Improved Cy3 and Cy5 DNA Labeling Efficiency

Linker-optimized Cy3- and Cy5-modified dUTPs

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Labeling of DNA probes for in situ hybridization is most often performed by enzymatic incorporation of labeled dUTP using Taq DNA polymerase (= Polymerase Chain Reaction (PCR))[1-2].   More information...

We now offer linker-optimized Cy3- and Cy5-modified dUTPs (dUTP-XX-Cy3 and dUTP-XX-Cy5) that possess a longer linker resulting in higher labeling efficiencies at similar substitution rates (Fig. 1, Tab. 1)[3].

Figure 1: The longer the linker the higher the labeling efficiency at a similar dTTP substitution rate. PCR conditions: A 500 bp DNA fragment has been amplified from 10 ng genomic lambda DNA with Taq Polymerase. 10 µl probe were subsequently analyzed by agarose gel electrophoresis (1.8 % gel) without (A) or with DNA intercalator EvaGreen (B), M214: 100 bp DNA Ladder (Jena Bioscience), 0 % - 100 %: Increasing amount of dTTP substitution by Cy3-modified dUTP.

Table 1: Spectroscopic and substrate properties of Cy3- and Cy5-labeled dUTPs.


[nm] **

[nm] **

[L x mmol-1 cm-1] **

Recommended dTTP
substitution by modified dUTP [%]
(PCR (Taq Pol)) *





30 - 50 %







20 - 40 %

* Please note: Optimal final concentration of the dye-labeled dUTP may vary depending on the application and assay conditions. For optimal product yields and optimal incorporation rates an individual optimization of the dye-labeled dUTP/ dTTP ratio is recommended.
** free acid

Jena Bioscience is a primary manufacturer offering

Selected References:
[1] Morrison et al. (2003) Labeling Fluorescence In Situ Hybridization Probes for Genomic Targets. Methods in Molecular Biology 204:21.
[2] Wiegant et al. (1997) Probe Labeling and Fluorescence In Situ Hybridization. In: Current Protocols in Cytometry 8.3.1, John Wiley & Sons Inc.
[3] Zhu et al. (1994) Directly labeled DNA probes using fluorescent nucleotides with different length linkers. Nucleic Acids Research 22:16.

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