Modified oligonucleotides for triple helix studies and for the obtention of structures with biomedical and technological interest

Abstract

Oligonucleotides are short fragments of DNA (10-100nt) which are of great interest because their applications in molecular biology, biomedicine and nanotechnology. As a result of their ability to base pairing, oligonucleotides can be used as primers, hybridization probes in biosensors, agents for controlling gene expression, structural material in nanotechnology or as substrates for a variety of biochemical and biophysical studies. Chemical modification of oligonucleotides as well as conjugation to different functional molecules allows for modulation of both therapeutical and biotechnological properties.

This thesis is focused in the nucleic acid chemistry field and the main objective is the synthesis of modified oligonucleotides for obtaining structures with therapeutical and/or biotechnological interest.

Oligonucleotides capable to form structures other than the canonical DNA double helix have received considerable attention in the last years. The ability of triplex forming oligonucleotides (TFOs) to bind specifically to certain duplex DNA regions provides a strategy for site-directed modification of genomic DNA. Besides, G-quadruplexes are four-stranded DNA structures stabilized by stacking of guanine tetrads which have been found in telomeres and some promoters and play a role in regulation of transcription and translation. In addition, they are also interesting for nanotechnological devices.

In this context, the first part of the research work was addressed to synthesize parallel stranded oligonucleotide clamps carrying LNA (locked nucleic acid) residues and study the stability of the triplex formed with DNA and RNA target sequences. Secondly, a novel strategy to obtain parallel clamps using the non-templated chemical ligation of two oligonucleotides by 5’-5’ linkages was developed. For this purpose, several protocols for introduce azido and alkyne moieties in the 5’-end of different sequences were developed so that the modified DNA strands could form a parallel hairpin after their chemical ligation by click chemistry. Thirdly, a system composed of four DNA strands whose 5’ ends are covalently attached was designed to form a monomolecular parallel G-quadruplex, which was used to study the effects of some nucleobase modifications in quadruplex structure. Finally, oligonucleotide conjugates carrying Cu(II) complexes were synthesized to construct arrays of electrochemical oscillators for nanotechnology applications.