Abstract: Chemical (e.g., click chemistry), enzymatic- or photo-induced polymerization or other polymerization approaches (e.g., thermally activated) of (1) single dyes (monomer) can be used to produce an extended dye network in which each successive dye is arranged in a head-to-tail arrangement (J-like packing arrangement) of their transition dipole moments or (2) dye aggregate sub-units to achieve polymer branching. Furthermore, various routing patterns are achieved by templating a linear series of dyes onto DNA oligomers of various configurations. Dye aggregate dye sub-unit junctions (e.g., triad, tetrad, pentad, hexad, etc.) are used to achieve polymer branching enable creating various circuit patterns and circuit elements (e.g., optical transistors, gates, etc.). Branched configurations can occur on any surface (e.g., DNA nanostructure, chips substrate, hydrogel, etc.) using DNA (or any similar specific [bio]chemistry).

Abstract: Dye aggregates that are templated to deoxyribonucleic acid (DNA) can exhibit different packing arrangements and, as an optically active medium, spectral properties of interest. Steric effects and properties of the linker that tethers the dye to a DNA scaffold (a simple nucleotide oligomer or more complex architectures) can used to fine tune the packing arrangement of the dyes to obtain desirable spectral properties. To gain access to J-aggregates (head-to-tail packing arrangement) as a source of fluorescent materials, the present disclosure is directed to two strategies that utilize rigid linkers to promote J-packing. Devices and methods of use also are disclosed herein.

Abstract: New phosphoramidite Cy5 derivatives can be used in automated DNA synthesis, allowing the labeling of DNA sequences with a wider array of chromophores than are presently commercially available. In addition to varying dye hydrophobicity/hydrophilicity, the 5,5?-substituents (including hexyloxy, triethyleneglycol monomethyl ether, tert-butyl, and chloro groups) can modulate electron donating/withdrawing character while also tuning resulting absorption and emission properties. Modification of the Cy5 periphery enables the tuning of photophysical properties, such as absorption and emission maxima, fluorescence quantum yield, and fluorescence lifetime.

Abstract: DNA has been employed to template dyes into controllable networks of dyes. However, dye-DNA constructs involving covalent tethering often suffer from the lack of structural rigidity due to DNA structural effects (e.g., DNA breathing). Moreover, attachment of a dye to DNA might result in more pronounced structural effects and loss of DNA structural integrity. Employing a dye as a nucleic acid crosslink will reduce deficiencies in DNA structural integrity by creating more rigid, stable, and robust dye-DNA networks while retaining the photophysical benefits of the desired dyes. The utilization of dye crosslinks offers a controllable spacing and orientation of dyes leading to a greater variety in the design of DNA-templated dye networks. Tetrapyrrole type dyes are of a particular interest. A notable chemical diversity of synthetic photo- and chemically stable tetrapyrroles with a variable substitution pattern allows fine-tuning of their chemical and photophysical properties within DNA-templated dye network.

Abstract: Bacteriochlorin of Formula I: wherein R is H or silyl are described, along with compositions containing the same and methods of making and using the same.

Abstract: Bacteriochlorin of Formula I: wherein R is H or silyl are described, along with compositions containing the same and methods of making and using the same.