Improved Denaturation of Small RNA Duplexes and Its Application for Northern Blotting

  • C. Jake Harris
  • David C. Baulcombe
  • Attila MolnarEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1580)


Small RNAs (sRNAs) are short (18–30 nucleotide) noncoding RNA molecules, which control gene expression and pathogen response in eukaryotes. They are associated with and guide nucleases to target nucleic acids by nucleotide base pairing. We found that current techniques for small RNA detection are adversely affected by the presence of complementary RNA. Thus we established FDF-PAGE (fully denaturing formaldehyde polyacrylamide gel electrophoresis), which dramatically improves denaturation efficiency and subsequently the detection of sequestered sRNAs.

Key words

Small RNA Sequestration Polyacrylamide gel electrophoresis Denaturation Improved detection 



C.J.H was supported by a BBSRC PhD Studentship. D.C.B. is the Royal Society Edward Penley Abraham Research Professor. This work was supported by the ERC Advanced Investigator grant ERC-2013-AdG 340642 TRIBE. A.M. is a Chancellor’s Fellow at the University of Edinburgh.


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • C. Jake Harris
    • 1
  • David C. Baulcombe
    • 1
  • Attila Molnar
    • 2
    Email author
  1. 1.Department of Plant SciencesUniversity of CambridgeCambridgeUK
  2. 2.School of Biological SciencesUniversity of EdinburghEdinburghUK

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