PCR and qPCR
Support and Educational Content

Alternative dyes for FISH, FRET, and qPCR

ATTO™ Dyes


ATTO™ dye labeled oligonucleotides offer additional alternatives for applications including fluorescence in situ hybridization (FISH), fluorescence resonance energy transfer (FRET), and dual-labeled probes used in qPCR experiments.* ATTO dyes are a group of patented fluorescent markers that feature strong absorption and sensitivity, enhanced photostability, and high fluorescence quantum yield. The ATTO dyes are perfect substitutes for dyes such as ROX™, VIC®, LIZ®, and Alexa Fluor® dyes. For qPCR applications, dye calibration will be needed for each qPCR instrument.

Catalog ATTO dyes can be attached to the 5’ or 3’ ends of 100 nmole, 250 nmole, and 1 μmole DNA and RNA oligonucleotides or duplex products. All ATTO dye labeled oligos will be HPLC purified. More information on ATTO dyes can be found at http://www.idtdna.com/catalog/Modifications/Dyes.aspx and www.atto-tec.com.

Order ATTO dye labeled oligonucleotides from the Custom DNA Oligos ordering page at http://www.idtdna.com/pages/products/dna-rna/custom-dna-oligos. Select the desired ATTO dye as either a 5’ or 3’ modification.

For questions about ATTO dye modifications or products not found on this list, including internal dye placement or dual-labeled probes, please contact Customer Care at custcare@idtdna.com.

Figure 1. Strong fluorescence of ATTO™ Dyes. Rat stomach stained with mouse anti-smooth muscle α-actin antibody followed by ATTO 488 anti-mouse IgG (green); and polyclonal rabbit anti-cytokeratin followed by ATTO 647N anti-rabbit IgG (red) [Image courtesy of ATTO-TEC GmbH].

*ATTO dyes have not been tested on Applied Biosystems genetic analyzers for use with certain fluorescent applications, such as sequencing, genotyping, and fragment analysis. Researchers must perform independent optimization for such use.


Additional reading

Fluorescent dyes with no licensing restrictions (Freedom™ Dyes)—a growing portfolio—Need fluorescent dyes suitable for commercial and diagnostic applications that have no patent licensing restrictions? View this table of Freedom Dye alternatives for commonly used proprietary dyes.


qPCR Probes—selecting the best reporter dye and quencher—Recommendations for choosing dyes and quenchers, taking into account instrument compatibility and multiplex probe applications.


Design efficient PCR and qPCR primers and probes using online tools—To facilitate experimental planning, IDT offers a variety of free, online tools for oligonucleotide analysis and PCR primer design. This article provides an overview of our predesigned qPCR assays and the basics of designing customized PCR primers and hydrolysis probes with the PrimerQuest® Tool.

Author: Ellen Prediger is a senior scientific writer at IDT.

© 2013, 2016 Integrated DNA Technologies. All rights reserved. Trademarks contained herein are the property of Integrated DNA Technologies, Inc. or their respective owners. For specific trademark and licensing information, see www.idtdna.com/trademarks.


Predesigned qPCR Assays

Probe-based qPCR assays for quantification of human, mouse, and rat gene expression. Order in plates or tubes.

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