(Q27654467)

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The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs

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The structure of the human tRNALys3 anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs (English)

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author name string

Yann Bilbille

1

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Franck A P Vendeix

2

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Richard Guenther

3

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Andrzej Malkiewicz

4

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Xavier Ariza

5

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Jaume Vilarrasa

6

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Paul F Agris

7

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language of work or name

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publication date

June 2009

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Nucleic Acids Research

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37

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10

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3342-53

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NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA

1 reference

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20 March 2017

A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture

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20 March 2017

Functional anticodon architecture of human tRNALys3 includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t6A

1 reference

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20 March 2017

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

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20 March 2017

HIV-1 A-rich RNA loop mimics the tRNA anticodon structure

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20 March 2017

The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of stable RNA structures and the diversity of recognition sites

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20 March 2017

Structure of an RNA double helix including uracil-uracil base pairs in an internal loop

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20 March 2017

NMR View: A computer program for the visualization and analysis of NMR data

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20 March 2017

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

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20 March 2017

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

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20 March 2017

MOLMOL: a program for display and analysis of macromolecular structures

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20 March 2017

NMRPipe: a multidimensional spectral processing system based on UNIX pipes

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20 March 2017

Initiation of HIV-1 reverse transcription is regulated by a primer activation signal

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

20 March 2017

Primer tRNAs for reverse transcription

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20 March 2017

HIV-1 reverse transcription initiation: a potential target for novel antivirals?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Decoding the genome: a modified view

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

The annealing mechanism of HIV-1 reverse transcription primer onto the viral genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Effect of altering the tRNA(Lys)(3) concentration in human immunodeficiency virus type 1 upon its annealing to viral RNA, GagPol incorporation, and viral infectivity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Destabilization of tRNA3(Lys) from the primer-binding site of HIV-1 genome by anti-A loop polyamide nucleotide analog

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Resonance assignment and structure determination for RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

NMR and biochemical characterization of recombinant human tRNA(Lys)3 expressed in Escherichia coli: identification of posttranscriptional nucleotide modifications required for efficient initiation of HIV-1 reverse transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Thermodynamics of RNA-RNA duplexes with 2- or 4-thiouridines: implications for antisense design and targeting a group I intron.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Structural and functional roles of the N1- and N3-protons of psi at tRNA's position 39

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

The RNA Modification Database: 1999 update

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29 September 2017

Mutational analysis of the tRNA3Lys/HIV-1 RNA (primer/template) complex.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Placement of tRNA primer on the primer-binding site requires pol gene expression in avian but not murine retroviruses

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Nucleotide substitutions within U5 are critical for efficient reverse transcription of human immunodeficiency virus type 1 with a primer binding site complementary to tRNA(His)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

The importance of the A-rich loop in human immunodeficiency virus type 1 reverse transcription and infectivity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Identification of a sequence within U5 required for human immunodeficiency virus type 1 to stably maintain a primer binding site complementary to tRNA(Met).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Mutations in both the U5 region and the primer-binding site influence the selection of the tRNA used for the initiation of HIV-1 reverse transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Specific initiation and switch to elongation of human immunodeficiency virus type 1 reverse transcription require the post-transcriptional modifications of primer tRNA3Lys

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Psoralen crosslinking between human immunodeficiency virus type 1 RNA and primer tRNA3(Lys)

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Stabilization of RNA stacking by pseudouridine

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Construction of a type 1 human immunodeficiency virus that maintains a primer binding site complementary to tRNA(His).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

DNA strand exchange and selective DNA annealing promoted by the human immunodeficiency virus type 1 nucleocapsid protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Structural requirements for the binding of tRNA Lys3 to reverse transcriptase of the human immunodeficiency virus type 1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

A specific orientation of RNA secondary structures is required for initiation of reverse transcription.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Modified nucleotides of tRNA(3Lys) modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Nuclear Overhauser effect study of yeast tRNAVal 1: evidence for uridine-pseudouridine base pairing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

