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2024

D'Agostino Mattia, Simonetti Angelita, Motta Stefano, Wolff Philippe, Romagnoli Alice, Piccinini Astra, Spinozzi Francesco, Marino Daniele Di, Teana Anna La, Ennifar Eric

Crystal structure of archaeal IF5A-DHS complex reveals insights into the hypusination mechanism Journal Article

In: Structure, 2024, ISSN: 1878-4186.

Abstract | Links | BibTeX | Tags: ARN-MS, ENNIFAR, Unité ARN

Brillet Karl, Janczuk-Richter Marta, Poon Amanda, Laukart-Bradley Joanne, Ennifar Eric, Lebars Isabelle

Characterization of SLA RNA promoter from dengue virus and its interaction with the viral non-structural NS5 protein Journal Article

In: Biochimie, vol. 222, pp. 87–100, 2024, ISSN: 1638-6183.

Abstract | Links | BibTeX | Tags: ENNIFAR, Unité ARN

Compain Guillaume, Monsarrat Clément, Blagojevic Julie, Brillet Karl, Dumas Philippe, Hammann Philippe, Kuhn Lauriane, Martiel Isabelle, Engilberge Sylvain, Oliéric Vincent, Wolff Philippe, Burnouf Dominique Y, Wagner Jérôme, Guichard Gilles

Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp Journal Article

In: JACS Au, vol. 4, no. 2, pp. 432–440, 2024, ISSN: 2691-3704.

Abstract | Links | BibTeX | Tags: ARN-MS, ENNIFAR, PPSE, Unité ARN

2023

Giuliodori Anna Maria, Belardinelli Riccardo, Duval Melodie, Garofalo Raffaella, Schenckbecher Emma, Hauryliuk Vasili, Ennifar Eric, Marzi Stefano

CspA stimulates translation in the cold of its own mRNA by promoting ribosome progression Journal Article

In: Front Microbiol, vol. 14, pp. 1118329, 2023, ISSN: 1664-302X.

Abstract | Links | BibTeX | Tags: ENNIFAR, ROMBY, Unité ARN

2022

Mráziková Klaudia, Kruse Holger, Mlýnský Vojtěch, Auffinger Pascal, Šponer Jiří

Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions Journal Article

In: J Chem Inf Model, vol. 62, iss. 23, pp. 6182-6200, 2022, ISSN: 1549-960X.

Abstract | Links | BibTeX | Tags: ENNIFAR, Unité ARN

Mair Stefan, Erharter Kevin, Renard Eva, Brillet Karl, Brunner Melanie, Lusser Alexandra, Kreutz Christoph, Ennifar Eric, Micura Ronald

Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA Journal Article

In: Nucleic Acids Res, vol. 50, iss. 11, pp. 6038-6051, 2022, ISSN: 1362-4962.

Abstract | Links | BibTeX | Tags: ENNIFAR, Unité ARN

Roovers Martine L, Labar Geoffray, Wolff Philippe, Feller Andre, Elder Dany Van, Soin Romuald, Gueydan Cyril, Kruys Veronique, Droogmans Louis

The Bacillus subtilis open reading frame ysgA encodes the SPOUT methyltransferase RlmP forming 2'-O-methylguanosine at position 2553 in the A-loop of 23S rRNA Journal Article

In: RNA, vol. 28, iss. 9, pp. 1185-1196, 2022, ISSN: 1469-9001.

Abstract | Links | BibTeX | Tags: ARN-MS, ENNIFAR, Unité ARN

Bereiter R., Renard E., Breuker K., Kreutz C., Ennifar E., Micura R.

1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis Journal Article

In: J Am Chem Soc, vol. 144, iss. 23, pp. 10344-10352, 2022, ISBN: 35666572, (1520-5126 (Electronic) 0002-7863 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: ENNIFAR, Unité ARN

2021

Bec G, Ennifar E

switchSENSE Technology for Analysis of DNA Polymerase Kinetics Book Chapter

In: Rederstorff, M (Ed.): vol. 2247, pp. 145-153, Springer Protocols, Humana Press, New York, NY, Small Non-Coding RNAs, 2021.

