Most functional RNA molecules have characteristic structures that are highly conserved in evolution. Many of them contain pseudoknots. Here, we present a method for computing the consensus structures including pseudoknots based on alignments of a few sequences. The algorithm combines thermodynamic and covariation information to assign scores to all possible base pairs, the base pairs are chosen with the help of the maximum weighted matching algorithm. We applied our algorithm to a number of different types of RNA known to contain pseudoknots. All pseudoknots were predicted correctly and more than 85 percent of the base pairs were identified.

<p> An improved method for the synthesis of oligoribonucleotides of defined sequence was developed. The general phosphotriester synthesis of Neilson and co-workers was modified by the introduction of a new condensing agent, mesitylenesulfonyl-1,2,4-triazole, and by the replacement of the bis(cyclohexylammonium) salt of mono-2,2,2-trichloroethyl phosphate with its acid salt. These modifications provided significant increases in the yields for the condensation of protected nucleosides - especially in the case of purine residues. Finally, modification of the three-step procedure for the deprotection of protected oligoribonucleotides resulted in the isolation of oligomers of exceptional purity and biological activity.</p> <p> Oligomers corresponding to natural sequences in transfer RNA molecules were obtained by this improved method of synthesis. These oligomers were then used to study: 1. The formation of short double-stranded RNA helices and 2. The interactions of aminoacyl-tRNA ligases with tRNA fragments.</p> / Thesis / Doctor of Philosophy (PhD)

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