Chemi-Northern: a versatile chemiluminescent northern blot method for analysis and quantitation of RNA molecules

Katherine M. Mckenney, Robert P. Connacher, Elise B. Dunshee, Aaron C. Goldstrohm

Research output: Contribution to journalArticlepeer-review

Abstract

This report describes a chemiluminescence-based detection method for RNAs on northern blots, designated Chemi- Northern. This approach builds on the simplicity and versatility of northern blotting, while dispensing of the need for expensive and cumbersome radioactivity. RNAs are first separated by denaturing gel electrophoresis, transferred to a nylon membrane, and then hybridized to a biotinylated RNA or DNA antisense probe. Streptavidin conjugated with horseradish peroxidase and enhanced chemiluminescence substrate are then used to detect the probe bound to the target RNA. Our results demonstrate the versatility of this method in detecting natural and engineered RNAs expressed in cells, including messenger and noncoding RNAs. We show that Chemi-Northern detection is sensitive and fast, detecting attomole amounts of RNA in as little as 1 sec, with high signal intensity and low background. The dynamic response displays excellent linearity. Using Chemi-Northern, we measure the reproducible, statistically significant reduction of mRNA levels by human sequence-specific RNA-binding proteins, PUM1 and PUM2. Additionally, wemeasure the interaction of the poly(A) binding protein, PABPC1, with polyadenylated mRNA. Thus, the Chemi-Northern method provides a versatile, simple, and costeffective method to enable researchers to analyze expression, processing, binding, and decay of RNAs.

Original languageEnglish (US)
Pages (from-to)448-462
Number of pages15
JournalRNA
Volume30
Issue number4
DOIs
StatePublished - Apr 2024

Bibliographical note

Publisher Copyright:
© 2024 McKenney et al.

Keywords

  • RNA
  • biotinylation
  • chemiluminescence
  • northern blot
  • streptavidin

PubMed: MeSH publication types

  • Journal Article

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