PABLO analysis of RNA: 5'-phosphorylation state and 5'-end mapping

Methods Enzymol. 2008:447:83-98. doi: 10.1016/S0076-6879(08)02205-2.

Abstract

Recent studies have revealed that 5'-end-dependent RNA degradation in prokaryotes is triggered by pyrophosphate removal from the 5'-terminus to generate a monophosphorylated intermediate that is readily degraded. This chapter describes how to examine the 5'-phosphorylation state of any specific bacterial RNA by PABLO analysis. The method is based on the ability of monophosphorylated, but not triphosphorylated, RNA 5'-ends to undergo splinted ligation to a DNA oligonucleotide when juxtaposed by base pairing to a bridging oligonucleotide. PABLO analysis not only makes it possible to quantify the proportion of a particular RNA that is monophosphorylated in bacterial cells but also provides a more reliable method than primer extension for high-resolution mapping of RNA 5'-termini.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Sequence
  • Blotting, Northern
  • Diphosphates / isolation & purification
  • Electrophoresis, Polyacrylamide Gel
  • Molecular Sequence Data
  • Phosphorylation
  • RNA, Messenger / chemistry
  • RNA, Messenger / metabolism*
  • Reverse Transcriptase Polymerase Chain Reaction

Substances

  • Diphosphates
  • RNA, Messenger