Alternative dyes for oligonucleotides/probes labeling

Why choose alternative dyes instead of “genuine” dyes? First, they are cheaper, and second, they can give the same results. Another reason is that the number of suppliers who can provide modified oligonucleotides is restricted – only a patent or a licence owner is usually allowed to produce them.

Oligonucleotides/probes labelled with fluorescent dyes are widely used in a considerable number of different types of methods, like qPCR, genotyping, hybridization, sequencing, FISH, and others.

These methods require a wide range of various fluorescent dyes.

Some fluorescent dyes (alternative dyes) can be used as an excellent replacement for other fluorescent dyes (classical/typical dyes). An overview of the most widely used replacement dyes is presented in Table 1 below.

Note: Users should always check if the substitute dye is suitable for their needs and if it is compatible with the method used. Products shown in the table may have a trademark or a patent associated with them.

If you decide to choose an alternative dye, please keep in mind that choosing an alternative dye is subject to the same conditions and rules as choosing a typical dye.

The most important conditions include:

* Absorption and emission spectra of the selected dye

* pH stability of the dye

* Photostability of the dye, fluorescence yield etc.

It is also necessary to consider the method and properties of the instrument to be used when choosing the correct alternative dyes, for example, the range of excitation source and range of detector of the instrument, etc.

Published by: Zuzana Havlínová
September 2018
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