The L2Hs sequences are a polymorphic, interspersed, middle repetitive DNA family unique to human genomes. Genomic fingerprinting indicates that these DNAs vary from one individual to another and between tissues of the same individual. Sequence analysis reveals that they are AT-rich (76%) and contain many unusual sequence arrangements (palindromes, inverted and direct repeats). These sequence properties confer on the L2Hs elements the potential to fold into non-B-form structures, a characteristic of recombination hot spots. To test this hypothesis carbodiimide, osmium tetroxide and S$\sb1$ nuclease were used as single-strand specific probes to study a recombinant plasmid, pN6.4.39, containing a single L2Hs segment. Different forms of the plasmid substrate were analyzed, including linear molecules and circular forms of low, intermediate and high superhelical densities. In addition, plasmid DNA in growing E. coli cells were analyzed. Modified plasmid DNA was analyzed by primer extension in a sequencing-type reaction format. These studies demonstrate that the L2Hs sequences: (1) assume non-B-form structures both in vitro and in vivo, (2) map to predicted cruciform structures, (3) behave as C-type extrusion sequences, and (4) that these unusual DNA structures are dependent on plasmid superhelicity.

This thesis examines the synthesis, photophysical properties, and sensory responses of hydroxy-substituted 1,4-distyryl-2,5-bis(arylethynyl)benzenes (Cruciforms, XFs). These two-dimensional cross-conjugated materials possess spatially separated frontier molecular orbitals (FMOs). This spatial separation allows the HOMO and LUMO to be addressed independently by analytes, which leads to significant changes in their absorption and emission. These properties allow XFs to be utilized for the detection of various analytes. These studies highlight the benefits of utilizing XFs for the development of advanced functional solid state materials for sensory applications.

The design of chromophores targets materials with optoelectronic properties necessary for advanced applications. Organic materials possess properties which emerge from the collective impact of the constituent backbone and substituents as well as their connectivity (i.e. molecular architecture), necessitating the exploration of novel conjugated architectures. This thesis chronicles our examination of 1,4-distyryl-2,5-bis(arylethynyl)benzenes (cruciforms, XFs). Electronic substitution of this 'X-shaped' cross-conjugated scaffold tunes both the energy levels and the spatial distribution of the frontier molecular orbitals (FMOs) in XFs. The resulting fluorophores exhibit FMO separation, imbuing XFs with desirable properties for sensory applications. Using model analytes, we examine how the underlying FMO arrangement and the nature of analyte interaction elicit observable responses. These studies provide a foundation for future access of functional responsive ratiometric cores. This case study demonstrates the importance and unique potential of FMO-separated fluorophores.

This research serves as a meticulous examination into cross-conjugated materials and how alterations of the frontier molecular orbitals can be utilized for applications in "chemical tongue" organic sensing devices. With conjugated materials being used in the development of new sensory devices for detection of metals, bacteria, and chemical warfare agents, the field of organic sensing is growing faster than ever. The purpose of this dissertation is to provide a precedence for the synthesis of new cross-conjugated compounds and outline potential applications of these materials as chemical sensors and molecular probes.