Stereocontrolled synthesis of oligodeoxyribonucleoside boranophosphates by an oxazaphospholidine approach using acid-labile N-protecting groups

Stereocontrolled synthesis and nuclear magnetic resonance analysis of boranophosphate/phosphate chimeric oligonucleotides

This report describes the stereoselective synthesis of boranophosphate/phosphate (PB/PO) chimeric oligodeoxynucleotides (ODNs) and the nuclear magnetic resonance (NMR) analysis of oligomers containing PB linkages. This stereoselective synthesis involved dimer building blocks containing highly stereopure boranophosphotriester linkages, which enabled the synthesis of PB/PO chimeric ODNs via the standard phosphoramidite method. The stereochemistry of dinucleoside and trinucleoside PBs was confirmed by nuclear Overhauser effect spectroscopy (NOESY) experiments. In the NOESY experiments, the stereochemistry was determined from the correlation of the protons of the borane (BH3) group with those of neighbouring 2'-deoxyribose moieties or nucleobases. Thus, the stereochemistry of the PB linkages within the oligomer was determined, and the stereopurity was also confirmed. A PB linkage was introduced into ODNs with retention of the P-configuration of the dimer building blocks without any loss of stereopurity during solid-phase synthesis. This synthetic approach is expected to be a reliable method for introducing PB linkages with precise stereochemistry. Additionally, detailed analysis of the PB linkages via NMR allowed accurate determination of the stereochemistry.

Solid-Phase Synthesis of Phosphate/Boranophosphate Chimeric DNAs Using the H-Phosphonate-H-Boranophosphonate Method

Boranophosphate (PB) DNAs are promising antisense oligonucleotide candidates because of their attractive features, such as high nuclease resistance and low toxicity. However, a full boranophosphate backbone modification to antisense DNAs causes reduced duplex formation with complementary RNAs and reduced antisense activity. In this study, an efficient solid-phase synthesis of phosphate/boranophosphate (PO/PB) chimeric DNA was achieved by the combination of the H-phosphonate and H-boranophosphonate methods. The physiological and biological properties of the synthesized PO/PB chimeric DNAs were also evaluated. The strategy employed herein can facilitate the design and synthesis of PO/PB chimeric DNAs containing site-specific boranophosphate modifications.

Stereocontrolled Synthesis of Boranophosphate DNA by an Oxazaphospholidine Approach and Evaluation of Its Properties

In this paper, we describe the first stereocontrolled synthesis and properties of boranophosphate DNA (PB-DNA), which contains all of the four nucleobases longer than 10mer. Synthesis was accomplished via an oxazaphospholidine approach combined with acid-labile protecting groups on nucleobases. It was demonstrated that there were significant differences between all-( Rp)- and all-( Sp)-PB-DNA in terms of the duplex-formation ability, nuclease resistance, and ribonuclease H (RNase H) activity. In particular, all-( Sp)-PB-DNA was demonstrated to show a duplex-formation ability with RNA and RNase H activity, both of which are necessary for antisense-type nucleic acid therapeutics.

Borane phosphonate DNA: a versatile unnatural internucleotide linkage

Borane phosphonate DNA is a promising molecule for biological applications as well as post-synthesis DNA modification, including DNA functionalization.

Recent advances in H-phosphonate chemistry. Part 1. H-phosphonate esters: synthesis and basic reactions

This review covers recent progress in the preparation of H-phosphonate mono- and diesters, basic studies on mechanistic and stereochemical aspects of this class of phosphorus compounds, and their fundamental chemistry in terms of transformation of P-H bonds into P-heteroatom bonds. Selected recent applications of H-phosphonate derivatives in basic organic phosphorus chemistry and in the synthesis of biologically important phosphorus compounds are also discussed.

Oxidative substitution of boranephosphonate diesters as a route to post-synthetically modified DNA

The introduction of modifications into oligonucleotides is important for a large number of applications in the nucleic acids field. However, the method of solid-phase DNA synthesis presents significant challenges for incorporating many useful modifications that are unstable to the conditions for preparing synthetic DNA. Here we report that boranephosphonate diesters undergo facile nucleophilic substitution in a stereospecific manner upon activation by iodine. We have subsequently used this reactivity to post-synthetically introduce modifications including azides and fluorophores into DNA by first synthesizing boranephosphonate-linked 2'-deoxyoligonucleotides and then treating these oligomers with iodine and various nucleophiles. In addition, we show that this reaction is an attractive method for preparing stereodefined phosphorus-modified oligonucleotides. We have also examined the mechanism of this reaction and show that it proceeds via an iodophosphate intermediate. Beyond nucleic acids synthesis, due to the ubiquity of phosphate derivatives in natural compounds and therapeutics, this stereospecific reaction has many potential applications in organophosphorus chemistry.

Enhancement of the affinity of 2′-O-Me-oligonucleotides for complementary RNA by incorporating a stereoregulated boranophosphate backbone

P-stereodefined boranophosphate 2′-O-Me-oligoribonucleotides (2′-O-Me-PB-ORNs) were synthesized and we revealed that an all-(Sp)-PB-backbone largely stabilized the duplex with RNA.

Solid-phase synthesis of P-boronated oligonucleotides by the H-boranophosphonate method

Recently, P-boronated oligonucleotides have been attracting much attention as potential therapeutic oligonucleotides. In this study, we developed H-boranophosphonate oligonucleotide bearing a borano group and hydrogen atom on the internucleotidic phosphorus and demonstrated that this novel P-boronated oligonucleotide is a versatile precursor to various P-boronated oligonucleotides such as boranophosphate, boranophosphorothioate, and boranophosphoramidate. The method was also applicable to the synthesis of a locked nucleic acid-modified boranophosphate oligonucleotide, which exhibited a dramatically enhanced affinity to complementary oligonucleotides.