Enhancing the functionality of nucleic acids

In Chapter One, the synthesis and characterization of nine modified DNA hairpins for electron transfer studies is presented. A new pyrene modified 2'-deoxyuridine phosphoramidite was synthesized and then incorporated into DNA hairpins using automated DNA synthesis. These hairpins were purified by reversed-phase HPLC and analyzed by optical melting experiments. The hairpins are 18-24 bases long, have a central tetra-T loop, and have a single U PE (5-(2-pyren-1-yl-ethylenyl)-2'-deoxyuridine) substitution in the central region of their stems. Three of the hairpins are also substituted with 5-XdU traps, where X = Br or F, to learn about the effects of these traps on charge transfer excited state lifetimes and emission quantum yields in UPE substituted DNA. All of the hairpins were studied at Georgia State University to observe their pyrene•+/dU•- charge transfer excited state dynamics following photoexcitation at 355 nm with a 25-ps laser pulse.; Chapter Two describes the synthesis of four 5-position modified uridine nucleosides, six new 5-position modified 2'-deoxyuridine triphosphates, and 2 new modified 2'-deoxycytidine triphosphates. Four new 5-position modified uridine nucleosides were synthesized using a previously reported palladium catalyzed carboxyamidation procedure. This synthetic route was then modified for the synthesis of 5-position modified 2'-deoxyuridine and 2'-deoxycytidine triphosphates. Carboxyamidation has now been demonstrated to be a facile method for introduction of several types of functional groups to 2'-deoxypyrimidines. The synthesis of a novel 4,5-bis modified 2'-deoxycytidine was also accomplished using carboxyamidation. The expansion of palladium-catalyzed carboxyamidation to 2'-deoxypyrimidines provides a route to previously unknown class of modified 2'-pyrimidine triphosphates.; In Chapter Three, two UTP derivatives modified at the 5-position through an amide linkage with either a 2-pyridyl or isobutyl group were tested as substrates for T7 RNA polymerase (T7 RNAP) transcription. A gel-based kinetic assay was used to determine the relative Km and Vmax for T7 RNAP transcription using these two modified UTP's. The Km and Vmax found for both modified UTP's were similar to those found for the natural substrate, UTP, indicating that insertion of these modified bases into the transcript did not impede its elongation.; In Chapter Four, six 5-position modified dUTP derivatives were tested for compatibility with the enzymatic steps of in vitro selection. Six commercially available DNA polymerases were tested for their ability to efficiently incorporate each of these UTP derivatives during PCR. It was not possible to perform PCR using any of the modified UTP derivatives studied. In contrast, primer extension reactions of random templates as well as defined sequence templates were successful. KOD XL and D. Vent polymerase were found to be the most efficient at synthesizing full-length primer extension product with all the dUTP derivatives tested giving yields similar to those obtained with dTTP. Deep Vent and KOD XL were also capable of synthesizing an unmodified complement strand to a modified template. Lastly, in order to provide a more quantitative comparison between modified dUTP's and dTTP as substrates for primer extension reactions, a gel-shift assay was used to investigate dUTP insertion at a specified site during primer extension reactions with KOD XL. While the assay demonstrated that none of the modified dUTP's tested are as good of substrates as the native dTTP for KOD XL polymerase incorporation, under normal primer extension conditions, all of the modified dUTP's tested would be incorporated efficiently. In summary, all of the modified dUTP's studied were demonstrated to be compatible with the enzymatic steps of in vitro selection.