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Boronate esters formed by reaction of an oligonucleotide carrying a 5′‐boronic acid moiety with the 3′‐terminal cis‐diol of another have been shown previously to assist assembly of fragmented DNAzymes. Here we demonstrate that boronate esters replacing the natural phosphodiester linkage at selected sites of two functional RNAs, the hairpin ribozyme and the Mango aptamer, allow assembly of functional structures. The hairpin ribozyme, a small naturally occurring RNA that supports the reversible cleavage of appropriate RNA substrates, is very sensitive to fragmentation. Splitting the ribozyme at four different sites led to a significant decrease or even loss of cleavage and ligation activity. Ribozymes assembled from fragments capable of boronate ester formation showed restoration of cleavage activity in some but not all cases, dependent on the split site. Ligation proved to be more challenging, no supportive effect of the boronate ester was observed. Split variants of the Mango aptamer also showed a dramatic loss of functionality, which however, was restored when 5′‐boronic acid modified fragments were used for assembly. These studies show for the first time that boronate esters as internucleoside linkages can act as surrogates of natural phosphodiesters in functional RNA molecules. [ABSTRACT FROM AUTHOR]

Over the last decades, boron and nucleic acids chemistries have gained a lot of attention for biological, medicinal and analytical applications. Our laboratory has a long‐standing interest in both chemistries and owing to the ability of boronic acids to react with cis‐diol function in aqueous media we developed over the years a variety of applications ranging from molecular recognition and sensing to the development of reversible dynamic systems in which the natural phosphodiester linkage was replaced by a boronate. In this account, we summarize research results from our group from our preliminary studies on molecular recognition of ribonucleosides to the dynamic assembly of functional DNAzymes. In particular, the various parameters influencing the dynamic nature of these reversible covalent bonds able to respond to external stimuli are discussed. Finally, current challenges and opportunities for boron‐based nucleic acids are also addressed. [ABSTRACT FROM AUTHOR]

It has long been debated whether easily reducible azide groups can withstand the conditions of oligonucleotide synthesis by phosphoramidite chemistry. We have synthesized various 2′‐ and 3′‐azido modified nucleosides and immobilized them on controlled pore glass (CPG) to be used as starting material for the synthesis of oligonucleotides (ONs) with 3′‐terminal azide (attached to C2′ or C3′). In a model study, immobilized 3′‐azidoadenosine was used as a starting block for the synthesis of a series of oligodeoxynucleotides (ODNs) of increasing length. Upon synthesis, the ODNs were enzymatically digested into monomers and analyzed by RP‐HPLC. A peak corresponding to 3′‐azidoadenosine was clearly identified in all samples. Quantitative analysis showed that 3′‐azidoadenosine was present in nearly the expected ratio to deoxycytidine, which was used as an internal standard. Most importantly, the ratio remained the same for all three ODNs regardless of their length, demonstrating that a higher number of coupling cycles does not lead to higher degradation of the azide. Thus, 2′‐ or 3′‐azido nucleosides attached to a solid support are excellent starting materials for the synthesis of oligonucleotides with 3′‐terminal azide. [ABSTRACT FROM AUTHOR]

The 10–23 DNAzyme is an artificially developed Mg2+‐dependent catalytic oligonucleotide that can cleave an RNA substrate in a sequence‐specific fashion. In this study, new split 10–23 DNAzymes made of two nonfunctional fragments, one of which carries a boronic acid group at its 5′ end, while the other has a ribonucleotide at its 3′ end, were designed. Herein it is demonstrated that the addition of Mg2+ ions leads to assembly of the fragments, which in turn induces the formation of a new boronate internucleoside linkage that restores the DNAzyme activity. A systematic evaluation identified the best‐performing system. The results highlight key features for efficient control of DNAzyme activity through the formation of boronate linkages. [ABSTRACT FROM AUTHOR]

The use of the Cu(I)-catalyzed azide–alkyne cycloaddition (CuAAC) reaction for the preparation of oligonucleotide conjugates is by now familiar. However, the selective introduction of boronic acids into DNA and RNA sequences by CuAAC reactions has long been considered impossible due to the incompatibility of the boronic acid moiety with copper salts. Here we describe two new methods for the selective on-column functionalization of oligonucleotides with boronic acids via two different CuAAC reactions. The first one allows the introduction of a phenylboronic acid at the 5′-extremity of oligonucleotides, while the selective intrastrand positioning of the modification can be achieved with the second one. Both methods were applied to the DNA and RNA series (up to a 20-mer) with good isolated yields and excellent purities. These results illustrate the potential of the reported methods for selective incorporation of boronic acids into oligonucleotides. [ABSTRACT FROM AUTHOR]

A simple metal-free borylation of aryl iodides mediated by a fluoride sp²-sp³ diboron adduct is described. The reaction conditions are compatible with various functional groups. Electronic effects of substituents do not affect the borylation while steric hindrance does. The reaction proceeds via a radical mechanism in which pyridine serves to stabilize the boryl radicals, generated in situ. [ABSTRACT FROM AUTHOR]

Boronate esters formed by reaction of an oligonucleotide carrying a 5'-boronic acid moiety with the 3'-terminal cis-diol of another have been shown previously to assist assembly of fragmented DNAzymes. Here we demonstrate that boronate esters replacing the natural phosphodiester linkage at selected sites of two functional RNAs, the hairpin ribozyme and the Mango aptamer, allow assembly of functional structures. The hairpin ribozyme, a small naturally occurring RNA that supports the reversible cleavage of appropriate RNA substrates, is very sensitive to fragmentation. Splitting the ribozyme at four different sites led to a significant decrease or even loss of cleavage and ligation activity. Ribozymes assembled from fragments capable of boronate ester formation showed restoration of cleavage activity in some but not all cases, dependent on the split site. Ligation proved to be more challenging, no supportive effect of the boronate ester was observed. Split variants of the Mango aptamer also showed a dramatic loss of functionality, which however, was restored when 5'-boronic acid modified fragments were used for assembly. These studies show for the first time that boronate esters as internucleoside linkages can act as surrogates of natural phosphodiesters in functional RNA molecules., (© 2023 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

The first bio-inspired N-Heterocyclic Carbene (NHC)-catalyzed Stetter reaction in aqueous medium is reported with benzaldehyde and chalcone as model substrates. A screening of azolium salts as precatalysts revealed the remarkable efficiency of synthetic thiazolium salt 8 (up to 90% conversion in pure water at 75 °C). The reaction was successfully extended to various simple aldehyde substrates. The effect of temperature was also investigated in order to extend the reaction to lower temperature allowing a potential application to sensitive biomolecules. This study highlighted the influence of both solvent and temperature on the 1,4-diketone 3/benzoin 4 ratio. New precatalysts 26 and 27 were designed and synthesized to explore a possible compartmentalization of the reaction in aqueous conditions. Owing to the use of inexpensive metal-free N-Heterocyclic Carbene (NHC) as a bioinspired catalyst, we anticipate that this green strategy in aqueous conditions will be attractive for bioconjugation of many biomolecule-type aldehydes and enone derivatives., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)