I've worked with PNA probes and they work well. FITC is quite bright, I wouldn't think that would be a great deal different. I think the AF's big advantage is that they are more stable. There are tons of nucleic acid probes but given that your telomere probe is likely to be significantly dimmer than your total DNA probe I think you may want to consider using a different excitation - ie why not use a more standard DAPI stain? Or pick a far-red stain. Anything that'll avoid spectral overlap. You could also consider using a centromere targeting PNA probe as the control if you want to get really fancy. As a word of caution: PNA probes and the like are great for in situ staining but I really don't know if this is a good approach for a flow cytometry experiment. You may not get a good enough signal to noise ratio to see anything. RNA binds PNA probes and so cells not RNAse treated have higher background. Furthermore, telomere shortening is stochastic so cells often have one or a few very short telomeres while the remaining telomeres are normal in length. Whole cell assays like flow will not capture this. If you are going to look at whole cells between patients really should just use a qPCR approach - these are by far the most common for this type of bulk measurement and far cheaper, easier, and more proven than a flow experiment. I think you might also want to consider microscopy based experiments if you can - the good news is if you have a flow sorter you can look at the same cells by flow and microscopy so you can directly compare the two methods. In any case you definitely want to make sure your staining is robust by microscopy before you attempt the more risky flow experiment.