15N-labeled Escherichia coli tRNAfMet, tRNAGlu, tRNATyr, and tRNAPhe. Double resonance and two-dimensional NMR of N1-labeled pseudouridine.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

NMR and molecular modeling evidence for a G.A mismatch base pair in a purine-rich DNA duplex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

29 September 2017

Nucleotide sequences within the U5 region of the viral RNA genome are the major determinants for an human immunodeficiency virus type 1 to maintain a primer binding site complementary to tRNA(His).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

2 June 2018

Retroviral nucleocapsid proteins possess potent nucleic acid strand renaturation activity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

2 June 2018

A major family of motifs involving G.A mismatches in ribosomal RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

2 June 2018

Recombinant human immunodeficiency virus type 1 nucleocapsid (NCp7) protein unwinds tRNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

2 June 2018

The role of 5-methylcytidine in the anticodon arm of yeast tRNA(Phe): site-specific Mg2+ binding and coupled conformational transition in DNA analogs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

2 June 2018

A magnesium-induced conformational transition in the loop of a DNA analog of the yeast tRNA(Phe) anticodon is dependent on RNA-like modifications of the bases of the stem

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

2 June 2018

Pseudouridines in rRNA helix 69 play a role in loop stacking interactions

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27 November 2018

The role of modifications in codon discrimination by tRNA(Lys)UUU.

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

27 November 2018

Structural variability of the initiation complex of HIV-1 reverse transcription.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

27 November 2018

An RNA complex of the HIV-1 A-loop and tRNA(Lys,3) is stabilized by nucleoside modifications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

27 November 2018

Prediction of proton chemical shifts in RNA. Their use in structure refinement and validation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

27 November 2018

Heteronuclear NMR studies of the interaction of tRNA3Lys with HIV-1 nucleocapsid protein11Edited by M. F. Summers

1 reference

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27 November 2018

Single atom modification (O-->S) of tRNA confers ribosome binding.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

27 November 2018

Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation.

1 reference

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27 November 2018

Site-selected introduction of modified purine and pyrimidine ribonucleosides into RNA by automated phosphoramidite chemistry.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2691828

27 November 2018

Purification of transfer RNA species by single-step ion-exchange high-performance liquid chromatography

1 reference

https://pubmed.ncbi.nlm.nih.gov/19324888

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Solution structure of (rGGCAGGCC)2 by two-dimensional NMR and the iterative relaxation matrix approach

1 reference

https://pubmed.ncbi.nlm.nih.gov/19324888

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Base pairing within the psi32,psi39-modified anticodon arm of Escherichia coli tRNA(Phe)

1 reference

https://pubmed.ncbi.nlm.nih.gov/19324888

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Three-dimensional heteronuclear NMR studies of RNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/19324888

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Initiation of reverse transcription of HIV-1: secondary structure of the HIV-1 RNA/tRNA(3Lys) (template/primer)

1 reference

https://pubmed.ncbi.nlm.nih.gov/19324888

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Solution structure of a GA mismatch DNA sequence, d(CCATGAATGG)2, determined by 2D NMR and structural refinement methods

1 reference

https://pubmed.ncbi.nlm.nih.gov/19324888

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs

1 reference

https://pubmed.ncbi.nlm.nih.gov/19324888

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Crystal structure of unmodified tRNA(Gln) complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure

1 reference

https://pubmed.ncbi.nlm.nih.gov/19324888

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Quantitative enzymatic hydrolysis of tRNAs: reversed-phase high-performance liquid chromatography of tRNA nucleosides

1 reference

https://pubmed.ncbi.nlm.nih.gov/19324888

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

High-yielding preparation of

1 reference

https://pubmed.ncbi.nlm.nih.gov/19324888

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKP187

1 reference

Consolidated OpenCitations Corpus – April 2017

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OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

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