I like carboxyfluorescein. It is bright, it doesn’t alter how the oligo behaves, and most labs already have a fluorescein cube (filters and dichroic mirror) for their fluorescent microscopes. The down side is that fluorescein photobleaches, so you should minimize its exposure to intense light and only observe it with the microscope when you are ready to take pictures and turn off the lamp soon. Carboxyfluorescein emits green.
Gene Tools Blue is not as bright as fluorescein but it too doesn’t alter how the oligo behaves. The problem is that it is a non-standard fluorochrome and it is expensive to purchase a cube optimized for the fluor (the wavelengths for excitation and emission are here: https://www.gene-tools.com/custom_morpholinos_controls_endmodifications#3'-GeneToolsBlue). A DAPI cube will produce some fluorescent signal, but it is not very good. Gene Tools blue emits blue.
Lissamine, also called Rhodamine B, is a bright fluorochrome and it doesn’t bleach easily but it makes the oligos less water soluble, which can be a practical problem. Lissamine emits red.
https://www.gene-tools.com/custom_morpholinos_controls_endmodifications#...
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