(Q39698136)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:12364603%20AND%20SRC:MED&resulttype=core&format=json

13 December 2019

title

The bulge region of HIV-1 TAR RNA binds metal ions in solution (English)

1 reference

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13 December 2019

0 references

1

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13 December 2019

Zofia Gdaniec

2

1 reference

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13 December 2019

Ryszard Adamiak

6

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13 December 2019

author name string

Artur Fischer

3

1 reference

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13 December 2019

Tomasz Grabarkiewicz

4

1 reference

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13 December 2019

Lukasz Bielecki

5

1 reference

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13 December 2019

language of work or name

English

0 references

publication date

1 October 2002

1 reference

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13 December 2019

published in

Nucleic Acids Research

1 reference

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13 December 2019

volume

30

1 reference

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13 December 2019

issue

19

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13 December 2019

page(s)

4241-4249

1 reference

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describes a project that uses

13 December 2019

ImageQuant

1 reference

11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC140541/fullTextXML

inferred from PubMed Central ID database lookup

cites work

Brownian-dynamics simulations of metal-ion binding to four-way junctions

1 reference

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The reactivity of phosphodiester bonds within linear single-stranded oligoribonucleotides is strongly dependent on the base sequence

14 September 2017

1 reference

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A thermodynamic framework for Mg2+ binding to RNA.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Identification and characterization of metal ion binding sites in RNA.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Dissection of the ion-induced folding of the hammerhead ribozyme using 19F NMR.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

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

14 September 2017

1 reference

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Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B

14 September 2017

1 reference

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Solution structure of Cobalt(III)hexammine complexed to the GAAA tetraloop, and metal-ion binding to G.A mismatches

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Structure and thermodynamics of metal binding in the P5 helix of a group I intron ribozyme

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

On the role of magnesium ions in 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=140541

Crystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Lead-catalysed specific cleavage of ribosomal RNAs

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

An inhibitor of the Tat/TAR RNA interaction that effectively suppresses HIV-1 replication

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Secondary structure of the r(CUUCGG) tetraloop

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Crystal structure of a group I ribozyme domain: principles of RNA packing

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Control of RNA initiation and elongation at the HIV-1 promoter

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Physiological concentrations of purines and pyrimidines

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Effects of site-specific substitution of 5-fluorouridine on the stabilities of duplex DNA and RNA

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Fluorine-19 nuclear magnetic resonance studies of the structure of 5-fluorouracil-substituted Escherichia coli transfer RNA.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Site-specific cleavage by metal ion cofactors and inhibitors of M1 RNA, the catalytic subunit of RNase P from Escherichia coli

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Lead cleavage sites in the core structure of group I intron-RNA.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

A crystallographic study of metal-binding to yeast phenylalanine transfer RNA

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

The environment of two metal ions surrounding the splice site of a group I intron

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Determination of metal ion binding sites within the hairpin ribozyme domains by NMR.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudoknot

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Iron regulatory element and internal loop/bulge structure for ferritin mRNA studied by cobalt(III) hexammine binding, molecular modeling, and NMR spectroscopy

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Analysis of magnesium, europium and lead binding sites in methionine initiator and elongator tRNAs by specific metal-ion-induced cleavages.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Nonenzymatic cleavage of oligoribonucleotides.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Structural equilibria in RNA as revealed by 19F NMR.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Metal ion probing of rRNAs: evidence for evolutionarily conserved divalent cation binding pockets.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=140541

Docking of cationic antibiotics to negatively charged pockets in RNA folds

20 August 2018

1 reference

12 December 2020

Characterization of the solution conformations of unbound and Tat peptide-bound forms of HIV-1 TAR RNA

1 reference

12 December 2020

Does 29-mer RNA hairpin of the HIV-1 TAR RNA sequence bind magnesium? 19F-NMR and modelling studies

1 reference

12 December 2020

Conformation of the TAR RNA-Arginine Complex by NMR Spectroscopy

1 reference

12 December 2020

Correlations between fluorine-19 nuclear magnetic resonance chemical shift and the secondary and tertiary structure of 5-fluorouracil-substituted tRNA

1 reference

12 December 2020

Metallobiochemistry of RNA. Co(NH3)6(3+) as a probe for Mg2+(aq) binding sites

1 reference

12 December 2020

Solution structures of 5-fluorouracil-substituted RNA duplexes containing G-U wobble base pairs

1 reference

12 December 2020

A magnesium ion core at the heart of a ribozyme domain

1 reference

12 December 2020

Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKF541

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:12364603%20AND%20SRC:MED&resulttype=core&format=json

13 December 2019

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:12364603%20AND%20SRC:MED&resulttype=core&format=json

13 December 2019

PubMed publication ID

12364603

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:12364603%20AND%20SRC:MED&resulttype=core&format=json