Abstract | BibTeX | Tags: Biosensor, DNA polymerase, ENNIFAR, HIV reverse transcriptase, Kinetics, switchSENSE technology, Unité ARN

Chagot M E, Quinternet M, Manival X, Lebars I

Application of NMR Spectroscopy to Determine the 3D Structure of Small Non-Coding RNAs Journal Article

In: Methods Mol Biol, vol. 2300, pp. 251-266, 2021, ISBN: 33792884, (1940-6029 (Electronic) 1064-3745 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: 3D structure, dynamics, ENNIFAR, NMR, RNA, Unité ARN

Velours C, Aumont-Nicaise M, Uebel S, England P, Velazquez-Campoy A, Stroebel D, Bec G, Soule P, Quetard C, Ebel C, Roussel A, Charbonnier J B, Varela P F

Macromolecular interactions in vitro, comparing classical and novel approaches Journal Article

In: Eur Biophys J, vol. 50, no. 3-4, pp. 313-330, 2021, ISBN: 33792745, (1432-1017 (Electronic) 0175-7571 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: Artificial binders, Double-stranded DNA breaks repair factors, ENNIFAR, Macromolecular interactions, Molecular scale biophysics, Unité ARN

Bereiter R, Himmelstoss M, Renard E, Mairhofer E, Egger M, Breuker K, Kreutz C, Ennifar E, Micura R

Impact of 3-deazapurine nucleobases on RNA properties Journal Article

In: Nucleic Acids Res, vol. 49, no. 8, pp. 4281-4293, 2021, ISBN: 33856457, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: ENNIFAR, Unité ARN

Schenckbecher E, Bec G, Sakamoto T, Meyer B, Ennifar E

Biophysical Studies of the Binding of Viral RNA with the 80S Ribosome Using switchSENSE Journal Article

In: Methods Mol Biol, vol. 2263, pp. 341-350, 2021, ISBN: 33877606, (1940-6029 (Electronic) 1064-3745 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: Biophysics, ENNIFAR, Kinetics, Ribosome, RNA, switchSENSE, Unité ARN

Velazquez-Campoy A, Claro B, Abian O, Horing J, Bourlon L, Claveria-Gimeno R, Ennifar E, England P, Chaires J B, Wu D, Piszczek G, Brautigam C, Tso S C, Zhao H, Schuck P, Keller S, Bastos M

A multi-laboratory benchmark study of isothermal titration calorimetry (ITC) using Ca(2+) and Mg(2+) binding to EDTA Journal Article

In: Eur Biophys J, vol. 50, no. 3-4, pp. 429-451, 2021, ISBN: 33864101, (1432-1017 (Electronic) 0175-7571 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: Benchmark study, Data treatment, ENNIFAR, Isothermal Titration Calorimetry (ITC), Ligand-binding, Sample preparation, Standard reaction, Unité ARN

Ramos-Morales E, Bayam E, Del-Pozo-Rodriguez J, Salinas-Giege T, Marek M, Tilly P, Wolff P, Troesch E, Ennifar E, Drouard L, Godin J D, Romier C

The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination Journal Article

In: Nucleic Acids Res, vol. 49, no. 11, pp. 6529-6548, 2021, ISBN: 34057470, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: ARN-MS, ENNIFAR, Unité ARN

Himmelstoss M, Erharter K, Renard E, Ennifar E, Kreutz C, Micura R

2'-O-Trifluoromethylated RNA - a powerful modification for RNA chemistry and NMR spectroscopy Journal Article

In: Chem Sci, vol. 11, no. 41, pp. 11322-11330, 2021, ISBN: 34094374, (2041-6520 (Print) 2041-6520 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: ENNIFAR, Unité ARN

Thepaut M, Campos-Silva R, Renard E, Barloy-Hubler F, Ennifar E, Boujard D, Gillet R

Safe and easy in vitro evaluation of tmRNA-SmpB-mediated trans-translation from ESKAPE pathogenic bacteria Journal Article

In: Rna, 2021, ISBN: 34353925, (1469-9001 (Electronic) 1355-8382 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: ENNIFAR, Unité ARN

Andre C, Veillard F, Wolff P, Lobstein A M, Compain G, Monsarrat C, Reichhart J M, Burnouf D Y, Guichard G, Wagner J E

Antibacterial activity of a dual peptide targeting the Escherichia coli sliding clamp and the ribosome Journal Article

In: RSC Chem Biol, vol. 2, no. 4, pp. 1296, 2021, ISBN: 34459830, (2633-0679 (Electronic) 2633-0679 (Linking) Published Erratum).

