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Article ; Online: Native Top-Down Mass Spectrometry Uncovers Two Distinct Binding Motifs of a Functional Neomycin-Sensing Riboswitch Aptamer.

Heel, Sarah Viola / Bartosik, Karolina / Juen, Fabian / Kreutz, Christoph / Micura, Ronald / Breuker, Kathrin

Journal of the American Chemical Society

2023 Volume 145, Issue 28, Page(s) 15284–15294

Abstract: Understanding how ligands bind to ribonucleic acids (RNA) is important for understanding RNA recognition in biological processes and drug development. Here, we have studied neomycin B binding to neomycin-sensing riboswitch aptamer constructs by native ... ...

Abstract	Understanding how ligands bind to ribonucleic acids (RNA) is important for understanding RNA recognition in biological processes and drug development. Here, we have studied neomycin B binding to neomycin-sensing riboswitch aptamer constructs by native top-down mass spectrometry (MS) using electrospray ionization (ESI) and collisionally activated dissociation (CAD). Our MS data for a 27 nt aptamer construct reveal the binding site and ligand interactions, in excellent agreement with the structure derived from nuclear magnetic resonance (NMR) studies. Strikingly, for an extended 40 nt aptamer construct, which represents the sequence with the highest regulatory factor for riboswitch function, we identified two binding motifs for neomycin B binding, one corresponding to the bulge-loop motif of the 27 nt construct and the other one in the minor groove of the lower stem, which according to the MS data are equally populated. By replacing a noncanonical with a canonical base pair in the lower stem of the 40 nt aptamer, we can reduce binding to the minor groove motif from ∼50 to ∼30%. Conversely, the introduction of a CUG/CUG motif in the lower stem shifts the binding equilibrium in favor of minor groove binding. The MS data reveal site-specific and stoichiometry-resolved information on aminoglycoside binding to RNA that is not directly accessible by other methods and underscore the role of noncanonical base pairs in RNA recognition by aminoglycosides.
MeSH term(s)	Neomycin ; Riboswitch ; Framycetin ; Anti-Bacterial Agents/metabolism ; Aminoglycosides ; RNA ; Mass Spectrometry ; Binding Sites ; Nucleic Acid Conformation ; Ligands
Chemical Substances	Neomycin (I16QD7X297) ; Riboswitch ; Framycetin (4BOC774388) ; Anti-Bacterial Agents ; Aminoglycosides ; RNA (63231-63-0) ; Ligands
Language	English
Publishing date	2023-07-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.3c02774
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Article ; Online: Resolving the intricate binding of neomycin B to multiple binding motifs of a neomycin-sensing riboswitch aptamer by native top-down mass spectrometry and NMR spectroscopy.

Heel, Sarah Viola / Juen, Fabian / Bartosik, Karolina / Micura, Ronald / Kreutz, Christoph / Breuker, Kathrin

Nucleic acids research

2023 Volume 52, Issue 8, Page(s) 4691–4701

Abstract: Understanding small molecule binding to RNA can be complicated by an intricate interplay between binding stoichiometry, multiple binding motifs, different occupancies of different binding motifs, and changes in the structure of the RNA under study. Here, ...

Abstract	Understanding small molecule binding to RNA can be complicated by an intricate interplay between binding stoichiometry, multiple binding motifs, different occupancies of different binding motifs, and changes in the structure of the RNA under study. Here, we use native top-down mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy to experimentally resolve these factors and gain a better understanding of the interactions between neomycin B and the 40 nt aptamer domain of a neomycin-sensing riboswitch engineered in yeast. Data from collisionally activated dissociation of the 1:1, 1:2 and 1:3 RNA-neomycin B complexes identified a third binding motif C of the riboswitch in addition to the two motifs A and B found in our previous study, and provided occupancies of the different binding motifs for each complex stoichiometry. Binding of a fourth neomycin B molecule was unspecific according to both MS and NMR data. Intriguingly, all major changes in the aptamer structure can be induced by the binding of the first neomycin B molecule regardless of whether it binds to motif A or B as evidenced by stoichiometry-resolved MS data together with titration data from 1H NMR spectroscopy in the imino proton region. Specific binding of the second and third neomycin B molecules further stabilizes the riboswitch aptamer, thereby allowing for a gradual response to increasing concentrations of neomycin B, which likely leads to a fine-tuning of the cellular regulatory mechanism.
MeSH term(s)	Aptamers, Nucleotide/chemistry ; Aptamers, Nucleotide/metabolism ; Aptamers, Nucleotide/genetics ; Riboswitch ; Framycetin/chemistry ; Framycetin/metabolism ; Binding Sites ; Nucleic Acid Conformation ; Magnetic Resonance Spectroscopy/methods ; Neomycin/chemistry ; Mass Spectrometry/methods ; Nucleotide Motifs ; Nuclear Magnetic Resonance, Biomolecular
Chemical Substances	Aptamers, Nucleotide ; Riboswitch ; Framycetin (4BOC774388) ; Neomycin (I16QD7X297)
Language	English
Publishing date	2023-03-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkae224
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Article ; Online: Synthesis of Bisubstrate Analogues for RNA Methylation Studies using two Transition-Metal-Catalyzed Reactions.

