Synthesis and biophysical properties of 5'-thio-2',4'-BNA/LNA oligonucleotide

Furan ring opening reaction for the synthesis of 2,5-dicarbonyl-3-ene-phosphates

Furan ring opening reactions are essential in organic synthesis, enabling the incorporation of diverse functional groups and the construction of complex molecular structures. A highly efficient and practical method for synthesizing 2,5-dicarbonyl-3-ene-phosphates from readily available biomass furan and dialkyl phosphonates is reported. The reaction, catalyzed by FeCl3, demonstrated wide substrate scope and high synthetic efficiency. Gram-scale synthesis was achieved, and a one-pot reaction provided a quick access route to the desired compounds. Additionally, a successful Diels-Alder reaction highlighted the versatility of the methodology.

Synthesis of ortho-Phosphated (Hetero)Arylamines through Cascade Atherton-Todd Reaction/[3,3]-Rearrangement from Arylhydroxylamines and Dialkyl Phosphites

A practical and facile strategy for the synthesis of ortho-phosphated (hetero)arylamines from readily available arylhydroxylamines and dialkyl phosphites via cascade Atherton-Todd reaction/[3,3]-rearrangement was developed. This method is amenable to various arylhydroxylamines such as phenylhydroxylamines, naphthylhydroxylamines, and pyridylhydroxylamines, has mild reaction conditions, is oxidant-free, and has good functional-group compatibility and excellent regioselectivity.

Modified internucleoside linkages for nuclease-resistant oligonucleotides

In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.

In vitro and in vivo properties of therapeutic oligonucleotides containing non-chiral 3' and 5' thiophosphate linkages

The introduction of non-bridging phosphorothioate (PS) linkages in oligonucleotides has been instrumental for the development of RNA therapeutics and antisense oligonucleotides. This modification offers significantly increased metabolic stability as well as improved pharmacokinetic properties. However, due to the chiral nature of the phosphorothioate, every PS group doubles the amount of possible stereoisomers. Thus PS oligonucleotides are generally obtained as an inseparable mixture of a multitude of diastereoisomeric compounds. Herein, we describe the introduction of non-chiral 3′ thiophosphate linkages into antisense oligonucleotides and report their in vitro as well as in vivo activity. The obtained results are carefully investigated for the individual parameters contributing to antisense activity of 3′ and 5′ thiophosphate modified oligonucleotides (target binding, RNase H recruitment, nuclease stability). We conclude that nuclease stability is the major challenge for this approach. These results highlight the importance of selecting meaningful in vitro experiments particularly when examining hitherto unexplored chemical modifications.

Synthesis and Properties of Oligonucleotides Having Ethynylphosphonate Linkages

Ethynylphosphonate (EP)-linked thymidine dimers were synthesized via a palladium-catalyzed cross-coupling reaction and successfully incorporated into oligonucleotides. The oligonucleotides containing EP linkages appropriately formed a duplex with their complementary single-stranded RNA (ssRNA) and single-stranded DNA. The oligonucleotides containing both the EP linkages and 2'-O,4'-C-methylene-bridged nucleic acid/locked nucleic acid exhibited strong duplex-forming ability toward the complementary ssRNA. The EP-modified oligonucleotides exhibited higher exonuclease resistances than their natural counterparts. Moreover, one EP modification to a gapmer-type antisense oligonucleotide resulted in a switch of the cleavage site in the target ssRNA. Therefore, the EP modification can be applied for controlling the cleavage site in the RNase H-dependent mechanism.

Synthesis and biophysical properties of carbamate-locked nucleic acid (LNA) oligonucleotides with potential antisense applications

Antisense oligonucleotides (ASOs) are becoming important drugs for hard to treat diseases. Modifications to their DNA backbones are essential to inhibit degradation in vivo, but they can reduce binding affinity to RNA targets. To address this problem we have combined the enzymatic resistance of carbamate (CBM) DNA backbone analogues with the thermodynamic stability conferred by locked nucleic acid sugars (LNA). Using a dinucleotide phosphoramidite strategy and automated solid phase synthesis, we have synthesised a set of oligonucleotides modified with multiple LNA-CBM units. The LNA sugars restore binding affinity to RNA targets, and in this respect LNA position with respect to the CBM linkage is important. Oligonucleotides containing carbamate flanked on its 5'and 3'-sides by LNA form stable duplexes with RNA and unstable duplexes with DNA, which is desirable for antisense applications. Carbamate-LNA modified oligonucleotides also show increased stability in the presence of snake venom and foetal bovine serum compared to LNA or CBM backbones alone.

Nearest-neighbour parameters optimized for melting temperature prediction of DNA/RNA hybrids at high and low salt concentrations

Gene editing technologies sparked a renewed interest in the hybridization of DNA/RNA duplexes, yet little improvement on nearest-neighbour parameters was made over the past two decades. For low sodium concentration no parameter set was yet calculated. Here, we revised the existing experimental datasets and used an expanded set of sequences from which we recalculated the nearest-neighbour parameters, reducing the average temperature prediction uncertainty to 1.6 °C. Two experimental sets using temperatures extracted via different methods were used with similar results, with the curve-fitting method achieving a slight advantage in prediction quality over other methods. Additionally, we obtained new parameters for low salt with an average uncertainty of 0.98 °C. We also tested several types of salt correction factors and concluded that it is advisable to use those originally developed for RNA/RNA rather than for DNA/DNA.

A scalable electrochemical dehydrogenative cross-coupling of P(O)H compounds with RSH/ROH

A practical, scalable electrochemical dehydrogenative cross-coupling of P(O)H compounds with thiols, phenols and alcohols in both an undivided cell and a continuous-flow setup is disclosed. Its broad substrate scope (>50 examples), good functional-group tolerance and scalability (>10 g) show potential for practical synthesis. A preliminary mechanistic study suggests that the phosphorus radicals are involved in the catalytic cycle.