Abstract | Links | BibTeX | Tags: ARN-MS, ENNIFAR, reichhart, Unité ARN

Mrazikova K., Sponer J., Mlynsky V., Auffinger P., Kruse H.

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose.Nucleobase Lone-Pair.pi Contacts in Nucleic Acids Journal Article

In: J Chem Inf Model, vol. 61, no. 11, pp. 5644-5657, 2021, ISBN: 34738826, (1549-960X (Electronic) 1549-9596 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: ENNIFAR, Unité ARN

Monsarrat C., Compain G., Andre C., Engilberge S., Martiel I., Olieric V., Wolff P., Brillet K., Landolfo M., da Veiga C. Silva, Wagner J., Guichard G., Burnouf D. Y.

Iterative Structure-Based Optimization of Short Peptides Targeting the Bacterial Sliding Clamp Journal Article

In: J Med Chem, 2021, ISBN: 34806883, (1520-4804 (Electronic) 0022-2623 (Linking) Journal Article).

Abstract | Links | BibTeX | Tags: ARN-MS, ENNIFAR, Unité ARN

2020

Abaeva I S, Vicens Q, Bochler A, Soufari H, Simonetti A, Pestova T V, Hashem Y, Hellen C U T

The Halastavi árva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism Journal Article

In: Cell Reports, vol. 33, no. 10, pp. 108476, 2020.

Abstract | Links | BibTeX | Tags: Cricket paralysis virus, Dicistrovirus, ENNIFAR, Halastavi árva virus; IRES, intergenic region, internal ribosomal entry site, pseudoknot, Ribosome, SERBP1, SERPINE1 mRNA binding protein 1, Unité ARN

Auffinger P, Ennifar E, D'Ascenzo L

Deflating the RNA Mg 2+ bubble. Stereochemistry to the rescue! Journal Article

In: RNA, vol. 27, no. 3, pp. 243-252, 2020.

Abstract | Links | BibTeX | Tags: cryo-EM, ENNIFAR, ionic atmosphere, solvent, Unité ARN, validation, X-Ray

Abel S, Marchi M, Solier J, Finet S, Brillet K, Bonneté F

Structural insights into the membrane receptor ShuA in DDM micelles and in a model of gram-negative bacteria outer membrane as seen by SAXS and MD simulations Journal Article

In: Biochim Biophys Acta Biomembr, vol. in press, 2020.

Abstract | Links | BibTeX | Tags: DDM, ENNIFAR, Membrane transporter ShuA, Molecular dynamics simulations, Outer membrane model, SEC-MALLS, SEC-SAXS, Unité ARN

Wolff P, Villette C, Zumsteg J, Heintz D, Antoine L, Chane-Woon-Ming B, Droogmans L, Grosjean H, Westhof E

Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea Journal Article

In: RNA, vol. 26, no. 12, pp. 1957-1975, 2020.

Abstract | Links | BibTeX | Tags: (hyper)thermophiles Archaea mass spectrometry modifications tRNA, ARN-MS, ENNIFAR, Unité ARN, WESTHOF

Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y

Structural Insights Into the Mammalian Late-Stage Initiation Complexes Journal Article

In: Cell Rep, vol. 31, no. 1, pp. 107497, 2020, ISBN: 32268096.

Abstract | Links | BibTeX | Tags: ENNIFAR, PPSE, Unité ARN

Werner S, Schmidt L, Marchand V, Kemmer T, Falschlunger C, Sednev M V, Bec G, Ennifar E, Höbartner C, Micura R, Motorin Y, Hildebrandt A, Helm M

Machine Learning of Reverse Transcription Signatures of Variegated Polymerases Allows Mapping and Discrimination of Methylated Purines in Limited Transcriptomes Journal Article

In: Nucleic Acids Res, vol. 48, no. 7, pp. 3734-3746, 2020, ISBN: 32095818.

Abstract | Links | BibTeX | Tags: ENNIFAR, Unité ARN

Vigouroux A, Aumont-Nicaise M, Boussac A, Marty L, Bello L Lo, Legrand P, Brillet K, Schalk I J, Moréra S

A unique ferrous iron binding mode is associated to large conformational changes for the transport protein FpvC of Pseudomonas aeruginosa Journal Article

In: FEBS J, vol. 287, no. 2, pp. 295-309, 2020, ISBN: 31318478.

