Methylene Blue II Phosphoramidite


3-Butyl-3-[2-(2-cyanoethyl)(N,N-diisopropyl)phosphoramidityl)ethyl]amino-7-(2-(4,4'-dimethoxytrityloxy)ethyl)-7-(butylamino)phenothiazin-5-ium chloride

Product Specifications

Catalog Number: Select Pack Size and Format to Reveal


Methylene Blue, which belongs to the phenothiazine family of dyes, is a unique dye with a variety of useful properties. Despite its high extinction coefficient in the visible region (81,000 L/, it is weakly fluorescent due to its high rate of intersystem crossing from the S1 excited state to the T1 triplet state. This property makes it an excellent photosensitizer, and it has been used extensively to produce highly reactive singlet oxygen. Methylene blue has the ability to both intercalate in duplex DNA, preferring G:C over T:A base pairs, and can act as an electrochemical redox probe. Methylene blue has also been shown to be unmatched in performance as a redox-active reporter for electrochemical biosensors.

Earlier, we introduced Methylene Blue C3 Phosphoramidite but this product proved to have quite limited stability and has been discontinued. As an alternative option, we introduced Methylene Blue NHS Ester to allow researchers to label amino-modified oligonucleotides with this interesting dye. With the encouragement and technical expertise of Carole Chaix and her colleagues at the University of Lyon, we decided to prepare an alternative structure that seemed to have a much superior stability profile - Methylene Blue II Phosphoramidite. Fortunately, this structure did indeed prove more stable and we are now able to offer again a Methylene Blue Phosphoramidite.



  • Coupling: 3 minute coupling time recommended. The use of UltraMILD monomers are required. (Catalog Numbers: dA: 10-1601-xx, dC: 10-1015-xx, dG: 10-1621-xx, dT: 10-1030-xx). To avoid any exchange of the iPr-Pac group on the dG with acetyl, use the UltraMild Cap Mix A (40-4210-xx/ 40-4212-xx). Some branching off the Methylene Blue will occur when incorporated internally within an oligo, so we recommend the dye be placed at or near the 5' terminus of the oligo sequence.
  • Deprotection: UltraMILD deprotection: 0.05M potassium carbonate in methanol (60-4600-30) for 4 hours at room temperature
Diluent Anhydrous Acetonitrile
Storage Storage: Freezer storage, -10 to -30C, dry
Stability 1-2 Days

Dilution/Coupling Data

The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.

ABI 392/394

Catalog # Pack Size Grams/Pack 0.1M Dil. (mL) Approximate Number of Additions
LV40 LV200 40nm 0.2μm 1μm 10μm
10-5961-02 0.25 g 0.25 2.58 72.67 43.6 27.25 19.82 14.53 3.63
10-5961-90 100 µmol 0.1 1 20 12 7.5 5.45 4 1
10-5961-95 50 µmol 0.05 0.5 3.33 2 1.25 0.91 0.67 0.17


Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-5961-02 0.25 g 0.25 3.86 0.07 70.8 44.25 32.18 4.43
10-5961-90 100 µmol 0.1 1.5 0.07 23.6 14.75 10.73 1.48
10-5961-95 50 µmol 0.05 0.75 0.07 8.6 5.38 3.91 0.54