Coelho, Dylan / Le Corre, Laurent / Bartosik, Karolina / Iannazzo, Laura / Braud, Emmanuelle / Ethève-Quelquejeu, Mélanie

Chemistry (Weinheim an der Bergstrasse, Germany)

2023 Volume 29, Issue 44, Page(s) e202301134

Abstract: RNA methyltransferases (RNA MTases) are a family of enzymes that catalyze the methylation of RNA using the cofactor S-adenosyl-L-methionine. While RNA MTases are promising drug targets, new molecules are needed to fully understand their roles in disease ... ...

Abstract	RNA methyltransferases (RNA MTases) are a family of enzymes that catalyze the methylation of RNA using the cofactor S-adenosyl-L-methionine. While RNA MTases are promising drug targets, new molecules are needed to fully understand their roles in disease and to develop effective drugs that can modulate their activity. Since RNA MTases are suitable for bisubstrate binding, we report an original strategy for the synthesis of a new family of m6A MTases bisubstrate analogues. Six compounds containing a S-adenosyl-L-methionine (SAM) analogue unit covalently tethered by a triazole ring to the N-6 position of an adenosine were synthesized. A procedure using two transition-metal-catalyzed reactions was used to introduce the α-amino acid motif mimicking the methionine chain of the cofactor SAM. First, a copper(I)-catalyzed alkyne-azide iodo-cycloaddition (iCuAAC) reaction afforded the 5-iodo-1,4-disubstituted-1,2,3-triazole which was functionalized by palladium-catalyzed cross-coupling to connect the α-amino acid substituent. Docking studies of our molecules in the active site of the m6A ribosomal MTase RlmJ show that the use of triazole as a linker provides additional interactions and the presence of the α-amino acid chain stabilizes the bisubstrate. The synthetic method developed here enhances the structural diversity of bisubstrate analogues to explore the active site of RNA modification enzymes and to develop new inhibitors.
MeSH term(s)	Methylation ; S-Adenosylmethionine/chemistry ; Methyltransferases ; RNA/metabolism ; Catalysis
Chemical Substances	S-Adenosylmethionine (7LP2MPO46S) ; Methyltransferases (EC 2.1.1.-) ; RNA (63231-63-0)
Language	English
Publishing date	2023-07-06
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1478547-X
ISSN	1521-3765 ; 0947-6539
ISSN (online)	1521-3765
ISSN	0947-6539
DOI	10.1002/chem.202301134
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Article ; Online: Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons.

Kompatscher, Maria / Bartosik, Karolina / Erharter, Kevin / Plangger, Raphael / Juen, Fabian Sebastian / Kreutz, Christoph / Micura, Ronald / Westhof, Eric / Erlacher, Matthias D

Nucleic acids research

2023 Volume 52, Issue 3, Page(s) 1374–1386

Abstract: tRNA superwobbling, used by certain bacteria and organelles, is an intriguing decoding concept in which a single tRNA isoacceptor is used to decode all synonymous codons of a four-fold degenerate codon box. While Escherichia coli relies on three tRNAGly ... ...

