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Alternative dyes for FISH, FRET, and qPCR

ATTO™ Dyes

Product spotlight: Use ATTO-labeled oligonucleotides as alternatives in applications including fluorescence in situ hybridization (FISH), fluorescence resonance energy transfer (FRET), and dual-labeled probes used in qPCR experiments.

ATTO-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, photostability, and 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 [1].

Ordering ATTO dyes

Catalog ATTO dyes can be attached to 100 nmol, 250 nmol, and 1 μmol DNA and RNA oligonucleotides, or duplex products. To order, visit the DNA Oligos or RNA Oligos ordering pages, where you can choose an ATTO dye as either a 5′ or 3′ modification. All ATTO-labeled oligos from IDT will be HPLC-purified.

Catalog ATTO dye

Alternative for:

5' or 3' ATTO 488 (NHS Ester) Alexa Fluor 488
5' or 3' ATTO 532 (NHS Ester) VIC
5' or 3' ATTO 550 (NHS Ester) NED™ and Alexa Fluor 555
5' or 3' ATTO 565 (NHS Ester) PET™
5' or 3' ATTO Rho101 (NHS Ester) ROX™
5' or 3' ATTO 590 (NHS Ester) Alexa Fluor 594
5' or 3' ATTO 633 (NHS Ester) LIZ
5' or 3' ATTO 647N (NHS Ester) Alexa Fluor 647

For questions about ATTO dye modifications or products not found on this list, including internal dye placement or dual-labeled probes, reach out at contact us.

FOF-ATTO Dyes-Fig 1
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]. For detailed information on these (and other) ATTO dyes, visit ATTO-TEC.

*ATTO dyes have not been tested on Illumina® platforms for use with certain fluorescent applications, such as sequencing, genotyping, and fragment analysis. Researchers must perform independent testing for such use.


  1. Buschmann V, Weston KD, Sauer M. Spectroscopic study and evaluation of red-absorbing fluorescent dyes. Bioconjug Chem. 2003;14(1):195-204.

For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations. Doc ID: RUO23-1956_001

Published Jan 18, 2013
Revised/updated May 11, 2023