Glyoxal‐Linked Nucleotides and DNA for Bioconjugations and Crosslinking with Arginine‐Containing Peptides and Proteins

Leone, Denise‐Liu'; Pohl, Radek; Hubálek, Martin; Kadeřábková, Marta; Krömer, Matouš; Sýkorová, Veronika; Hocek, Michal

doi:10.1002/chem.202104208

Cited by 10 publications

(8 citation statements)

References 65 publications

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“…Glutaraldehyde (Figure a) has been used extensively for cross-linking proteins, but studies with RNA are scarce, although it is likely that it can cross-link nucleic acids. The dialdehyde glyoxal has recently been used as well for temporary caging of nucleobases and when incorporated in the backbone of DNA it was shown to cross-link to proteins . Formaldehyde forms adducts and cross-links with biomolecules that protects them from degradation.…”

Section: Chemistry Of Current Technologiesmentioning

confidence: 99%

Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications

Velema

2023

JACS Au

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In recent years, RNA has emerged as a multifaceted biomolecule that is involved in virtually every function of the cell and is critical for human health. This has led to a substantial increase in research efforts to uncover the many chemical and biological aspects of RNA and target RNA for therapeutic purposes. In particular, analysis of RNA structures and interactions in cells has been critical for understanding their diverse functions and druggability. In the last 5 years, several chemical methods have been developed to achieve this goal, using chemical cross-linking combined with high-throughput sequencing and computational analysis. Applications of these methods resulted in important new insights into RNA functions in a variety of biological contexts. Given the rapid development of new chemical technologies, a thorough perspective on the past and future of this field is provided. In particular, the various RNA cross-linkers and their mechanisms, the computational analysis and challenges, and illustrative examples from recent literature are discussed.

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Section: Chemistry Of Current Technologiesmentioning

confidence: 99%

Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications

Velema

2023

JACS Au

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“…This was utilized to prepare heterodimeric DVD‐IgG1 s with two different cargos using a one‐pot protocol, demonstrating the strength of this method. In a very recent study, Hocek and co‐workers enzymatically incorporated phenylglyoxal modified nucleoside triphosphates into oligonucleotides for conjugation of the oligonucleotides to arginine‐containing peptides and proteins [78] . Arginine conjugation has also been used for identification of highly reactive Arg residues on proteins using a azide‐cyclohexanedione probe for reaction and enrichment [79] .…”

Section: Alkaline Amino Acid Residuesmentioning

confidence: 99%

“…In a very recent study, Hocek and co-workers enzymatically incorporated phenylglyoxal modified nucleoside triphosphates into oligonucleotides for conjugation of the oligonucleotides to arginine-containing peptides and proteins. [78] Arginine conjugation has also been used for identification of highly reactive Arg residues on proteins using a azide-cyclohexanedione probe for reaction and enrichment. [79] Furthermore, Arg-selective crosslinkers have been used to improve structural mass spectrometry analysis of proteins containing Lys-deficient regions.…”

Section: Argininementioning

confidence: 99%

Chemical Conjugation to Less Targeted Proteinogenic Amino Acids

2022

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Protein bioconjugates are in high demand for applications in biomedicine, diagnostics, chemical biology and bionanotechnology. Proteins are large and sensitive molecules containing multiple different functional groups and in particular nucleophilic groups. In bioconjugation reactions it can therefore be challenging to obtain a homogeneous product in high yield. Numerous strategies for protein conjugation have been developed, of which a vast majority target lysine, cysteine and to a lesser extend tyrosine. Likewise, several methods that involve recombinantly engineered protein tags have been reported. In recent years a number of methods have emerged for chemical bioconjugation to other amino acids and in this review, we present the progress in this area.

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“…A reactive glyoxal functional group was incorporated by the Sonogashira coupling of 5‐ethynyl‐dUTP and a glyoxyl‐substituted aryl bromide using a Pd/TPPTS catalyst system (Scheme 24). [68] The resulting glyoxal‐substituted nucleotide derivatives were obtained in modest yield. The glyoxal moiety undergoes selective bioconjugation with the guanidine group of arginine.…”

Section: Applications Of Hydrophilic Pd Catalysts In Modification Of ...mentioning

confidence: 99%

Covalent Modification of Nucleobases using Water‐Soluble Palladium Catalysts

Shaughnessy

2022

The Chemical Record

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Nucleosides represent one of the key building blocks of biochemistry. There is significant interest in the synthesis of nucleoside-derived materials for applications as probes, biochemical models, and pharmaceuticals. Palladium-catalyzed cross-coupling reactions are effective methods for making covalent modification of carbon and nitrogen sites on nucleobases under mild conditions. Water-soluble catalysts derived from palladium and hydrophilic ligands, such as tris(3-sulfonatophenyl)phosphine trisodium (TPPTS), are efficient catalysts for a range of coupling reactions of unprotected halonucleosides. Over the past two decades, these methods have been extended to direct functionalization of halonucleotides, as well as RNA and DNA oligonucleotides (ONs) containing halogenated bases. These methods can be run under biocompatible conditions, including examples of Suzuki coupling of modified DNA in whole cells and tissue samples. In this account, development of this methodology by our group and others is highlighted along with the extension of these catalyst systems to modification of nucleotides and ONs.

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Glyoxal‐Linked Nucleotides and DNA for Bioconjugations and Crosslinking with Arginine‐Containing Peptides and Proteins

Cited by 10 publications

References 65 publications

Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications

Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications

Chemical Conjugation to Less Targeted Proteinogenic Amino Acids

Covalent Modification of Nucleobases using Water‐Soluble Palladium Catalysts

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