Carbon-based materials hold exciting prospects for the future of miniaturized electronics, potentially replacing silicon in next generation devices. However, a stronger fundamental understanding of the charge transport phenomena and structure-function relationships is necessary to effectively employ the favorable properties of these materials. To achieve this we sought to develop a precisely defined model system that emulates aromatic, π-stacked organic semiconductors. We first drew inspiration from the nucleobase stacking structure of deoxyribonucleic acid (DNA) in order to take advantage of well-established oligonucleotide synthesis and self-assembly methodologies. We demonstrated the exquisite control offered by these methodologies through implementation in a microfluidic-encapsulated, DNA-modified carbon nanotube field effect transistor (CNT FET) capable of highly sensitive and sequence specific detection of a prototypical DNA binding protein. We then expanded our studies to include perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs), a well-known class of organic materials that have been incorporated within DNA as base surrogates but were generally unstudied in terms of assembly dynamics and kinetics. By examining molecular dynamics simulated and synthetic variants of DNA-PTCDI hybrid systems, we established a foundation for the rational design and construction of precisely defined one-dimensional organic nanowires. We proceeded to prepare a novel class of chemically well-defined PTCDI-based organic semiconductor ensembles that could serve as a platform for investigating the emergent electronic phenomena in organic semiconductor materials. Altogether, our studies hold general relevance for fundamentally understanding structure-function relationships in arbitrary organic materials, nanoscale charge transfer phenomena at device-relevant organic/inorganic interfaces, and electrical conductivity in biological and bioinspired systems.