Abstract	tRNA superwobbling, used by certain bacteria and organelles, is an intriguing decoding concept in which a single tRNA isoacceptor is used to decode all synonymous codons of a four-fold degenerate codon box. While Escherichia coli relies on three tRNAGly isoacceptors to decode the four glycine codons (GGN), Mycoplasma mycoides requires only a single tRNAGly. Both organisms express tRNAGly with the anticodon UCC, which are remarkably similar in sequence but different in their decoding ability. By systematically introducing mutations and altering the number and type of tRNA modifications using chemically synthesized tRNAs, we elucidated the contribution of individual nucleotides and chemical groups to decoding by the E. coli and M. mycoides tRNAGly. The tRNA sequence was identified as the key factor for superwobbling, revealing the T-arm sequence as a novel pivotal element. In addition, the presence of tRNA modifications, although not essential for providing superwobbling, was shown to delicately fine-tune and balance the decoding of synonymous codons. This emphasizes that the tRNA sequence and its modifications together form an intricate system of high complexity that is indispensable for accurate and efficient decoding.
MeSH term(s)	Anticodon/genetics ; Base Sequence ; Codon/genetics ; Escherichia coli/genetics ; Glycine/genetics ; RNA, Transfer/genetics ; RNA, Transfer, Gly/genetics ; Mycoplasma mycoides/genetics ; Mycoplasma mycoides/metabolism ; RNA, Bacterial/genetics
Chemical Substances	Anticodon ; Codon ; Glycine (TE7660XO1C) ; RNA, Transfer (9014-25-9) ; RNA, Transfer, Gly ; RNA, Bacterial
Language	English
Publishing date	2023-12-05
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad1136
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Article ; Online: Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data.

Berg, Kevin / Lodha, Manivel / Delazer, Isabel / Bartosik, Karolina / Garcia, Yilliam Cruz / Hennig, Thomas / Wolf, Elmar / Dölken, Lars / Lusser, Alexandra / Prusty, Bhupesh K / Erhard, Florian

Nucleic acids research

2024 Volume 52, Issue 7, Page(s) e35

Abstract: Nucleoside analogues like 4-thiouridine (4sU) are used to metabolically label newly synthesized RNA. Chemical conversion of 4sU before sequencing induces T-to-C mismatches in reads sequenced from labelled RNA, allowing to obtain total and labelled RNA ... ...

Abstract	Nucleoside analogues like 4-thiouridine (4sU) are used to metabolically label newly synthesized RNA. Chemical conversion of 4sU before sequencing induces T-to-C mismatches in reads sequenced from labelled RNA, allowing to obtain total and labelled RNA expression profiles from a single sequencing library. Cytotoxicity due to extended periods of labelling or high 4sU concentrations has been described, but the effects of extensive 4sU labelling on expression estimates from nucleotide conversion RNA-seq have not been studied. Here, we performed nucleotide conversion RNA-seq with escalating doses of 4sU with short-term labelling (1h) and over a progressive time course (up to 2h) in different cell lines. With high concentrations or at later time points, expression estimates were biased in an RNA half-life dependent manner. We show that bias arose by a combination of reduced mappability of reads carrying multiple conversions, and a global, unspecific underrepresentation of labelled RNA emerging during library preparation and potentially global reduction of RNA synthesis. We developed a computational tool to rescue unmappable reads, which performed favourably compared to previous read mappers, and a statistical method, which could fully remove remaining bias. All methods developed here are freely available as part of our GRAND-SLAM pipeline and grandR package.
MeSH term(s)	Thiouridine/metabolism ; Thiouridine/chemistry ; RNA-Seq/methods ; Humans ; RNA/genetics ; Sequence Analysis, RNA/methods ; Nucleotides/genetics
Chemical Substances	Thiouridine (13957-31-8) ; RNA (63231-63-0) ; Nucleotides
Language	English
Publishing date	2024-02-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkae120
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Article ; Online: Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post-Synthetic Approach.

Bartosik, Karolina / Debiec, Katarzyna / Czarnecka, Anna / Sochacka, Elzbieta / Leszczynska, Grazyna

Molecules (Basel, Switzerland)

2020 Volume 25, Issue 15

Abstract: The chemical synthesis of modified oligoribonucleotides represents a powerful approach to study the structure, stability, and biological activity of RNAs. Selected RNA modifications have been proven to enhance the drug-like properties of RNA oligomers ... ...

