Temperature-Dependent Photoisomerization Quantum Yields for Azobenzene-Modified DNA

Abstract

We study the photoisomerization quantum yield of azobenzene-modified DNA as a function of temperature for various DNA sequences. We find that even though the photoisomerization quantum yield of free azobenzene is essentially temperature-independent, the trans-to-cis photoisomerization quantum yield depends strongly on temperature when the azobenzene is incorporated into DNA. We show that this temperature dependence is DNA-sequence-dependent and closely linked to the melting temperature of the host DNA. While the trans-to-cis isomerization quantum yield is sequenceand temperature-dependent, in contrast, the thermal cis-totrans isomerization of azobenzene embedded in DNA is sequence-independent and exhibits Arrhenius-like behavior with an activation energy of 88.8 ± 0.693 kJ/mol and a smaller pre-exponential factor than free azobenzene, yielding first-order cis-to-trans kinetics with a rate constant of (2.08 ± 0.00952) × 10 −6 s −1 at 25 °C. These results provide an understanding of the azobenzene isomerization mechanisms in DNA sequences to enable more efficient design of optically reprogrammable nanomaterials and biosensors.

Azobenzene as a photoregulator covalently attached to RNA: a quantum mechanics/molecular mechanics-surface hopping dynamics study

“…These results are in qualitative agreement with recent experimental 55 , 56 and MD-based computational 35 studies on the photoisomerisation quantum yield of azobenzene in DNA where the quantum yield for the trans -to- cis conversion was found to depend largely on the local DNA sequence 35 as well as on temperature, 56 and strongly decreases with decreasing local volume in the nucleic acid environment. Specifically, the experimentally determined quantum yields reported in ref. 56 vary in the range 0.01 < Φ t → c < 0.05 for various azobenzene-substituted DNA double strands with a threoninol linker, below the melting temperature T m .…”

Azobenzene as a Photoregulator Covalently Attached to RNA: A Quantum Mechanics/Molecular Mechanics-Surface Hopping Dynamics Study

“…These results are in qualitative agreement with recent experimental 55,56 and MD-based computational 35 studies on the photoisomerisation quantum yield of azobenzene in DNA where the quantum yield for the trans-to-cis conversion was found to depend largely on the local DNA sequence 35 as well as on temperature, 56 and strongly decreases with decreasing local The striking lengthening of the S 1 lifetime in the trans-to-cis photodynamics and the decrease in the F t/c quantum yield must clearly be due to steric constraints of the RNA (or DNA) environment that are much less effective in the cis-to-trans case. A slowing down of the azobenzene trans-to-cis photoisomerization and excited state decay in viscous solvents and constrained environments has been previously reported, 32,47,[49][50][51]57 even though the effect was by far not as pronounced and typically limited to an increase of the isomerization time by a factor of two to three.…”

“…Downloaded on 5/31/2021 3:39:14 AM.This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.volume in the nucleic acid environment. Specically, the experimentally determined quantum yields reported in ref 56. vary in the range 0.01 < F t/c < 0.05 for various azobenzenesubstituted DNA double strands with a threoninol linker, below the melting temperature T m .…”

Synthesis of Bis-β-Diketonate Lanthanide Complexes with an Azobenzene Bridge and Studies of Their Reversible Photo/Thermal Isomerization Properties

“…There are many factors that affect the azobenzene photoisomerization properties, which include the isomerization mechanism, rate, and pathway, such as the intensity of light, irradiation wavelength, temperature, pressure, solvent, and substituted groups on the azobenzene. 16−26 Up to date, four mechanisms have been proposed to explain the possible mechanism for azobenzene photoisomerization—rotation, inversion, concerted inversion, and inversion-assisted rotation. These theories can be referred to in some previously published reviews.…”