For fixed samples, has anyone used anything other than DAPI? We are looking for something that works as well as DAPI but isn’t excited by UV light. Specifically, can anyone comment on SYTO, SYTOX, TOTO, TO-PRO? or Propidium Iodide? And has anyone used DNA dyes on living embryos?
We have used TOTO-3 to stain DNA when doing immunofluorescence on worm embryos. See Ai et al. 2009, for example. Or Geles et al. 2002 or Severson and Bowerman 2003. After you wash off the secondary, incubate with 1:4000 TOTO-3 (T3604 from Invitrogen) for 5 min and wash 1 more time before mounting in Vectashield.
Many labs use strain AZ212 made by Vida Praitis when imaging live embryos. Do you have to use a dye?
Thanks for the suggestions. Yes, it would be more useful to have a DNA dye, as we are performing structure/function analysis and have multiple integrated transgenes in a mutant background - crossing in another integrated array at this point would make for messy genetics!