Synthesis and evaluation of 2'-O-substituted oligoribonucleotide analogues with new properties

During a previous, exploratory project in our group, it was observed that duplexes formed by oligonucleotides modified with polar 2'-O-substituents were more tolerant towards the addition of 1,2-dimethoxyethane (DME) than RNA and DNA duplexes [1]. Inspired by these results, we developed the hypothesis that such polar 2'-O-substituents could provide some kind of "autonomous" solvation of nucleic acid duplexes through H-bonding with the polar sites of the minor groove (that are normally associated with water molecules). In this work, the systematic study of the pairing properties of such oligoribonucleotide analogues is presented. A total of 18 different modifications were prepared on the basis of a general design, consisting of polyhydroxylated chains linked to the 2'-O-position of ribonucleosides by a formacetal linker. The variation among the different modifications included the length and the configuration of the polyol chains. For the synthesis of the corresponding phosphoramidite building blocks, an efficient general method was developed and the assembly of the oligonucleotides could be carried out under standard RNA or DNA coupling conditions. The pairing properties of these analogues were determined under various conditions, including the presence of organic solvents. The configuration of the stereocenters of the modifications was very important for the strength of the pairing of these new oligonucleotides, with a very strong preference for a DL-configuration at the first two stereocenters. Among the 18 different systems, the (DL)-C4 modified oligonucleotides (2'-O-substituents derived from L-threitol) showed the strongest pairing with RNA and DNA, while the pairing with itself was much weaker. The length of the modifications did not influence the stability of RNA-Mod and DNA-Mod duplexes to a great extent, whereas a strong effect on the stability of the Mod-Mod duplexes was observed. In general, the order of stability of the different duplexes was: Mod-Mod < DNA-Mod < RNA-DNA < DNA-DNA < RNA-Mod < RNA-RNA. Substitution of the canonical set of nucleotides by 2,6-diaminopurine riboside (D), 5-methyluridine (T), 5-methylcytidine (M) and guanosine led to a strong increase of the stability of all the duplexes, but qualitatively, the pairing properties remained unchanged. With this new pairing system, RNA-Mod and DNA-Mod duplexes were stronger than their corresponding natural RNA or DNA duplexes, respectively. The addition of up to 40% of DME led to a decrease of the stability of DNA and RNA duplexes, whereas all duplexes containing at least one of our modified strands were stabilized. Importantly, these oligonucleotides were able to induce an efficient and highly selective strand invasion of RNA duplexes and RNA hairpins, which was the basis for a new design of molecular beacons, combining a high affinity for the RNA target, fast kinetics at room temperature and a high signal-to-noise ratio. With (the more interesting) DNA duplexes, however, such a double-strand invasion did not occur, most likely because the Mod-Mod duplexes were too stable. The introduction of amino groups in our modifications led to a strong decrease of the stability of Mod-Mod duplexes, while DNA-Mod duplexes were more stable as compared to their HO-homologues. Consequently, these new modifications allowed us to induce a double-strand invasion of DNA duplexes, which was, however, less efficient than the one of RNA with HO-modifications, and still needs to be optimized. An NMR structure analysis of an RNA duplex containing (DL)-C4 modified nucleotides revealed that the modifications were, as originally expected, pointed towards the minor groove of the duplex. However, the polar groups were not directly interacting with the nucleobases, but covering the groove by contacting each other. The C4-NH2 modified building blocks could be used to introduce a tether with a reactive NH2-group at a specific position of a RNA hairpin, which then could be used for conjugation reactions. In this context, we developed a new EDTA building block for the preparation of EDTA-oligonucleotide conjugates. Such oligonucleotide conjugates are used for accurate structural investigations of RNA folding and help to identify intermolecular contacts between two oligonucleotides. In collaboration with Philipp Wenter [2], we have prepared the four 13C5-ribose labeled 2'-O-TOM phosphoramidites and their corresponding solid supports. These labeled building blocks were used for the preparation of short oligoribonucleotides with labeled ribose units at specific positions. In the group of Prof. Frédéric Allain (ETH Zurich), these labeled oligoribonucleotides were very successfully used for the structure determination of protein-RNA complexes.