A major thrust in bioenergy research is to develop innovative methods for deconstructing plant cell wall polymers, such as cellulose and lignin, into simple monomers that can be biologically converted to ethanol and other fuels. Current techniques for monitoring a broad array of cell wall materials and specific degradation products are expensive and time consuming. To monitor various polymers and assay their breakdown products, molecular probes for detecting specific carbohydrates and lignins are urgently needed. These new probes would extend the limited biochemical techniques available, and enable realtime imaging of ultrastructural changes in plant cells. Furthermore, degradation of plant biomass could be greatly accelerated by the development of catalysts that can hydrolyze key cell wall polysaccharides and lignin. The objective of this project was to develop cheap and efficient DNA reagents (aptamers) used to detect and quantify polysaccharides, lignin, and relevant products of their breakdown. A practical goal of the research was to develop electrochemical aptamer biosensors, which could be integrated into microfluidic devices and used for high-throughput screening of enzymes or biological systems that degrade biomass. Several important model plant cell wall polymers and compounds were targeted for specific binding and purification of aptamers, which were then tested by microscopic imaging, circular dichroism, surface plasmon resonance, fluorescence anisotropy, and electrochemical biosensors. Using this approach, it was anticiated that we could provide a basis for more efficient and economically viable biofuels, and the technologies established could be used to design molecular tools that recognize targets sought in medicine or chemical and biological defense projects.