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Understanding the assembly of monomeric components into specific molecular motifs is a central theme in materials and surface engineering. Motif designs, specifically using a controllable template, can yield materials with desired optical or electronic properties. The objective of this thesis is to understand the aggregate size, packing, and monomer orientation for the cationic dye, pseudoisocyanine. These organic molecules assemble into crystals in solution, on planar bilayer templates, and on the membranes of living cells. Pseudoisocyanine J-aggregates were found to form on top of the heterogeneous lipid domains in a phospholipid bilayer. This behaviour is limited to a few headgroup chemistries and lateral packing motifs, allowing one to control aggregation via a combination of these two factors. These aggregates are low-dimensional and display polymorphism. Using atomic force microscopy and visible-light spectroscopy, distinct optical characteristics can be correlated to different bilayer templated J-aggregate morphologies. The molecular packing of a similar J-aggregate crystal was resolved using both atomic force microscopy and selected area electron diffraction. The infrared absorption spectra of different polymorphs also displayed distinct differences. These separate examinations enabled a perspective that clarifies the geometry, packing, orientation, and size of templated J-aggregates. Insights into the templating of J-aggregates on the molecular scale reveals that they are sensitive reporters of membrane phase in adherent cells, and are compatible with established cell biology techniques. Lipid domains in live mammalian cells were visualized using fluorescent J-aggregates in combination with endogenous marker proteins of the endocytic process. Analysis of live cell images and additional biophysical work revealed that pseudoisocyanine J-aggregates formed on domains of the anionic lipid bis(monoacylglycerol)phosphate. Only by using J-aggregates can this lipid be shown to form well-ordered domains during endosomal maturation, leading to multivesicular body formation. These data demonstrate that a correlated optical and topographical approach is necessary to understand the structure of fluorescent molecular assemblies, and form the basis for utilizing such aggregates in a biological context.

Understanding the assembly of monomeric components into specific molecular motifs is a central theme in materials and surface engineering. Motif designs, specifically using a controllable template, can yield materials with desired optical or electronic properties. The objective of this thesis is to understand the aggregate size, packing, and monomer orientation for the cationic dye, pseudoisocyanine. These organic molecules assemble into crystals in solution, on planar bilayer templates, and on the membranes of living cells. Pseudoisocyanine J-aggregates were found to form on top of the heterogeneous lipid domains in a phospholipid bilayer. This behaviour is limited to a few headgroup chemistries and lateral packing motifs, allowing one to control aggregation via a combination of these two factors. These aggregates are low-dimensional and display polymorphism. Using atomic force microscopy and visible-light spectroscopy, distinct optical characteristics can be correlated to different bilayer templated J-aggregate morphologies. The molecular packing of a similar J-aggregate crystal was resolved using both atomic force microscopy and selected area electron diffraction. The infrared absorption spectra of different polymorphs also displayed distinct differences. These separate examinations enabled a perspective that clarifies the geometry, packing, orientation, and size of templated J-aggregates. Insights into the templating of J-aggregates on the molecular scale reveals that they are sensitive reporters of membrane phase in adherent cells, and are compatible with established cell biology techniques. Lipid domains in live mammalian cells were visualized using fluorescent J-aggregates in combination with endogenous marker proteins of the endocytic process. Analysis of live cell images and additional biophysical work revealed that pseudoisocyanine J-aggregates formed on domains of the anionic lipid bis(monoacylglycerol)phosphate. Only by using J-aggregates can this lipid be shown to form well-ordered domains during endosomal maturation, leading to multivesicular body formation. These data demonstrate that a correlated optical and topographical approach is necessary to understand the structure of fluorescent molecular assemblies, and form the basis for utilizing such aggregates in a biological context.