Currently we're using SYBR Green and Gold to stain cyanophages but the natural florescence of Synechococcus sp. WH7803 makes it much harder to quantify the adsorption rates of the cyanophages. Are there other DNA stains that can be used to study viral infection but emit different wavelengths other than green (or any range not detected by FIT-C or FSC-H)?
SYBR Gold can be used. SYBR green II, and SYBR Safe can also be used but definitely they demonstrate much less fluorescent intensity than SYBR Green. You can further refer to the following links to get details:-
1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC92618/
2. http://mbio.asm.org/content/3/6/e00373-12.full.html
Molecular Probes now provides SYTO Orange nucleic acid stain. Although the excitation maximum is around 540 nm, it could also be excited with a blue laser (488 nm) with ca. 30% efficiency.
Synechococcus also have orange (and red) fluorescence but it should be possible to detect an intensity increase after virus adsorption.
You will find more information on their website.
Re-thinking about your question Vinh Tran, if you cannot measure an increase in the background green fluorescence of Synechococcus after SYBR-labelled cyanophages adsorption, it is unlikely that an orange DNA stain will provide better results.
A red stain would probably not work either, because of chlorophyll fluorescence around 680 nm.
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