Cleavage of oligonucleotides containing a P3'→N5' phosphoramidate linkage mediated by single-stranded oligonucleotide templates.

Double-stranded DNA (dsDNA) templates can hybridize to and accelerate cleavage of oligonucleotides containing a P3'→N5' phosphoramidate (P-N) linkage. This dsDNA-templated cleavage of P-N linkages could be due to conformational strain placed on the linkage upon triplex formation. To determine whether duplex formation also induced conformational strain, we examined the reactivity of the oligonucleotides with a P-N linkage in the presence of single-stranded templates, and compared these reactions to those with dsDNA templates. P-N oligonucleotides that are cleaved upon duplex formation could be used as probes to detect single-stranded nucleic acids.

Double-stranded DNA-templated cleavage of oligonucleotides containing a P3'->N5' linkage triggered by triplex formation: the effects of chemical modifications and remarkable enhancement in reactivity.

We recently reported double-stranded DNA-templated cleavage of oligonucleotides as a sequence-specific DNA-detecting method. In this method, triplex-forming oligonucleotides (TFOs) modified with 5'-amino-2',4'-BNA were used as a DNA-detecting probe. This modification introduced a P3'→N5' linkage (P-N linkage) in the backbone of the TFO, which was quickly cleaved under acidic conditions when it formed a triplex. The prompt fission of the P-N linkage was assumed to be driven by a conformational strain placed on the linkage upon triplex formation. Therefore, chemical modifications around the P-N linkage should change the reactivity by altering the microenvironment. We synthesized 5'-aminomethyl type nucleic acids, and incorporated them into TFOs instead of 5'-amino-2',4'-BNA to investigate the effect of 5'-elongation. In addition, 2',4'-BNA/LNA or 2',5'-linked DNA were introduced at the 3'- and/or 5'-neighboring residues of 5'-amino-2',4'-BNA to reveal neighboring residual effects. We evaluated the triplex stability and reaction properties of these TFOs, and found out that chemical modifications around the P-N linkage greatly affected their reaction properties. Notably, 2',5'-linked DNA at the 3' position flanking 5'-amino-2',4'-BNA brought significantly higher reactivity, and we succeeded in indicating that a TFO with this modification is promising as a DNA analysis tool.

Acid-mediated cleavage of oligonucleotide P3' --> N5' phosphoramidates triggered by sequence-specific triplex formation.

The P-N bond in oligonucleotide P3' --> N5' phosphoramidates (5'-amino-DNA) is known to be chemoselectively cleaved under mild acidic conditions. We prepared homopyrimidine oligonucleotides containing 5'-amino-5'-deoxythymidine (5'-amino-DNA thymine monomer) or its conformationally locked congener, 5'-amino-2',4'-BNA thymine monomer, at midpoint of the sequence. The effect of triplex formation with homopurineohomopyrimidine dsDNA targets on acid-mediated hydrolysis of the P3' --> N5' phosphoramidate linkage was evaluated. Very interestingly, it was found that the triplex formation significantly accelerates the P-N bond cleavage.

Synthesis of novel 2'-deoxy type trans-3',4'-bridged nucleic acid.

We newly designed and synthesized a 2'-deoxy type trans-3',4'-bridged nucleic acid (trans-3',4'-BNA) analogues bearing a 4,7-dioxabicyclo[4.3.0]nonane structure. The synthesis of the trans-3',4'-BNA was carried out successfully from thymidine over 21 steps. The structure of trans-3',4'-BNA was confirmed by x-ray crystallographic analysis, indicating that the furanose ring has a typical S-type conformation with C(3')-exo puckering.

Synthesis and properties of a 2'-deoxy analogue of trans-3',4'-BNA with an S-type sugar conformation.

We previously synthesized bridged nucleic acid (BNA) analogues possessing an S-type sugar conformation. Recently, we achieved the synthesis of a 2'-deoxy analogue of trans-3',4'-BNA. The structure of this compound was confirmed by X-ray crystallography, which indicated that its sugar ring had an S-type conformation. The hybridization ability of the 2'-deoxy-trans-3',4'-BNA-modified oligonucleotide with DNA and RNA complements was evaluated, and it was found that 2'-deoxy-trans-3',4'-BNA showed superior hybridization ability compared with other BNA analogues with S-type sugar conformation.

Nucleotides and nucleic acids: a source of inspiration for the development of new, phosphorus-centered functional groups.

Synthetic methodologies aiming at the creation of new phosphorus-centered functional groups are reported, as well as applications to the field of nucleotide chemistry. Thus, difluorophosphonothioate-based, ionic reagents 3b and 3d are shown to allow the stereocontrolled and efficient synthesis of phosphonodifluoromethyl analogues of nucleoside-3'-phosphates. An alternate, radical approach describes the use of hypophosphorous acid to stereoselectively link two furanosyl units in positions 3 and 5, and to provide an access to alpha,alpha-difluoro-H-phosphinates. These intermediates are shown to be precursors to the corresponding fluorinated phosphonic acids, phosphonothioic acids and variously substituted phosphinates.

Synthesis and properties of trans-3',4'-bridged nucleic acids having typical S-type sugar conformation.

The synthesis of nucleoside analogues with a conformationally restricted sugar moiety is of great interest. The present research describes the synthesis of BNA (bridged nucleic acid) monomers 1 and 2 bearing a 4,7-dioxabicyclo[4.3.0]nonane skeleton and a methoxy group at the C2' position. Conformational analysis showed that the sugar moiety of these monomers is restricted in a typical S-type conformation. It was difficult to synthesize the phosphoramidite derivative of the ribo-type monomer 1, while the phosphoramidite of the arabino-type monomer 2 was successfully prepared and incorporated into oligodeoxynucleotides (ODNs). The hybridization ability of the obtained ODN derivatives containing 2 with complementary strands was evaluated by melting temperature (T(m)) measurements. As a result, the ODN derivatives hybridized with DNA and RNA complements in a sequence-selective manner, though the stability of the duplexes was lower than that of the corresponding natural DNA/DNA or DNA/RNA duplex.

Synthesis and properties of 2'-O,4'-C-methyleneoxymethylene bridged nucleic acid.

A novel bridged nucleic acid (BNA) analogue, 2'-O,4'-C-methyleneoxymethylene bridged nucleic acid (2',4'-BNA(COC)), was synthesized and incorporated into oligonucleotides. The 2',4'-BNA(COC) modified oligonucleotides showed high binding affinity with an RNA complement and significant enzymatic stability against snake venom phosphodiesterase.

trans-3',4'-BNAs, novel nucleic acid analogues with an S-type conformation: synthesis and incorporation into oligonucleotides.

We designed and successfully synthesized novel nucleic acid analogues with a C3'-C4' trans-fused six-membered ring, trans-3',4'-BNAs from D-glucose. A 1H-NMR experiment and X-ray crystallographic analysis demonstrated that the sugar puckering of trans-3',4'-BNA was restricted in an S-type conformation. We also achieved its incorporation into oligonucleotides using automated DNA synthesizer.

Synthesis and properties of oligonucleotides containing novel 2',4'-BNA analogues (2',4'-BNACOC).

Preorganization of the nucleoside into proper conformation is one of the most promising approaches to develop the oligonucleotides strongly interacting with nucleic acid targets in a sequence-specific manner. We designed and synthesized the 2',4'-BNACOC monomer as a novel bridged nucleic acid analogue possessing a fixed N-type sugar conformation, and also successfully achieved its incorporation into oligonucleotides. The 2',4'-BNACOC modified oligonucleotides were found to have selective and strong binding-affinity for complementary RNA rather than DNA, and to show an excellent nuclease resistance ability.