Peptide-rna recognition: investigation of non-covalent interactions using esi-mass spectrometry and proton nmr spectroscopy

• Main Author: Sanh, Alan Dominique
• Format: Dissertation
• Language: English
• Published: ProQuest Dissertations & Theses 01-01-2004
• Subjects: Biophysics

Non-covalent interactions between amino acids, peptides and proteins with RNA play significant roles in many biological systems. Therefore, the aim of this thesis was to investigate the interactions between specific RNA bases and sequences thereof with appropriate uncharged di/tri-peptides using the technique of LC-MS and 1H NMR. For these studies, cytidine and uridine-3'-phosphoamidites were synthesised in a suitably protected form. A variety of 2'-OH protecting groups were explored and Tetrahydropyranyl (THP) and allyl were found to be the best for our purposes. Alternative transient 5', 3'-OH protecting groups were also examined in order to overcome limitations of the normal 1,1,3,3-tetraisopropyldisiloxane (TIPDS) group.?? Since the premise of this research was based on the theory that the third base of the codon is not required for selective recognition, we prepared abasic RNA monomers and introduced them into RNA oligomers to check their influence on binding. In addition, peptide analogous and heterocyclic compounds (naphthyridine derivatives), designed to mimic RNA bases, were prepared and their ability to hydrogen bond to suitable nucleotide bases determined. The binding studies performed using LC-MS involved RNA oligomers, immobilised onto a controlled pore glass (CPG) solid support, being subjected to a continuos flow of a solution of the selected peptide in methanol. The binding parameters were evaluated using curve fit models. This technique proved to be sensitive since only 3% in weight of RNA anchored to the resin was sufficient to estimate discrimination between peptides. The data presented when analysed in a certain way may show some differnces between the interaction of two tripeptides with the supported oligonucleotides.