Affinity capillary electrophoresis with magnetic beads for multiplex quantitative analysis of bacterial 16S rRNA

Ken Adachi, Masahiro Yamaguchi, Makoto Nakashige, Takahiro Kanagawa, Masaki Torimura, Satoshi Tsuneda, Yuji Sekiguchi, Naohiro Noda*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


We have developed a novel method for microbial community analysis of bacterial 16S rRNAs based on affinity capillary electrophoresis using 16S rRNA-conjugated magnetic beads. We called this method magnetic beads affinity capillary electrophoresis (MB-ACE) which can be used for sequential and quantitative analysis of 16S rRNA. In this method, RNA extracted from a microbial community is biotin-modified and mixed with streptavidin-modified paramagnetic beads. This mixture is then injected into a capillary and localized in the middle of the capillary using a magnet held adjacent to the capillary. Subsequently, a fluorescent-labeled probe to detect the target 16S rRNA is injected into the capillary, and voltage is applied. The probe trapped on the RNA is dissociated by formamide and detected at its anodic end by measuring the fluorescence. Next, another fluorescent probe is injected, and thus the target 16S rRNA in the sample is quantified one by one. MB-ACE was used for the quantification of the 16S rRNAs of Escherichia coli and Pseudomonas putida in samples that were prepared by mixing RNA extracted from activated sludge and 16S rRNAs prepared by in vitro transcription. The two types of 16S rRNAs were quantified, indicating that MB-ACE can be used for sequential quantitative analysis of bacterial 16S rRNAs.

Original languageEnglish
Pages (from-to)662-667
Number of pages6
JournalJournal of Bioscience and Bioengineering
Issue number6
Publication statusPublished - 2009 Jun


  • 16S rRNA
  • Affinity capillary electrophoresis
  • Magnetic beads
  • Microbial community analysis
  • Quantitative detection

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology


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