Abstract | Links | BibTeX | Tags: ENNIFAR, Pseudomonas aeruginosa iron pyoverdine siderophore solute-binding protein, Unité ARN

Gasser C, Delazer I, Neuner E, Pascher K, Brillet K, Klotz S, Trixl L, Himmelstoß M, Ennifar E, Rieder D, Lusser A, Micura R

Thioguanosine Conversion Enables mRNA-Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC-seq DUAL) Journal Article

In: Angew Chem Int Ed Engl, vol. 59, no. 17, pp. 6881-6886, 2020, ISBN: 31999864.

Abstract | Links | BibTeX | Tags: ENNIFAR, RNA sequencing RNA structures gene expression nucleoside modifications oligonucleotides, Unité ARN

Brillet K, Martinez-Zapien D, Bec G, Ennifar E, Dock-Bregeon A C, Lebars I

Different views of the dynamic landscape covered by the 5'-hairpin of the 7SK small nuclear RNA Journal Article

In: RNA, vol. 26, no. 9, pp. 1184-1197, 2020, ISBN: 32430362.

Abstract | Links | BibTeX | Tags: 7SK HEXIM RNA Tat structure, ENNIFAR, Unité ARN

Wolff P, Ennifar E

Native Electrospray Ionization Mass Spectrometry of RNA-Ligand Complexes Book Chapter

In: Arluison, V; Wien, F (Ed.): RNA Spectroscopy: Methods and Protocols, vol. 2113, pp. 111-118, Springer Protocols, Humana Press, New York, NY, 2020, ISBN: 32006311.

Abstract | Links | BibTeX | Tags: ARN-MS, ENNIFAR, Native mass spectrometry RNA, Unité ARN

Lechner A, Wolff P, Leize-Wagner E, François Y N

Characterization of Post-Transcriptional RNA Modifications by Sheathless Capillary Electrophoresis-High Resolution Mass Spectrometry Journal Article

In: Anal Chem, vol. 92, no. 10, pp. 7363-7370, 2020, ISBN: 32343557.

Abstract | Links | BibTeX | Tags: ARN-MS, ENNIFAR, Unité ARN

Antoine L, Wolff P

Mapping of Posttranscriptional tRNA Modifications by Two-Dimensional Gel Electrophoresis Mass Spectrometry Book Chapter

In: Arluison, V; Wien, F (Ed.): RNA Spectroscopy: Methods and Protocols, vol. 2113, pp. 101-110, Springer Protocols, Humana Press, New York, NY, 2020, ISBN: 32006310.

Abstract | Links | BibTeX | Tags: 2D Gel isolation Nano-LC-MS/MS Posttranscriptional tRNA modifications, ARN-MS, ENNIFAR, ROMBY, Unité ARN

Bernacchi S, Ennifar E

Analysis of the HIV-1 Genomic RNA Dimerization Initiation Site Binding to Aminoglycoside Antibiotics Using Isothermal Titration Calorimetry Book Chapter

In: Arluison, V; Wien, F (Ed.): RNA Spectroscopy: Methods and Protocols, vol. 2113, pp. 237-250, Springer Protocols, Humana Press, New York, NY, 2020, ISBN: 32006318.

Abstract | Links | BibTeX | Tags: Aminoglycosides, dimerization, drug interaction, ENNIFAR, HIV-1, initiation site, ITC, MARQUET, PAILLART, RNA, Thermodynamics RNA, Unité ARN, Viral

Vileno B, Lebars I

Site-Specific Spin Labeling of RNA for NMR and EPR Structural Studies Book Chapter

In: Arluison, V; Wien, F (Ed.): RNA Spectroscopy: Methods and Protocols, vol. 2113, pp. 217-235, Springer Protocols, Humana Press, New York, NY, 2020, ISBN: 32006317.

Abstract | Links | BibTeX | Tags: ENNIFAR, RNA NMR EPR Paramagnetic Spin-label, Unité ARN

Kruse H, Mrazikova K, D'Ascenzo L, Sponer J, Auffinger P

Short but Weak! The Z-DNA lone-pair···π Conundrum Challenges Standard Carbon Van Der Waals Radii Journal Article

In: Angew Chem Int Ed Engl, pp. in press, 2020, ISBN: 32516461.

Abstract | Links | BibTeX | Tags: ENNIFAR, lp···pi interactions molecular recognition non-covalent interactions van der Waals radii Z-DNA, Unité ARN