Northern blot detection of endogenous small RNAs (approximately14 nt) in bacterial total RNA extracts

Nucleic Acids Res. 2010 Aug;38(14):e147. doi: 10.1093/nar/gkq437. Epub 2010 May 26.


Here we describe a northern blot procedure that allows the detection of endogenous RNAs as small as approximately 14 nt in total RNA extracts from bacteria. RNAs that small and as part of total bacterial RNA extracts usually escape detection by northern blotting. The approach combines LNA probes 5'-digoxigenin-endlabeled for non-radioactive probe detection with 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide-mediated chemical crosslinking of RNAs to nylon membranes, and necessitates the use of native PAGE either with the TBE or MOPS buffer system.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacillus subtilis / genetics
  • Base Sequence
  • Blotting, Northern / methods*
  • Buffers
  • Cross-Linking Reagents
  • Escherichia coli / genetics
  • Ethyldimethylaminopropyl Carbodiimide / chemistry
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Nucleic Acid Denaturation
  • Oligoribonucleotides / chemistry
  • RNA, Bacterial / analysis*
  • RNA, Bacterial / chemistry
  • RNA, Untranslated / analysis*
  • RNA, Untranslated / chemistry


  • Buffers
  • Cross-Linking Reagents
  • Oligoribonucleotides
  • RNA, Bacterial
  • RNA, Untranslated
  • Ethyldimethylaminopropyl Carbodiimide