Studies on the formation of i-motif structures at neutral pH. Use of cytidine analogues and importance of minor groove tetrads on mini i-motifs stabilization

Abstract

Given the increasing interest in i-motif structures, obtaining such structures as well as detailed structural information under physiological conditions have become hot topics in the structural biology field. In this context, the main objectives of this thesis are focused on the design and detailed characterization of several oligonucleotide sequences that may form stable i-motif structures at neutral pH. The starting point is the mini i-motif structure, extensively studied in the research group that exhibits unusual high pH and thermal stability. These are dimeric structures stabilized by the formation of two hemiprotonated C:C+ base pairs capped at both ends by minor groove G:T:G:T tetrads. With the aim of getting deeper insights in this type of structures and enhance their stability at physiological conditions, different approaches were followed. A first strategy consisted in the incorporation of a neutral analogue of protonated cytidine (pseudoisocytidine, psC) occupying specific positions of the motif. The 3H-tautomer of psC, thanks to the extra hydrogen-bond donor, can form neutral base pairs completely isomorphic to hemiprotonated C:C+ pairs. psC was incorporated in different positions of dimeric mini i-motifs and in the telomeric sequence (HT0). The effect of the incorporation of psC depends on its position in the structure, being in most cases destabilizing. Neutral psC:C base pairs stabilize i-motifs at neutral pH, but the stabilization only occurs when psC:C base pairs are located at the ends of intercalated C:C+ stacks. Structural and stability data on the incorporation of pseudocytidine in i-motifs suggest that positively charged base pairs in the core of the structure are necessary to stabilize this non-canonical DNA structure.

A second approach focused on exploring the compatibility of i-motif structures with other reported minor groove tetrads. The effect of different minor groove tetrads in i-motifs was studied in the context of short linear and cyclic oligonucleotides, affording dimeric mini i-motifs, but also in longer sequences that may form monomeric mini i-motif structures. The results show that the mini i-motif is compatible with different type of minor groove tetrads and a stability ranking could be established: G:C:G:T ≥ G:C:G:C >> G:T:G:T, exhibiting monomeric structures enhanced stability. Interestingly, a consensus sequence was outlined based on the results obtained for the set of mini i-motif-forming sequences. The mapping of this sequence throughout the human genome by bioinformatics analysis revealed a statistical prevalence. The distribution found for these sequences is not random, being much more frequent in regulatory regions

Finally, a fluorescent cytidine analogue (1,3-diaza-2-oxophenoxazine, tCo), capable to hybridize as a cytosine and maintaining the ability to form Watson-Crick as well as hemiprotonated base pairs, was tested as an internal probe for the characterization of local environments within i-motif structures. NMR spectroscopy indicated both types of hybridization (tCo:C+ and G:tCo) are compatible with the mini i-motif structure at neutral pH. Interestingly, the fluorescence signal of tCo suffers a sever quenching when forming an hemiprotonated base pair, compared to the very little quenching that shows upon WC hybridization. Hence, tCo was successfully used as fluorescent probe for monitoring conformational transitions between different species of tCo-containing sequences. Moreover, when replacing a cytosine residue involved in a C:C+ pair, the favorable stacking between tCo and G:C base pairs from the capping minor groove assemblies provokes enhanced stability of the structure against both pH and temperature. Very remarkably, the visualization of mini i-motif structures in cellular media was accomplished by confocal fluorescence microscopy after the successful transfection of HeLa cells with tCo-containing oligonucleotides.

En el marc de les estructures no canòniques dels àcids nucleics i les seves possibles implicacions biològiques, aquesta tesi te com a objectiu principal l’obtenció i caracterització estructural d’estructures i- motif que siguin estables a pH neutre. El punt de partida és l’estructura mini i-motif, un tipus de motiu que presenta una inusual elevada estabilitat front pH i temperatura. Es tracta d’una estructura dimèrica estabilitzada per la formació de dos parells hemiprotonats C:C+ que interaccionen per apilament amb dues tètrades G:T:G:T de solc menor que actuen de tapa de l’estructura. Per a aprofundir en l’estudi d’aquest tipus de motius i augmentar-ne la seva estabilitat a pH fisiològic, diferents aproximacions s’han dut a terme. En la primera aproximació, s’ha explorat la incorporació d’un anàleg neutre de citidina protonada (pseudoisocitidina, psC), capaç de formar parells neutres isomòrfics als parells hemiprotonats C:C+. Els estudis realitzats demostren que l’efecte de la psC en depèn fortament de la posició dins l’estructura. La formació de parells hemiprotonats al centre de l’estructura és fonamental i la formació de parells neutres només és tolerada pels parells terminals, produint-se en aquest cas una certa estabilització. Una segona línia de treball s’ha centrat en explorar la compatibilitat d’estructures i-motif amb altres tètrades de solc menor. S’han estudiat diferents seqüències, lineals i cícliques, que donarien lloc a estructures mini i-motif amb diferents associacions de nucleobases a les tètrades. Els estudis demostren que el mini i-motif és compatible amb diferents tètrades de solc menor i s’ha pogut establir el següent rànquing d’estabilitat G:C:G:T ≥ G:C:G:C >> G:T:G:T. Cal destacar que, la seqüència consens per aquest tipus d’estructures s’ha determinat que és prevalent al genoma humà. Finalment, s’ha incorporat un anàleg de citidina fluorescent (1,3-diaza-2-oxofenoxazina, tCo), substituint citosines en posicions especifiques de l’estructura. Els resultats demostren que tCo actua de forma eficient com a sonda local per a monitoritzar transicions conformacionals i que, en posicions específiques te un efecte força positiu en l’estabilitat tèrmica del motiu. Aquest fet ha permès utilitzat un d’aquests derivats per a visualitzar el plegament de l’estructura en medi cel·lular.