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

J Org Chem. 2015 Oct 16;80(20):10108-18. doi: 10.1021/acs.joc.5b01719. Epub 2015 Sep 30.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amides / chemistry*
  • Humans
  • Nucleic Acid Conformation
  • Phosphoric Acids / chemistry*
  • RNA / chemical synthesis*
  • RNA / chemistry*
  • RNA / metabolism
  • RNA Nucleotidyltransferases / antagonists & inhibitors
  • RNA Nucleotidyltransferases / chemistry*
  • RNA Splicing
  • Solid-Phase Synthesis Techniques

Substances

  • Amides
  • Phosphoric Acids
  • RNA
  • phosphoramidic acid
  • RNA Nucleotidyltransferases
  • lariat debranching enzyme