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Azobenzene photoisomerization-induced destabilization of B-DNA.

ABSTRACT: Molecular photoswitches provide a promising way for selective regulation of nanoscaled biological systems. It has been shown that conformational changes of azobenzene, one of the widely used photoswitches, can be used to reversibly control DNA duplex formation. Here, we investigate the conformational response of DNA upon azobenzene binding and isomerization, using a threoninol linker that has been experimentally investigated recently. To this end, nonequilibrium molecular dynamics simulations are carried out using a switching potential describing the photoinduced isomerization. Attachment of azobenzene leads to a distortion of the DNA helical conformation that is similar for the trans and cis forms. However, the trans form is stabilized by favorable stacking interactions whereas the cis form is found to remain flipped out of the basepair-stacked position. Multiple azobenzene attachment augments the distortion in DNA helical conformation. The distorted DNA retains nativelike pairing of bases at ambient temperatures, but shows weaker basepairing compared to native DNA at an elevated temperature.

SUBMITTER: Biswas M

PROVIDER: S-EPMC4142232 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature

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Azobenzene photoisomerization-induced destabilization of B-DNA.

Biswas Mithun M Burghardt Irene I

Biophysical journal 20140801 4

Molecular photoswitches provide a promising way for selective regulation of nanoscaled biological systems. It has been shown that conformational changes of azobenzene, one of the widely used photoswitches, can be used to reversibly control DNA duplex formation. Here, we investigate the conformational response of DNA upon azobenzene binding and isomerization, using a threoninol linker that has been experimentally investigated recently. To this end, nonequilibrium molecular dynamics simulations ar ...[more]

PMID: 25140428

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Project description:Two mononuclear and one binuclear ytterbium complexes with dual near-infrared (NIR) photoluminescence and reversible trans-to-cis photoisomerization functions were synthesized and characterized. The central ytterbium(III) ion coordinates with two β-diketonate (4,4,4-trifluoro-1-phenylbutane-1,3-dionate (tfd)) ligands and one deprotonated azobenzene-containing tetradentate ligand [(E)-4-(phenyldiazenyl)-N,N-bis(pyridin-2-ylmethyl) benzohydrazide (HL), (E)-4-((4-(dimethylamino)phenyl)diazenyl)-N,N-bis(pyridin-2-ylmethyl)benzohydrazide (HNL), or (E)-4,4'-N',N'-bis(pyridin-2-ylmethyl)benzohydrazide azobenzene (H2DL)] to form a neutral ternary complex ([Yb(tfd)2L], [Yb(tfd)2(NL)], or [Yb2(tfd)4(DL)], respectively), where the ytterbium(III) ion is eight-coordinated to N3O5 donor sets. X-ray crystallographic analysis shows that all three complexes form a trigonal dodecahedron geometry with similar -N=N- distances that are slightly longer than those of the pure azobenzene-containing ligands. The NIR luminescence properties of the Yb(III) complexes were determined at a wavelength of about 980 nm with quantum yields in the range of 0.4-0.6% in ethanol and acetonitrile solutions at room temperature, and trans-to-cis photoisomerization was determined with the quantum yields (Φt→c = 10-2) at the same level as their pure ligands. The trans-to-cis photoisomerization rates of the complexes (10-4 s-1) are slightly higher than those of the pure ligands and similar to azobenzene (10-5 to 10-4 s-1). From time-dependent density functional theory calculations of the energy levels of the first excited triplet states of the ligands, the energies of the lowest excited triplet states of all of the ligands are higher than the resonance level of Yb3+ (2F5/2, 1.2722 eV). We suggest that these azo-containing ligands may participate in energy transfer to the ytterbium ion, in addition to the main "antenna effect" ligand tfd. This is the first report of azobenzene group-functionalized ytterbium complexes with dual NIR luminescence and photoisomerization properties, indicating that azobenzene-containing lanthanide(III) complexes have potential applications as dual function materials in biological systems.

Dataset Information

Azobenzene photoisomerization-induced destabilization of B-DNA.

Publications

Azobenzene photoisomerization-induced destabilization of B-DNA.

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