Abstract	The chemical synthesis of modified oligoribonucleotides represents a powerful approach to study the structure, stability, and biological activity of RNAs. Selected RNA modifications have been proven to enhance the drug-like properties of RNA oligomers providing the oligonucleotide-based therapeutic agents in the antisense and siRNA technologies. The important sites of RNA modification/functionalization are the nucleobase residues. Standard phosphoramidite RNA chemistry allows the site-specific incorporation of a large number of functional groups to the nucleobase structure if the building blocks are synthetically obtainable and stable under the conditions of oligonucleotide chemistry and work-up. Otherwise, the chemically modified RNAs are produced by post-synthetic oligoribonucleotide functionalization. This review highlights the post-synthetic RNA modification approach as a convenient and valuable method to introduce a wide variety of nucleobase modifications, including recently discovered native hypermodified functional groups, fluorescent dyes, photoreactive groups, disulfide crosslinks, and nitroxide spin labels.
MeSH term(s)	Models, Molecular ; Nucleic Acid Conformation ; Oligoribonucleotides/chemical synthesis ; Oligoribonucleotides/chemistry ; Organophosphorus Compounds/chemistry ; RNA/chemistry ; RNA Stability
Chemical Substances	Oligoribonucleotides ; Organophosphorus Compounds ; phosphoramidite ; RNA (63231-63-0)
Language	English
Publishing date	2020-07-23
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules25153344
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Article ; Online: Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition.

Xu, Xiaochen / Egger, Michaela / Chen, Hao / Bartosik, Karolina / Micura, Ronald / Ren, Aiming

Nucleic acids research

2021 Volume 49, Issue 12, Page(s) 7139–7153

Abstract: Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind ... ...

Abstract	Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson-Crick base pair to junction J2. Xanthine inserts between a G-U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.
MeSH term(s)	Binding Sites ; Cations, Divalent ; Crystallography, X-Ray ; Ligands ; Magnesium/chemistry ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; RNA Folding ; Riboswitch ; Xanthine/chemistry
Chemical Substances	Cations, Divalent ; Ligands ; Riboswitch ; Xanthine (1AVZ07U9S7) ; Magnesium (I38ZP9992A)
Language	English
Publishing date	2021-06-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab486
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Article: Synthesis of various substituted 5-methyluridines (xm5U) and 2-thiouridines (xm5s2U) via nucleophilic substitution of 5-pivaloyloxymethyluridine/2-thiouridine

Bartosik, Karolina / Grazyna Leszczynska

Tetrahedron letters. 2015 Nov. 25, v. 56

2015

Abstract: 5-Pivaloyloxymethyluridine and its 2-thio analogue have been utilized as convenient substrates for the synthesis of various 5-methyluridines (xm5U) and 5-methyl-2-thiouridines (xm5s2U). The pivaloyloxy group (OPiv) located at the pseudobenzylic position ... ...

Abstract	5-Pivaloyloxymethyluridine and its 2-thio analogue have been utilized as convenient substrates for the synthesis of various 5-methyluridines (xm5U) and 5-methyl-2-thiouridines (xm5s2U). The pivaloyloxy group (OPiv) located at the pseudobenzylic position was effectively substituted with a series of nucleophiles: ammonia, primary and secondary amines including secondary cyclic amines, tetrabutylammonium salts of amino acids, an alkoxide and a thiolate.
Keywords	Lewis bases ; amino acids ; ammonia ; chemical reactions ; chemical structure ; salts ; secondary amines ; tetrabutylammonium compounds
Language	English
Dates of publication	2015-1125
Size	p. 6593-6597.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	204287-3
ISSN	1873-3581 ; 0040-4039
ISSN (online)	1873-3581
ISSN	0040-4039
DOI	10.1016/j.tetlet.2015.10.023
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Article ; Online: Post-synthetic conversion of 5-pivaloyloxymethyluridine present in a support-bound RNA oligomer into biologically relevant derivatives of 5-methyluridine.

Bartosik, Karolina / Sochacka, Elzbieta / Leszczynska, Grazyna

Organic & biomolecular chemistry

2017 Volume 15, Issue 9, Page(s) 2097–2103

Abstract: A post-synthetic reaction of 5-pivaloyloxymethyluridine (present in a support-bound RNA oligomer) with various nucleophilic reagents furnished efficiently the corresponding products bearing one of the tRNA wobble 5-methyluridines ( ... ...

Abstract	A post-synthetic reaction of 5-pivaloyloxymethyluridine (present in a support-bound RNA oligomer) with various nucleophilic reagents furnished efficiently the corresponding products bearing one of the tRNA wobble 5-methyluridines (mnm
Language	English
Publishing date	2017-03-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2097583-1
ISSN	1477-0539 ; 1477-0520
ISSN (online)	1477-0539
ISSN	1477-0520
DOI	10.1039/c6ob02674e
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