DNA polymerase mechanisms of base selection and catalysis are explored using a tool-kit of dNTP analogs that have bisphosphonates in place of the , ? -bridge oxygen. These analogs are Pol substrates that have leaving groups with widely dispirate electronic properties, pKa4 values ranging from 7.8 to 12.3, enabling us to use presteady state kinetic measurements to determine the selection of right and wrong deoxynucleotides occuring at the chemical transition state. Especially important members of the toolkit include all four individually synthesized (R)- and (S)- , ? -CHF and , ? -CHCI diastereomers. Our recent observation of a pronounced stereoselection for (R)-CHF in Pol , involving an electrostatic interaction of F with Arg183, unique to family X pols such as Pol , serves as the impetus for a scaffold strategy for the selective inhibition of Pol relative to the cellular replication Pols ?, ?, ?, and mitochondrial Pol ?. In Aim 1, Study a explores stereoselection in the cellular and mitochondrial pols. Studies b and c make use of the entire toolkit to explore chemistry vs. conformational change as a rate-limiting step In the transition-state of family X Pol ?, family Y error-prone Pol r\, and for a series of cancer-associated Pol variants. In Study d, newly synthesized bisphosphonate PPI analog leaving groups are used to reverse the polymerase reaction to attain a free energy reaction profile for Pol . Study e addresses an entirely new area of polymerase mechanistics, namely the use of EPR and ENDOR to elucidate the structure of the metal coordination site and Its role in fidelity. Aim 2, containing three interrelated studies, spells out a detailed scaffold strategy for the design and synthesis of selective Inhibitors of Pol and BER by the dual targeting of the dNTP binding site and active site Arg183 (Study a). In Study b, we develop a new approach, using pamoic acid analogs, to inhibit BER by selectively interfering with the Pol -assocated lyase. In Study c, we take an important step along the path toward translation, by evaluating the ability of cell permeabilized scaffold compounds to inhibit cultured cancer cells.