Date of Award
Doctor of Philosophy (PhD)
The stability of short, imperfect RNA double helices was investigated by proton magnetic resonance spectroscopy, since this physical technique can give conformational information of solution species at the individual nucleoside level. The short oligoribonucleotides used in these studies were chemically synthesized by the phosphotriester method of Neilson and associates, which is capable of preparing a wide variety of sequences in the quantities required for NMR spectroscopic experiments. The work reported in this thesis was the first to combine chemical synthesis of oligoribonucleotides with pmr spectroscopic techniques to investigate systematically the effect of imperfections on the stability of short RNA duplexes:
1. The mechanism by which a dangling base region stabilizes an adjacent duplex region was studied. The results of this study demonstrated, for the first time, that a dangling base stabilizes a double helix by increasing favourable base stacking interactions without reducing fraying of terminal base pairs.
2. The duplex set AGGA:UCCU was studied as a model of the Shine-Dalgarno mRNA-16 S rRNA binding site. The AGGA:UCCU duplex was more stable than two other duplexes with identical base composition, CAUG fray at the terminal A-U base pairs. This result was the first to demonstrate that fraying is a sequence related phenomenon.
3. The effect of small loops on the stability of short duplexes was investigated by the pentanucleotides CAXUG (X = A,G,C,U). These pentamers did not form double helices with a non-bonded base opposition under conditions where CAUG exists as a stable duplex. This result suggests that short duplex regions separating small loops may be more susceptible to transient opening than other duplex regions in native RNAs.
4. The study of the duplex set CAGUG:CAUUG was the first to investigate the formation of a G-U wobble base pair within-a regular Watson-Crick base paired double helix. The use of pmr spectroscopy allowed the observation that the G-U base pair was less stable than the surrounding Watson-Crick base-pairs.
5. Certain sequences, for example CGCG, are capable of forming both a perfect helix and a staggered helix. The results of a pmr study of CGGC, which can only form a staggered duplex, demonstrated that the staggered duplex formed in solution must have a special conformation different from the conformation of a perfect helix. The pmr study of CGCG was probably complicated by the existence of a complex series of equilibria between random coil, perfect double helix and staggered duplex. Sequences which can only form a perfect duplex should be chosen for study to keep the helix-coil transition under study relatively simple.
Some of the results presented in this thesis have appeared in the literature:
1. P.J. Romaniuk, D.W. Hughes, R.J. Gregoire, T. Neilson and R.A. Bell. "Contribution of a G-U Base Pair to the Stability of a Short RNA Helix." (1979) J. Chemical Soc. Chemical Commun., in press.
2. P.J. Romaniuk, D.W. Hughes, R.J. Gregoire, T. Neilson and R.A. Bell. "Stabilizing Effect of Dangling Bases on a Short RNA Double Helix as Determined by Proton Nuclear Magnetic Resonance Spectroscopy." (1978) J. American Chemical Soc. 100, 3971.
3. P.J. Romaniuk. T. Neilson. D.W. Hughes and R.A. Bell. "Proton Magnetic Resonance Studies on Short Duplexes. II. The Self- Complementary Oligoribonucleotide CpApUpG." (1978) Can. J. Chem. 56, 2249.
Romaniuk, Paul John, "Stability Studies of Short, Imperfect RNA Double Helices" (1979). Open Access Dissertations and Theses. Paper 3240.