Fluorescence In Situ Hybridization with Quantum Dot Labels in E. coli Cells

Yang Liu, Zhiyuan Han, Suresh Sarkar, Andrew M. Smith

Research output: Chapter in Book/Report/Conference proceedingChapter


In this chapter we describe the use of fluorescent quantum dots (QDs) as labels for microbial mRNA transcripts using fluorescence in situ hybridization (FISH). Unlike organic dyes, which are the standard labels in modern FISH methods, QDs provide fluorescence signals that are much brighter and resistant to photobleaching, with an expanded spectral range for multiplexing. We describe the preparation of QDs with compact sizes necessary for accurate labeling, their application for analyzing lacZ transcripts in Escherichia coli cells using FISH, and an assessment of signal stability. We further discuss differences between methods for mammalian cells and bacteria, for which individual nucleic acids cannot be discretely counted due to the small cell size and the optical diffraction limit.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages15
StatePublished - 2021

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Cytology
  • Imaging
  • Microscopy
  • Nanocrystal
  • Nanomedicine
  • Nanotechnology
  • Nucleic acid
  • Single-cell
  • Single-molecule

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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