The Double Face of Nucleic Acids

Nucleic acids have been the object of intense and thorough observations for more than a century, leading to the understanding of their structure and function. Their role as genetic information carriers is well established but there are evidences that they are also involved in a series of other less known processes. RNA for example is a single strand biopolymer that, dependently from the primary sequence, can assume complex three-dimensional foldings that allow binding to diverse target molecules or the involvement in catalysis. Being closely related to several cellular events, they are also useful therapeutic targets. This work is essentially divided in two parts, aimed at studying two different and complementary aspects of nucleic acids. While the first project goes into the understanding of the “RNA world” and of the applicability of extraordinary RNA conformational variability in a diagnostic and therapeutic system, the second topic is addressed to study the ability of two compounds to interfere with DNA integration, a genetic process that allows the viral DNA to be inserted into the host genome. Therefore nucleic acids demonstrate their “double face” meaning their ability to be leading actors in diagnosis and therapy but also indispensable supporting actors, being the main targets for several drugs. The first part of the PhD program was focused on the use of SELEX to discover a new diagnostic or therapeutic tool. A protocol for the selection of RNA aptamers binding folic acid was developed. In particular, after 12 cycles of SELEX using affinity chromatography, it was possible to select an enriched pool of single stranded RNA oligonucleotides with affinity for the target. Subcloning and sequencing of the above-mentioned pool allowed the subsequent analysis of the oligonucleotide three-dimensional structure and the determination of the minimum binding sequence to folic acid. Computer tools and RNase protection assay were associated in the experimental protocol to obtain the most probable outcome. A clear region of ligand interaction on RNA was identified; this minimum sequence was chemically synthesized and Isothermal Titration Calorimetry (ITC) used for the determination of the binding constant of folic acid, that resulted in the nanomolar range. The approval from FDA and EMEA of Macugen®, a pegylated aptamer selective for the binding to VEGF and used in the treatment of age-related macular degeneration, is a proof that SELEX can be used to develop good drugs and diagnostics. RNA aptamers against folic acid could now find their way for diagnostic or therapeutic application. Therefore further studies must be addressed to allow their applicability to the desired purpose. The second part of the PhD program was carried out in the Laboratory of Molecular Pharmacology of the National Cancer Institute (National Institute of Health - Bethesda -Maryland - USA) and it takes into consideration DNA integration as target of anti-HIV drugs. HIV-1 integrase is one of the viral enzymes encoded from the POL gene, that catalyses the insertion of the viral DNA into host chromosomes. Using synthetic oligonucleotides mimicking the terminal portion of the U5 viral LTR, it was analyzed the effect of two important drugs (raltegravir, the first integrase inhibitor approved by FDA last year, and elvitegravir, in advanced stage of human clinical trials) on the recombinant wild type integrase and on a series of resistant mutants. The study was addressed to compare raltegravir and elvitegravir on the same in vitro system, with the aim to understand how different aminoacidic point mutations of the protein sequence are responsible in the onset of drug resistance.