| This research is centered on two projects of biological importance composed of RNA-based compounds: C8 analogs of cyclic diguanosine monophosphate (c-di-GMP) and 5'-capped oligoribonucleotides.;c-di-GMP is an important bacterial second messenger molecule that is critical for the transition between a biofilm-protected sessile state and a virulent, single cellular motile state in species like V. Cholerae and S.Typhimurium. The synthesis and solution phase structural analysis of a family of C8-modified analogs is described. Starting from unmodified c-di-GMP, elaboration at the C8 position of both guanine moieties of c-di- GMP resulted in the bromo, thio, methylthio, phenyl, and meta-acetylphenyl analogs.;Biophysical studies of all five compounds was performed using 1D and (1H, 31P, 13C) and 2D (DOSY, HMBC/HMQC) NMR to ascertain the level of G-quadruplex formation. It was found that only c-di-Br-GMP as the K+ salt form adopts the formation of higher order complexes containing guanine quartet structures. All analogs have an NMR-visible amino resonance that is most prominent at low temperatures due to protection from exchange by the self-stacking, and that disappears at elevated temperatures, which does not occur in with the 8-bromo-GMP monomer illustrating the special structural characteristics of the symmetric dimer.;Capped RNA has a unique 5'-end structure containing a terminal N7-methylated guanosine that is joined via a triphosphate bridge to the 5'-OH of all eukaryotic mRNAs. This structure plays a vital role in regulating RNA maturation, processing, transport and translation, but capped RNA is extremely difficult to synthesize chemically due to its instability.;A new protection strategy was devised that uses a lipophilic dimethoxytrityl (DMT) group on the amino group of the N7-methylated guanine activated capping reagent. This allows efficient purification of the final capped RNA on reverse-phase HPLC. Additionally, the DMT group increases the capping reagent solubility in organic solvents which improves the final coupling step.;The synthetic method is general to include a variety of mixed sequence oligonucleotides, and is compatible with reverse-phase HPLC. This method has been used to synthesize and purify the unmodified cap structure m+GpppG, the individual diastereomers of the alpha-thiophosphate analog m 7Gppp(s)G, m7GpppT8 and mixed sequences of m7Gppp-(2'-O-Me-GAUGC), m 7Gppp-(2'-O-Me-GAUGC)2, m7Gppp-(2'- O-Me-GUAUC)4 and m7Gppp-(GUAUC)4. |
