Effect of the ortho Modification of Azobenzene on the Photoregulatory Efficiency of DNA Hybridization and the Thermal Stability of its cis Form

Abstract

We synthesized various azobenzenes methylated at their ortho positions with respect to the azo bond for more effective photoregulation of DNA hybridization. Photoregulatory efficiency, evaluated from the change of T(m) (DeltaT(m)) induced by trans-cis isomerization, was significantly improved for all ortho-modified azobenzenes compared with non-modified azobenzene due to the more stabilized trans form and the more destabilized cis form. Among the synthesized azobenzenes, 4-carboxy-2',6'-dimethylazobenzene (2',6'-Me-Azo), in which two ortho positions of the distal benzene ring with respect to carboxyl group were methylated, exhibited the largest DeltaT(m), whereas the newly synthesized 2,6-Me-Azo (4-carboxy-2,6-dimethylazobenzene), which possesses two methyl groups on the two ortho positions of the other benzene ring, showed moderate improvement of DeltaT(m). Both NMR spectroscopic analysis and computer modeling revealed that the two methyl groups on 2',6'-Me-Azo were located near the imino protons of adjacent base pairs; these stabilized the DNA duplex by stacking interactions in the trans form and destabilized the DNA duplex by steric hindrance in the cis form. In addition, the thermal stability of cis-2',6'-Me-Azo was also greatly improved, but not that of cis-2,6-Me-Azo. Solvent effects on the half-life of the cis form demonstrated that cis-to-trans isomerization of all the modified azobenzenes proceeded through an inversion route. Improved thermal stability of 2',6'-Me-Azo but not 2,6-Me-Azo in the cis form was attributed to the retardation of the inversion process due to steric hindrance between lone pair electrons of the pi orbital of the nitrogen atom and the methyl group on the distal benzene ring.

Femtosecond photoisomerization of azobenzene-derivative binding to DNA

“…This result suggests that the AzD is the much more efficient T-to-C photoisomerization molecule as a photoregulator compared to the already-reported Az 9 and its derivatives [3][4][5][6], with the advantage of the pump wavelength without damaging the living cell [7,8]. S -to-I T T C kinetic rate hardly changes.…”

“…Therefore, a number of photoisomerization groups have been taken as one of reactions to be controlled [2]. Among them, reversible control of DNA hybridization using photoisomerization of binding azobenzene (Az) derivatives by light irradiation of different wavelengths has attracted considerable attention because of ease of the preparation and efficient photoisomerization probability [1,[3][4][5]. In addition, Asanuma et al.…”

Ultrafast photoisomerization and its single-shot pump pulse efficiency of trans-azobenzene derivative: Compound for photosensitive DNA

“…1 is denoted by the corresponding absorption cross section  m (m=T or C). The half-life time of the thermal isomerization of the C-AzD solution is ~10 hours at even 60 °C, indicating the excellent thermal stability of the ten times larger than that of the C-Az solution [1,2].…”

“…Under the sample condition mentioned in the previous subsection, when the 360 nm femtosecond pulse pumps the T-AzD solution at a 1-kHz repetition rate, only T-to-C to dominantly isomerize to the C-form even for the AzD solution of the T-and Cmixture state [1,2]. While the 400 to 500 nm CW irradiation (S 1 -band excitation) dominantly isomerizes to the T-form for the T-and C-mixture solution, suggesting that S 1 -band excitation for the T solution does not effectively isomerize to the C-form.…”

“…1) is one of the most effective photoregulator with the highest thermal stability of the cis (C)-form [1,2].…”