Tadao Takada

Abstract Fluorescence imaging uses changes in the fluorescence intensity and emission wavelength to analyze multiple targets simultaneously. To increase the number of targets that can be identified simultaneously, fluorescence blinking can be used as an additional parameter. To understand and eventually control blinking, we used DNA as a platform to elucidate the processes of electron transfer (ET) leading to blinking, down to the rate constants. With a fixed ET distance, various blinking patterns were observed depending on the DNA sequence between the donor and acceptor units of the DNA platform. The blinking pattern was successfully described with a combination of ET rate constants. Therefore, molecules with various blinking patterns can be developed by tuning ET. It is expected that the number of targets that can be analyzed simultaneously will increase by the power of the number of blinking patterns.

Current understanding of electron transfer (ET) kinetics is largely based on ensemble measurements that obscure the underlying single-molecule behavior. We previously reported systematic distance-dependent single molecule ET measurements that show a large heterogeneity. Here we study and discuss this heterogeneity in more detail and suggest that it is a rather fundamental phenomenon that is difficult to explain solely by the distribution of DNA conformations. This heterogeneity may arise from the uniqueness of each molecule, or it may reflect the uncertainty of ET kinetics.

The molecular arrangement of functional chromophores is essential to construct functional nanomaterials. Synthetic DNA has been used as a structural scaffold to control and construct molecular assembly. We now describe the formation of artificial DNA/porphyrin complexes where porphyrins working as photoactive molecules were placed at specific locations on the DNA through a non-covalent interaction. Spectroscopic analysis by UV/vis, circular dichroism (CD), and melting temperature measurements showed that the binding of water-soluble porphyrin derivatives with methylpyridinium groups (TMPyP and DMPyP) to DNA can be directed by hydrophobic cavities composed of a pair of abasic site analogs (dS). CD measurements showed that the two porphyrins can be accommodated at two specific sites when the DNA molecule had two cavities, as evidenced by the exciton-coupled CD spectra of the porphyrins. Photoelectrochemical experiments showed that the DNA complexes accommodating DMPyP at specific locations can respond to light excitation to generate a photocurrent when immobilized on the electrode surface. Our results demonstrated that the control of the porphyrin binding using the dS/dS pair is a useful approach to construct artificial DNA with porphyrin molecules, leading to the design of photoresponsive materials and photoelectrochemical sensors.