Although EDANS, FAM, TAMRA, ROX, Cy3^® and Cy5^® have been widely used to develop a variety of FRET peptide and FRET oligonucleotide probes, there are still some limitations in the use of these dyes. For example, the weak absorption and environment sensitive fluorescence of EDANS have severely limited its sensitivity for developing protease assays and nucleic acid detection probes. Compared to EDANS, fluorescein-based probes (such as FAM, HEX, JOE and TET) have stronger absorption and fluorescence. However the fluorescence of fluorescein-based probes is strongly dependent on pH. They only exhibit the strongest fluorescence at higher pH. This pH dependence makes the fluorescein-based fluorescent probes inconvenient for the assays that require low pH. In addition, most of fluorescein-based probes have quite low photostability, which limits their applications in fluorescence imaging.

Among cyanine dyes, non-sulfonated Cy3^® and Cy5^® are widely used for developing a variety of peptide and oligonucleotide probes, but they have quite low fluorescence quantum yields in aqueous media. The sulfonated Cy3^® and Cy5^® have improved fluorescence quantum yields than those of non-sulfonate cyanines. Alexa Fluor™ dyes have improved performance, but are extremely expensive, thus are unpractical for preparing peptide and oligonucleotide conjugates in some cases.

To address these limitations, AAT Bioquest has developed Tide Fluor™ donor dyes that are optimized as building blocks for developing FRET peptides and FRET oligonucleotides for a variety of biological applications. Our Tide Fluor™ dyes (such as TF1, TF2, TF3, TF4, TF5, TF6, TF7 and TF8) have strong fluorescence and good photostability. TF2 dyes have the similar excitation and emission wavelengths to those of carboxyfluoresceins (FAM), making them readily used for the biological applications done with fluoresceins. TF2 dyes have much stronger fluorescence at physiological conditions and they are much more photostable than FAM probes. Compared to other fluorescent dyes alternative to fluoresceins and Cy dyes (such as Alexa Fluor^® and DyLight™ dyes), Tide Fluor™ dyes are much more cost-effective with comparable or even better performance for your desired biological applications. Tide Fluor™ dyes have almost identical spectral properties to Alexa Fluor^® dyes as discussed below. However, on oligonucleotides and peptides, TF3 dyes are much brighter and more photostable than Cy3^®, Alexa Fluor^® 555 and DyLight™ 555. We recommend you try our Tide Fluor™ dyes that are optimized for labeling oligonucleotides and peptides at much lower cost with comparable performance to Alexa Fluor^® dyes.