Investigations in Molecular Recognition Element Selection and Single-Wall Carbon Nanotube Properties

The in vitro selection of Molecular Recognition Elements (MREs) is a powerful tool for identifying molecules useful in numerous applications. This is achieved using the iterative Systematic Evolution of Ligands by EXponential Enrichment (SELEX) process. This technique utilizes a large library of 10 9-1015 different molecules which is enriched for those that bind to a target of interest. It also can be designed to enrich for molecules which do not bind to other, closely-related negative targets. We have developed a novel variation of this process called Decoy-SELEX. This enriches molecules that bind to the target of interest, but focuses on what the MRE should not bind to by using highly stringent negative selections with multiple targets. We have used this novel technique to identify separate MREs for three targets. First, a singlechain Fragment variable (scFv) antibody fragment MRE was identified that binds to prostate cancer cells but not benign prostatic cells. This molecule will be useful in the specific detection and targeted therapy of prostate cancer. Then, a single-stranded DNA (ssDNA) MRE was identified that binds to the herbicide atrazine but not other closely-related molecules. This molecule will be useful in the rapid, field-use detection of environmental contamination by atrazine. Finally, a ssDNA MRE binding to the pesticide malathion but not its metabolites was obtained. This molecule will also be useful as an environmental sensor for malathion contamination.;Single-wall carbon nanotubes (SWCNT) are a relatively new class of materials with novel mechanical, electrical, and optical properties. These properties are dependent upon the chirality and length of individual tubes, and can be altered with modifications, including chemical conjugates, DNA-wrapping, or protein adsorption. Therefore, SWCNT have many potential uses, including incorporation into electrical or optical molecular sensors. In order to determine the future potential of DNA-wrapped SWCNT in sensing applications, chirality identification, and purification, we tested their effect on the polymerase chain reaction (PCR). We determined the reaction-limiting concentration for different DNA sequences and SWCNT chiralities in addition to determining that DNA can be PCR-amplified directly from a SWCNT scaffold. This study identified parameters important in future studies for SWCNT application. Additionally, we determined the effect of DNA-wrapped SWCNT on a green algae model organism compared to sodium cholate-wrapped SWCNT. We determined that there was no effect of either type of SWCNT on algal growth at the concentrations assayed. This is important as the manufacture and application of SWCNT increases, making the likelihood of environmental exposure more prominent