriophage T7 RNA polymerase

7 July 2018

1 reference

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Rapid and efficient site-specific mutagenesis without phenotypic selection

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Production of single-stranded plasmid DNA

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Human hepatitis delta virus RNA subfragments contain an autocleavage activity

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Direct Brønsted analysis of the restoration of activity to a mutant enzyme by exogenous amines

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

General acid catalysis by the hepatitis delta virus ribozyme

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Role of an active site guanine in hairpin ribozyme catalysis probed by exogenous nucleobase rescue

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

A conformational switch controls hepatitis delta virus ribozyme catalysis

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Proton inventory of the genomic HDV ribozyme in Mg(2+)-containing solutions.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Direct pK(a) measurement of the active-site cytosine in a genomic hepatitis delta virus ribozyme

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Structure-function relationships in the hammerhead ribozyme probed by base rescue

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

Rescue of the catalytic activity of an H42A mutant of horseradish peroxidase by exogenous imidazoles

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1484427

A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion

26 October 2018

1 reference

12 December 2020

Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage

1 reference

12 December 2020

Buffers of constant ionic strength for studying pH-dependent processes

1 reference

12 December 2020

Identification and characterization of a catalytic base in bacterial luciferase by chemical rescue of a dark mutant

1 reference

12 December 2020

Energetics of a strongly pH dependent RNA tertiary structure in a frameshifting pseudoknot

1 reference

12 December 2020

Identifiers

DOI

10.1261/RNA.14106

1 reference

4 August 2017

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4 August 2017

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