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Sometimes the bleed-through of the blue nuclear label into the green channel seems higher than usual. There is a real phenomenon behind this increase; it's called photoconversion.

It is known for the blue nuclear labels DAPI, Hoechst and Vybrant DyeCyle Violet, but can happen to other labels too. Red-shifts of up to 80 nm have been observed in real samples, e.g. cy5-Beta-catenin on polyvinylidene (PVDF) membrane.

Note that the in-solution values stated in reference may differ from spectra in other conditions.

DAPI, Hoechst 33258 and Vybrant DyeCyle Violet Exhibit Photoconversion

  • Photoconversion by exposure to UV light
    • The 405 nm laser is far enough from the UV to not cause this
  • Photoconverted derivatives have low photostability
    • Bleached easily
    • Photobleaching of DAPI & Hoechst 33258 recovers 50% in 60 min
    • Photoconverted derivatives bleach at the same rate
  • The photoconversion is reversible
    • After the photoconversion reversal an equilibrium state lasts for at least 2 more hours
  • The photoconversion is dose dependent
    • The dose response of DAPI is stronger
    • 4x increase in 100 s
    • (Hoechst 2x in the same time)
  • Hydroxen peroxide induces similar photo-oxidation
    • Red-shift
    • Takes 4 h for Hoechst
    • 1.5 h for DAPI
    • ReversibleHigh concentrations of DAPI & Hoechst 33258 diminish blue signal
      • Self-quenching
      • Signal in RNA increased


Spectral Characteristics of the Red-shifted Label

  • Excitation at 450-490 nm
  • Emission at 480-600 nm
    • Maxima at 540 nm

1      DAPI Spectral Shift



Too High Label Concentrations Can Diminish Signal

  • High concentrations of DAPI & Hoechst 33258 diminish blue signal
  • Self-quenching
  • Signal in RNA increased

DAPI Spectral Shift

  • DAPI binding with DNA is solution specific.
  • It can change from groove-binding to intercalation.
  • It can also induce polymer-dye adducts.
  • Emission maximum blue-shifts when complexed with DNA.



DAPI Spectral Characteristics

  • Excitation maxima at 364 nm
  • Emission maximum at 454 nm

DAPI Red-shift Conditions

  • DAPI also binds to RNA
  • Emission maximum red-shifts when bound to RNA.
    • Binding to RNA minor groove.
    • Complexation with polyA-polyU.
  • Dissociation 100 times faster than from DNA.
  • High dye/phosphate ratio (1:10) reveals a new binding form.
  • Emission New emission maximum 540 nm.
  • Binding of DAPI to sites in polynucleotides in proximity to previously bound DAPI.
    • Disappears if background electrolyte is 0.4 M KCl.
    • Distrupts DAPI-DAPI electrostatic interactions.
    • DAPI-polyadenylic acid (polyA).
    • DAPI-Polyphosphate (polyppolyP)
      • Excitation 415 nm.
      • Emission 550 nm.
    • Inositol phosphates (IP5 & IP6)
      • Emission 550 nm.
    • Heparin
      • Emission 550 nm.
    • Amorphous calcium phosphate (ACP)
      • Emission 550 nm.
      • Not Hydroxyapatite (HAp)
  • “Red-shifted DAPI fluorescence is not due to specific substrate chemistry, but indicates the presence of a high density of negatively-charged surfaces or molecules that locally concentrate DAPI. This local, increased DAPI concentration enables DAPI–DAPI interactions and its resultant red-shifted fluorescence.”
  • High concentrations of glycerol (as mounting media) are proportional to the level of DAPI photoconversion.
  • DAPI photoconversion rate has two components
    • Fast half-life < 10 s
    • Slow half-life > 60 s
    • Both are UV illumination intensity dependent (non-linear)



Hoechst 33258 Red-shift

  • Excitation 355 nm
  • Emission 465 nm
  • Exposure to UV causes both photobleaching and photoconversion
    • Emission New emission maxima 540 nm
  • Protonation of the dye
    • Also by exposure to hydrogen peroxide
  • Similar properties in acidic environments (pH 0.5-3.0)
    • Quantum yield drops 80-fold
  • QY increased 20-fold in pH 4.5
  • Acid treatment reversible
  • Equilibrium at 60 min past UV exposure
  • Red-shifted protonated form shows up in nucleoli
    • RNA-binding
      • Excitation 369 nm
      • Emission 437 nm

Hoechst Spectral Characteristics

  • Excitation 355 nm
  • Emission 465 nm


Vybrant DyeCyle Violet



 Vybrant DyeCyle Violet also exhibits the photoconversion red-shift of it's spectra.

Mitigating the Red-shift

  • Minimize UV intensity when imaging the blue nuclear labels.
    • Total dose or exposure time?
  • Use low label concentration.
  • Use low glycerol concentration in mounting media.
  • Acquire blue nuclear channels last to minimize green channel false positives.
  • Use alternate nuclear dyes like DRAQ5 or RedDot which fluoresce in the far red region.
  • Red-shifts of up to 80 nm have been observed in real samples
    • cy5-Beta-catenin on polyvinylidene (PVDF) membrane
    • The in-solution values stated in reference may differ from spectra in other conditions

5      Spectral Red-shift in other labels?




  • “A cautionary (spectral) tail: red-shifted fluorescence by DAPI–DAPI interactions”; Sidney Omelon, John Georgiou, Wouter Habraken; Biochemical Society Transactions Feb 09, 2016, 44 (1) 46-49; DOI: 10.1042/BST20150231
  • “UV-induced Spectral Shift and Protonation of DNA Fluorescent Dye Hoechst 33258”; Dominika Żurek-Biesiada & Piotr Waligórski & Jurek W. Dobrucki; J Fluoresc (2014) 24:1791–1801; DOI 10.1007/s10895-014-1468-y
  • “UV-Activated Conversion of Hoechst 33258, DAPI, and Vybrant DyeCycle Fluorescent Dyes into Blue-Excited, Green-Emitting Protonated Forms”; Dominika Zurek-Biesiada, Sylwia Ke˛dracka-Krok, Jurek W. Dobrucki; Cytometry Part A (2013) 83A: 441-451; DOI: 10.1002/cyto.a.22260
  • “High UV Excitation Intensity Induces Photoconversion of DAPI During Wide-Field Microscopy”; Stefan Rodic, Claire Brown, Erika (Tse-Luen) Wee; McGill Science Undergraduate Research Journal 9.1 (2014)
  • Tanious, Farial A., et al. "DAPI (4', 6-diamidino-2-phenylindole) binds differently to DNA and RNA: minor-groove binding at AT sites and intercalation at AU sites." Biochemistry 31.12 (1992): 3103-3112.
  • “Inositol phosphates induce DAPI fluorescence shift.”; Kolozsvari, Parisi, Saiardi; Biochem J. 2014 Jun 15;460(3):377-85.; doi: 10.1042/BJ20140237.
  • “Chromatic shifts in the fluorescence emitted by murine thymocytes stained with Hoechst 33342”; Timothy W. Petersen, Sherrif F. Ibrahim, Alan H. Diercks, and Ger van den Engh; Cytometry Part A (2004): 173-181; DOI: 10.1002/cyto.a.20058