Chemical modification of RNA using DNA catalysts

Site-specific labelling of RNA is of significant importance in many areas of chemical biology. The synthesis of high-quality fluorescent or spin-labelled RNA is a challenging task and often requires multiple steps. This thesis describes the development of new strategies for RNA labelling based on catalytically active DNAs, called deoxyribozymes or DNA catalysts.
A new and efficient method was established that allows direct, postsynthetic labelling of long RNAs at internal ribose residues under mild conditions and in only one step. For implementing this DNA-catalysed RNA labelling approach, we capitalised on a 2',5'-branched RNA-forming deoxyribozyme that was shown to accept various labelled mononucleotides as substrates for ligation to adenosine branch-sites.
In addition, a new deoxyribozyme-based technique was developed for the ligation of labelled RNA fragments to synthesise long modified RNA samples for spectroscopic studies. This provides a valuable, mild alternative to traditional enzymatic approaches and substantially adds to broaden the scope of preparative deoxyribozyme applications. The DNA-catalysed ligation was used for the synthesis of spin-labelled riboswitch RNAs.