Figure 2. Confirmed chemical structures of cyanine dyes (Cy-, Alexa Fluor-, and the AF-series) frequently used for biological applications.

Please note that the AF-dye homologs of Cy5 are available in two distinct versions called AFD647 (n = 1) and AF647 (n = 2). Formerly unpublished structures were confirmed by NMR and MS/MS [34]. To highlight structural differences compared to the parental cyanine fluorophore, we coloured linkers for labelling, e.g., via maleimide groups in blue, sulfo-groups in purple and sulfonated alkyl groups in orange. Please note that linkers for other type of dyes might differ in length.