Azobenzene Phosphoramidite



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Photo-control, the use of ultraviolet or visible light to control a reaction, has a number of advantages over other external stimuli:

  • Light does not introduce contaminants into the reaction system,
  • Excitation wavelength can be controlled through the design of the photo-responsive molecule, and
  • It is now straightforward to control irradiation time and/or local excitation.

When a photo-responsive molecule is directly attached to DNA as a receptor, photo-regulation of the bioprocess regulated by that DNA molecule could, in principle, be achieved. Such photo-responsive DNA could also be used as a switch in a DNA-based nano-machine. Professor Hiroyuki Asanuma and his group at the department of Molecular Design and Engineering of the Graduate School of Engineering of the Nagoya University (Japan) have developed an efficient method to achieve this goal. They have attached azobenzene to DNA and made it photo-responsive1,2. Azobenzene is a typical photo-responsive molecule that isomerizes from its planar trans-form to the non-planar cis-form after UV-light irradiation with a wavelength between 300 nm and 400 nm (lmax is around 330 nm). Interestingly, the system reverts from the cis-form to the trans-form after further irradiation with visible light (wavelength over 400 nm). This process is completely reversible, and the azobenzene group does not decompose or induce undesirable side reactions even on repeated trans-cis isomerization. By introducing azobenzenes into DNA through D-threoninol as a linker, Asanuma and co-workers succeeded in achieving photo-regulation of:

  • Formation and dissociation of a DNA duplex3,4 and
  • Transcription by T7-RNA polymerase reaction5,6,7




  • Coupling: 10 minutes
  • Deprotection: As required by nucleobases. Compatible with Ammonium Hydroxide for 17 hours at room temperature, Ammonium hydroxide/40% methylamine 1:1 (AMA) for 10 minutes at 65 °C or UltraMild deprotection conditions.
Diluent Anhydrous Acetonitrile
Storage Freezer storage, -10 to -30°C, 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
10-5800-02 0.25 g .25grams 3.06 88.67 53.2 33.25 24.18 17.73 4.43
10-5800-90 100 µmol .082grams 1 20 12 7.5 5.45 4 1
10-5800-95 50 µmol .041grams 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
10-5800-02 0.25 g .25grams 4.57 0.07 85 53.13 38.64 5.31
10-5800-90 100 µmol .082grams 1.5 0.07 23.6 14.75 10.73 1.48
10-5800-95 50 µmol .041grams 0.75 0.07 8.6 5.38 3.91 0.54


REFERENCE(S)| 1 H. Asanuma, et al., Angew Chem Int Ed, 2001, 40, 2671-2673.| 2 T. Takarada, et al., Chem Lett., 2001, 30, 732.| 3 H. Asanuma, X.G. Liang, T. Yoshida, and M. Komiyama, Chembiochem, 2001, 2, 39-44.| 4 H. Asanuma, D. Matsunaga, and M. Komiyama, NUCLEIC ACIDS SYMP SER (OXF), 2005, 49, 35.| 5 H. Asanuma, et al., Chembiochem, 2002, 3, 786.| 6 M. Liu, H. Asanuma, and M. Komiyama, J. Amer. Chem. Soc., 2006 , 128, 1009.| 7 H. Asanuma, et al., Nature Protocols, 2007, 2, 203-212..