Conjugation of RNA <i>via</i> 2′-OH acylation: Mechanisms determining nucleotide reactivity

Jash, Biswarup; Kool, Eric T.

doi:10.1039/d2cc00660j

Cited by 11 publications

(9 citation statements)

References 35 publications

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“…19 The highest stereoselectivity was observed for compound 17, at 25.2:1 (R/S), more than 6-fold greater than that observed for lead compound 8. Reactivities also varied greatly, with the most reactive compounds (3,(6)(7)(8)10,13,14) achieving the target range of conversion at remarkably low concentrations of 100 μM. This is especially noteworthy, given that many RNA acylation experiments employ reagents at ca.…”

Section: T H Imentioning

confidence: 99%

“…The group is also essential to RNA splicing mechanisms, and it defines the site of instability in RNA, as thermal and enzymatic chain cleavage mechanisms begin with this nucleophilic hydroxyl group . Because the 2′–OH group occurs at virtually every position of RNA, it also can act as a useful handle for analysis and modification of the polymer. , The unusually low p K a of this group enables it to act as a nucleophile toward activated carbonyl and sulfonyl species at neutral pH. − Appropriately designed acyl and alkyl acylimidazoles and aryl isatoic anhydrides are widely used to acylate this group in trace yields for mapping the folding and interactions of RNA, , and reagents that can provide high-yield reactions at 2′–OH offer useful methods for conjugation of the biopolymer. , …”

Section: Introductionmentioning

confidence: 99%

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Second-Generation Chiral Amino Acid Derivatives Afford High Stereoselectivity and Stability in Aqueous RNA Acylation

Shioi,

Chatterjee,

Xiao

et al. 2024

J. Org. Chem.

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Activated acyl species have proven versatile in the esterification of 2′–OH groups in RNA, enabling structure mapping, caging, profiling, and labeling of the biopolymer. Nearly all reagents developed for this reaction have been achiral; however, a recent study reported that simple chiral amino acid acylimidazole derivatives could yield diastereoselective reactions at RNA 2′–OH in water, enabling up to 4:1 selectivity in screening. Here, we investigated the effect of steric bulk on the stereoselectivity of RNA reaction and on the stability of adducts with a library of 36 chiral acylimidazole scaffolds with increasing steric demand. The results document the highest stereoselectivity yet achieved in RNA acylation reactions, with as high as >99:1 diastereoselectivity at >70% conversion. Also notably, the bulky adducts were found to have markedly improved stability on RNA.

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Section: T H Imentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Second-Generation Chiral Amino Acid Derivatives Afford High Stereoselectivity and Stability in Aqueous RNA Acylation

Shioi,

Chatterjee,

Xiao

et al. 2024

J. Org. Chem.

Self Cite

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“…This was attributed to the substantial difference in p K a (∼6–7 for phosphate monoester and ∼1 for phosphate diester) . The 2′-OH position (yellow, Figure ) can be acylated with activated carbonyl reagents, which forms the basis of SHAPE, a widely used method to determine RNA secondary structure. ,, More recent bifunctional acylators target the 2′-OH position to establish cross-linking. − The unusual nucleophilicity of the 2′-OH position has been attributed to oxyanion formation at this position due to inductive effects provided by neighboring 3′ and 4′ oxygens and the nucleobase nitrogen. , Pyrimidine bases can undergo [2 + 2] photocycloadditions using their C5–C6 double bond (blue, Figure ). This feature has been extensively exploited with psoralen cross-linkers .…”

Section: Chemistry Of Current Technologiesmentioning

confidence: 99%

“… 40 − 42 The unusual nucleophilicity of the 2′-OH position has been attributed to oxyanion formation at this position due to inductive effects provided by neighboring 3′ and 4′ oxygens and the nucleobase nitrogen. 43 , 44 Pyrimidine bases can undergo [2 + 2] photocycloadditions using their C5–C6 double bond (blue, Figure 1 ). 28 This feature has been extensively exploited with psoralen cross-linkers.…”

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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“…[39][40][41] The unusual nucleophilicity of the 2'-OH position has been attributed to oxyanion formation at this position due to inductive effects provided by neighboring 3' and 4' oxygens and the nucleobase nitrogen. 42,43 Pyrimidine bases can undergo [2+2] photocycloadditions using their C5-C6 double bond (blue, Fig. 1).…”

Section: Rna's Chemical Reactivitymentioning

confidence: 99%

Chemical RNA Crosslinking: Mechanisms, Computational Analysis and Biological Applications

Velema

2022

Preprint

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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 crosslinking 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 review on the past and future of this field is provided. In particular, the various RNA crosslinkers and their mechanisms, the computational analysis and challenges and illustrative examples from recent literature are discussed.

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Conjugation of RNA via 2′-OH acylation: Mechanisms determining nucleotide reactivity

Abstract: The acylation reactivity of RNA 2'-OH groups has proven broadly useful for labeling and mapping RNA. Here we perform kinetics studies to test the mechanisms governing this reaction, and we...

Cited by 11 publications

References 35 publications

Second-Generation Chiral Amino Acid Derivatives Afford High Stereoselectivity and Stability in Aqueous RNA Acylation

Second-Generation Chiral Amino Acid Derivatives Afford High Stereoselectivity and Stability in Aqueous RNA Acylation

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

Chemical RNA Crosslinking: Mechanisms, Computational Analysis and Biological Applications

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