Solid-state NMR studies of RNA

Since conformations of nucleosides and nucleotides affect their functions both as biological molecules and constituents of nucleic acids, methods to investigate their conformational properties are essential. Conformations of nucleosides and nucleotides are usually described by three parameters; sugar puckering mode, glycosidic and C4$\sp\prime$-C5$\sp\prime$ exocyclic torsion angles. The objective of the first part of this thesis is to determine the sensitivity of $\sp{13}$C solid state sugar chemical shifts to the three conformational parameters in ribo-nucleosides and nucleotides. Here, it is found that two predominantly N and S sugar puckers are distinguished by the magnitudes of C$\sb4\sp\prime$ and C$\sb1\sp\prime$ resonances. Furthermore, in the N sugar conformers the gt, and in the S conformers the syn conformations are detectable by the values of other sugar resonances. Data analyses are carried out by using multivariate statistical techniques owing to interdependence of sugar chemical shifts to the conformational parameters. Once the data are analyzed and means to determine conformational parameters established, chemical shifts of various RNA polymers in solid and oligonucleotides in solution will be examined. Furthermore, it is found that the conformations of polyribonucleotides could be affected by base-unstacking and drug intercalation. Such conformational changes are detected by the magnitude of the C$\sb5\sp\prime$ resonance, indicating the occurrence of C$\sb4\sp\prime$-C$\sb5\sp\prime$ exocyclic torsion angle in the gt mode. From there the study will continue to the $\sp{31}$P nucleus, the other component in DNA and RNA backbone. Here, the changes in the conformation of sugar-phosphate backbone as the results of variations in the water content in the medium and intercalation of pyronin Y will be monitored by changes in $\sp{31}$P chemical shift. In the final chapter, a $\sp{31}$P single crystal study will be performed on a very important nucleotide, 5$\sp\prime$-adenosine monophosphate. This study will determine the chemical shift tensor that represents the three-dimensional electronic environment of phosphorus in 5$\sp\prime$-AMP