UNIT 7.3 Differential Staining of DNA and RNA

  1. Zbigniew Darzynkiewicz1,
  2. Gloria Juan1,
  3. Edward F. Srour2

Published Online: 1 NOV 2004

DOI: 10.1002/0471142956.cy0703s30

Current Protocols in Cytometry

Current Protocols in Cytometry

How to Cite

Darzynkiewicz, Z., Juan, G. and Srour, E. F. 2004. Differential Staining of DNA and RNA. Current Protocols in Cytometry. 30:7.3:7.3.1–7.3.16.

Author Information

  1. 1

    New York Medical College, Valhalla, New York

  2. 2

    Indiana University School of Medicine, Indianapolis, Indiana

Publication History

  1. Published Online: 1 NOV 2004
  2. Published Print: OCT 2004


Cell cycle analysis by means of differential staining of RNA and DNA permits determination of RNA content, which in turn allows one to discriminate G0 versus G1 cells and to detect cell differentiation. This unit presents two protocols for differential staining, one using the metachromatic dye acridine orange (AO) and the other a combination of pyronin Y (PY) and Hoechst 33342. Each method has its advantages and limitations, and the Hoechst-PY method is not applicable to single-laser instruments. A third protocol describes staining of viable cells to identify/sort hematopoietic stem cells, with an alternative that includes simultaneous immunostaining.


  • flow cytometry;
  • cell cycle analysis;
  • nucleic acid staining;
  • acridine orange;
  • DNA staining; RNA staining;
  • hematopoietic stem cells;
  • pyronin Y;
  • Hoechst 33342