The development of small molecule probes to investigate biological functions is integral to the elucidation of complex biological processes. Achieving a better understanding of biological systems facilitates the discovery of new therapeutics and technologies that can be employed in the treatment of a variety of diseases and disorders. The research described herein addresses the need for novel methodologies for the examination of biological questions via two general approaches. The first approach involves the development of new synthetic methodologies to rapidly access libraries of biologically relevant small molecules. These molecules can then be employed in biological screens to identify new targets for drug discovery. Specifically, the research has developed microwave-assisted [2+2+2] cyclotrimerization reactions towards carbo- and heterocyclic libraries. The second approach of the research involves the development of photochemical technologies to regulate biological processes in a highly specific spatio-temporal fashion using light. This has been applied to the photochemical regulation of DNA hybridization, DNAzyme catalysis, antisense gene regulation, RNA folding, and protein function.