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

Methods Mol Biol. 2017:1580:1-6. doi: 10.1007/978-1-4939-6866-4_1.

Abstract

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.

Keywords: Denaturation; Improved detection; Polyacrylamide gel electrophoresis; Sequestration; Small RNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Blotting, Northern / methods*
  • Electrophoresis, Polyacrylamide Gel / methods*
  • Formaldehyde / chemistry*
  • Nucleic Acid Denaturation*
  • Nucleic Acid Hybridization / methods
  • RNA, Complementary / analysis
  • RNA, Small Untranslated / analysis*
  • Urea / chemistry

Substances

  • RNA, Complementary
  • RNA, Small Untranslated
  • Formaldehyde
  • Urea