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Uracil‐Selective Cross‐Linking in RNA and Inhibition of miRNA Function by 2‐Amino‐6‐vinyl‐7‐deazapurine Deoxynucleosides

MicroRNAs (miRNAs) regulate gene expression through RNA interference. Consequently, miRNA inhibitors, such as anti‐miRNA oligonucleotides (AMOs), have attracted attention for treating miRNA overexpression. To achieve efficient inhibition, we developed 2‐amino‐6‐vinylpurine (AVP) nucleosides that for...

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Published in:Chembiochem : a European journal of chemical biology 2024-11, Vol.25 (21), p.e202400417-n/a
Main Authors: Soemawisastra, Nadya, Okamura, Hidenori, Abdelhady, Ahmed Mostafa, Onizuka, Kazumitsu, Ozawa, Mamiko, Nagatsugi, Fumi
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container_title Chembiochem : a European journal of chemical biology
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creator Soemawisastra, Nadya
Okamura, Hidenori
Abdelhady, Ahmed Mostafa
Onizuka, Kazumitsu
Ozawa, Mamiko
Nagatsugi, Fumi
description MicroRNAs (miRNAs) regulate gene expression through RNA interference. Consequently, miRNA inhibitors, such as anti‐miRNA oligonucleotides (AMOs), have attracted attention for treating miRNA overexpression. To achieve efficient inhibition, we developed 2‐amino‐6‐vinylpurine (AVP) nucleosides that form covalent bonds with uridine counterparts in RNA. We demonstrated that mRNA cross‐linked with AVP‐conjugated antisense oligonucleotides with AVP were protected from gene silencing by exogenous miRNA. However, endogenous miRNA function could not be inhibited in cells, probably because of slow cross‐linking kinetics. We recently developed ADpVP, an AVP derivative bearing a 7‐propynyl group – which boasts faster reaction rate than the original AVP. Here, we synthesized dADpVP – a deoxy analog of ADpVP – through a simplified synthesis protocol. Evaluation of the cross‐linking reaction revealed that the reaction kinetics of dADpVP were comparable to those of ADpVP. In addition, structural analysis of the cross‐linked adduct discovered N3 linkage against uridine. Incorporating dADpVP into two types of miRNA inhibitors revealed a marginal impact on AMO efficacy yet improved the performance of target site blockers. These results indicate the potential of cross‐linking nucleosides for indirect miRNA function inhibition. Herein, we report the synthesis of a cross‐linkable nucleoside (2‐amino‐7‐deaza‐7‐propynyl‐6‐vinylpurine deoxyriboside; dADpVP). dADpVP selectively reacted with counter uridine with high reactivity upon duplex hybridization. The structural determination of the cross‐linked adduct revealed that cross‐linking occurred at the N‐3 of uridine. We investigated if the incorporation of cross‐linking nucleosides into microRNA inhibitors enabled a more effective inhibition of endogenous miRNA function.
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subjects Anti-miRNA
Antisense oligonucleotides
Antisense RNA
Chemical synthesis
Covalent bonds
Cross-linking
Cross-Linking Reagents - chemical synthesis
Cross-Linking Reagents - chemistry
Gene expression
Gene silencing
Humans
Impact analysis
Inhibitors
Kinetics
Linkage analysis
MicroRNAs
MicroRNAs - antagonists & inhibitors
MicroRNAs - chemistry
MicroRNAs - metabolism
miRNA
miRNA inhibition
Nucleobase analogs
Nucleosides
Oligonucleotides
Purines - chemistry
Purines - pharmacology
Reaction kinetics
Ribonucleic acid
RNA
RNA - chemistry
RNA - metabolism
RNA-mediated interference
Structural analysis
Uracil
Uracil - analogs & derivatives
Uracil - chemistry
Uracil - pharmacology
Uridine
Vinyl Compounds - chemistry
Vinyl Compounds - pharmacology
title Uracil‐Selective Cross‐Linking in RNA and Inhibition of miRNA Function by 2‐Amino‐6‐vinyl‐7‐deazapurine Deoxynucleosides
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