Design and NMR characterization of reversible head-to-tail boronate-linked macrocyclic nucleic acids.

Inspired by the ability of boronic acids to bind with compounds containing diol moieties, we envisioned the formation in solution of boronate ester-based macrocycles by the head-to-tail assembly of a nucleosidic precursor that contains both a boronic acid and the natural 2',3'-diol of ribose. DOSY NMR spectroscopy experiments in water and anhydrous DMF revealed the dynamic assembly of this precursor into dimeric and trimeric macrocycles in a concentration-dependent fashion as well as the reversibility of the self-assembly process. NMR experimental values and quantum mechanics calculations provided further insight into the sugar pucker conformation profile of these macrocycles.

Synthesis and structural characterization of monomeric and dimeric peptide nucleic acids prepared by using microwave-promoted multicomponent reactions.

A solution phase synthesis of peptide nucleic acid monomers and dimers was developed by using microwave-promoted Ugi multicomponent reactions. A mixture of a functionalized amine, a carboxymethyl nucleobase, paraformaldehyde and an isocyanide as building blocks generates PNA monomers which are then partially deprotected and used in a second Ugi 4CC reaction, leading to PNA dimers. Conformational rotamers were identified by using NMR and MD simulations.

The biolabile 2'-O-pivaloyloxymethyl modification in an RNA helix: an NMR solution structure.

The pivaloyloxymethyl (PivOM) group is a biolabile 2'-O-ribose protection that is under development in a prodrug-based approach for siRNA applications. Besides an expected cellular uptake, nucleic acid sequences carrying PivOM showed also increased nuclease resistance and, in most cases, an affinity for complementary RNA. The r(CGCU*ACGC)dT:r(GCGUAGCG)dT model duplex containing a single modified residue (U*) was synthesized and its solution structure was determined by NMR. The duplex showed a maintained A-RNA helix. In U*, both 2'-O-acetal ester side chain and ring pucker presented a notable rigid conformation. The PivOM moiety was oriented with the carbonyl group turned outside the minor groove and with trans, -ac and -ac torsion angles around the C2'-O2', O2'-CA and CA-OB1 bonds respectively. Gauche effects and dipolar interactions between the PivOM and the backbone appeared to be the predominant factors influencing the PivOM conformation and the orientation of the two supplementary H acceptors suggested that hydration could also play a role in the duplex stability.

Synthesis and preliminary evaluation of pro-RNA 2'-O-masked with biolabile pivaloyloxymethyl groups in an RNA interference assay.

The cellular delivery of bioactive nucleic acid-based drugs such as small interfering RNA (siRNA) represents a major technical hurdle for their pharmaceutical application. Prodrug-like approaches provide an attractive concept to address the delivery problem. With the aim to prepare RNA-based prodrugs bearing biolabile protections which facilitate cellular uptake and are prone to be removed enzymatically inside cells in order to release functional RNA, we synthesized pro-RNA totally or partially masked in 2'-OH position with pivaloyloxymethyl (PivOM) groups. A suitable strategy has been developed to synthesize and to purify base-sensitive mixed 2'-OH/2'-O-PivOM oligoribonucleotides, and to include them in siRNA. In this strategy, the fluoride labile [(triisopropylsilyl)oxy]-benzyloxycarbonyl group (tboc) as nucleobase protection (for A and C), the TBS group as 2'-OH protection and the Q-linker to solid-support were compatible with the PivOM groups masking some 2'-OH. We have taken advantage of the specific stability of the PivOM group to apply selected acidic, basic, and fluoride ions treatment for the deprotection and release of pro-RNA. This kind of pro-siRNA was studied in a human cell culture-based RNAi assay and preliminary promising data are discussed.

Expanding the borononucleotide family: synthesis of borono-analogues of dCMP, dGMP and dAMP.

We previously reported the synthesis of a borononucleotide analogue of thymidine monophosphate and its association towards the formation of a new borono-linked dinucleotide. Here we describe the completion of the set of four 2'-deoxyborononucleotide analogues of natural nucleotide monophosphates, namely the previously unknown dCbn, dGbn and dAbn. These analogues were all prepared from the respective 5'-aldehydic nucleosides through a homologation/reduction sequence. The borononucleotides were subsequently obtained by either borylation (dCbn and dGbn) or cross-metathesis (CM) in the presence of the Hoveyda-Grubbs catalyst (dAbn). The reversible formation of the corresponding dinucleotides between these new analogues and uridine was studied by (1)H NMR, and semi-empirical calculations were carried out to provide bond length and electrostatic information that assess the structural similarities existing between these bioisosteres and their natural counterparts.

Synthesis of a new internucleosidic linkage: the borononucleotides.

The synthesis of a borononucleotide analogue of thymidine and its association with various nucleosides, nucleotides and saccharides is described.

Borononucleotides: synthesis, and formation of a new reversible boronate internucleosidic linkage.

The synthesis of a borononucleotide analogue of thymidine and its association towards the formation of new borono-linked dimers is described.

First evaluation of acyloxymethyl or acylthiomethyl groups as biolabile 2'-O-protections of RNA.

[reaction: see text] Short oligo-U sequences containing 2'-O-acyloxymethyl or acylthiomethyl groups as biolabile 2'-O-protections of RNA have been synthesized. These modified homouridylates are deprotected upon cellular esterase activation to release the parent RNA. They exhibit exceptional resistance to nuclease degradation, and the evaluation of their pairing properties shows that the 2'-acyloxymethyl groups do not prevent the duplex dsRNA formation. These biolabile 2'-modifications overcome the first hurdle to turn oligoribonucleotides into candidates for RNA interference drugs.