Design, Synthesis, and Properties of Phosphoramidate 2',5'-Linked Branched RNA: Toward the Rational Design of Inhibitors of the RNA Lariat Debranching Enzyme

Overview

Journal J Org Chem

Publisher American Chemical Society

Specialty Chemistry

Date 2015 Sep 18

PMID 26378468

Citations 4

Authors

Nobuhiro Tago

Adam Katolik

Nathaniel E Clark

Eric J Montemayor

Kohji Seio

Mitsuo Sekine

P John Hart

Masad J Damha

Affiliations

Soon will be listed here.

Abstract

Two RNA fragments linked by means of a 2',5' phosphodiester bridge (2' hydroxyl of one fragment connected to the 5' hydroxyl of the other) constitute a class of nucleic acids known as 2'-5' branched RNAs (bRNAs). In this report we show that bRNA analogues containing 2'-5' phosphoramidate linkages (bN-RNAs) inhibit the lariat debranching enzyme, a 2',5'-phosphodiesterase that has recently been implicated in neurodegenerative diseases associated with aging. bN-RNAs were efficiently generated using automated solid-phase synthesis and suitably protected branchpoint building blocks. Two orthogonally removable groups, namely the 4-monomethoxytrityl (MMTr) group and the fluorenylmethyl-oxycarbonyl (Fmoc) groups, were evaluated as protecting groups of the 2' amino functionality. The 2'-N-Fmoc methodology was found to successfully produce bN-RNAs on solid-phase oligonucleotide synthesis. The synthesized bN-RNAs resisted hydrolysis by the lariat debranching enzyme (Dbr1) and, in addition, were shown to attenuate the Dbr1-mediated hydrolysis of native bRNA.

Citing Articles

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Crystal Structure of the RNA Lariat Debranching Enzyme Dbr1 with Hydrolyzed Phosphorothioate RNA Product.

Clark N, Katolik A, Welch A, Schorl C, Holloway S, Schuermann J Biochemistry. 2022; 61(24):2933-2939.

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Synthesis of comb-shaped DNA using a non-nucleosidic branching phosphoramidite.

Ellipilli S, Phillips J, Heemstra J Org Biomol Chem. 2018; 16(25):4659-4664.

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Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1.

Clark N, Katolik A, Roberts K, Taylor A, Holloway S, Schuermann J Proc Natl Acad Sci U S A. 2016; 113(51):14727-14732.

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Mechanistic insights into the manganese-dependent phosphodiesterase activity of yeast Dbr1 with bis-p-nitrophenylphosphate and branched RNA substrates.

Schwer B, Khalid F, Shuman S RNA. 2016; 22(12):1819-1827.

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