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We herein report a method for site‐selective photo‐crosslinking of a DNA duplex. A stilbene pair was introduced into a DNA duplex and a ruthenium complex was conjugated with a triplex‐forming oligonucleotide. We demonstrated that [2+2] photocycloaddition of the stilbene pair occurred upon irradiation with visible light when the ruthenium complex was in close proximity due to triplex formation. No reaction occurred when the ruthenium complex was not in proximity to the stilbene pair. The wavelength of visible light used was of lower energy than the wavelength of UV light necessary for direct excitation of stilbene. Quantum chemical calculation indicated that ruthenium complex catalyzed the photocycloaddition via triplet‐triplet energy transfer. Site selectivity of this photo‐crosslinking system was evaluated using a DNA duplex bearing two stilbene pairs as a substrate; we showed that the site of crosslinking was precisely regulated by the sequence of the oligonucleotide linked to the ruthenium complex. Since this method does not require orthogonal photoresponsive molecules, it will be useful in construction of complex photoresponsive DNA circuits, nanodevices and biological tools. [ABSTRACT FROM AUTHOR]

Förster resonance energy transfer between identical chromophores (homo‐FRET) has been difficult to analyze since neither emission intensity nor lifetime changes with the occurrence of homo‐FRET. Herein we used a DNA scaffold to analyze homo‐FRET between pyrene moieties. The DNA scaffold was modified with two pyrenes and a quencher, anthraquinone. Homo‐FRET was detected by monitoring quenching of pyrene emission and the decrease in the fluorescence lifetime of pyrene. Homo‐FRET efficiencies could be calculated by excluding effects of hetero‐FRET. The experimentally determined efficiencies showed an excellent agreement with Förster theory. These results will inform design of novel molecular probes and light‐harvesting antennae. [ABSTRACT FROM AUTHOR]

Herein we report the construction of efficient light-harvesting antennae by hybridization of DNA oligonucleotides containing high densities of fluorophores into DNA junctions through d-threoninol. Six pyrene donors could be incorporated into each arm without self-quenching. A perylene acceptor was located at the center of the junction. Antenna effects of a duplex and three- to eight-way junctions were systematically compared. Six- and eight-way junctions had the highest antenna effects, and their effective absorption coefficients were 8.5 times higher than that of perylene. Interestingly, even-numbered junctions had higher efficiencies than odd-numbered junctions. Nondenaturing gel analyses and fluorescence lifetime measurements demonstrated that the strong odd-even effects were derived from differences in the stability of junctions. The results presented will guide the design of efficient artificial photosynthetic systems., (© 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)