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Satoshi Obika

Publications and source records attributed to Satoshi Obika.

At least 19 recordsLinked to original sources
PubMed2006

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.

Amides↗
PubMed2006

Synthesis of 2',4'-BNACOC bearing a purine nucleobase.

Recently, we have synthesized pyrimidine derivatives of 2',4'-BNA(COC) monomer, the sugar conformation of which was restricted in N-form by a seven-membered bridged structure. The oligonucleotides containing these monomers showed high affinity with complementary single-stranded RNA and significant resistance to nuclease degradation. For an application to antisense methodology, it is important to synthesize 2',4'-BNA(COC) monomers bearing a purine nucleobase. However, the formation of methyleneoxymethylene (COC) linkage in the purine derivatives failed under the acidic conditions used for the synthesis of 2',4'-BNA(COC) with pyrimidine nucleobases. After several examinations, we successfully achieved the synthesis of 2',4'-BNA(COC) monomers bearing a purine nucleobase via the formation of COC linkage using Pummerer-type reaction.

Bridged-Ring Compounds↗
PubMed2006

High-affinity RNA mimicking binding of 2',4'-BNANC towards complementary strands: a comparative study with 2',4'-BNA/LNA.

2',4'-BNA(NC), a bridged nucleic acid analogue, which was designed and synthesized in our laboratory, showed very high binding affinity towards complementary RNA and DNA strands. Its duplex-forming ability towards a single-stranded RNA was similar to or slightly higher than that of 2',4'-BNA and the overall triplex-forming ability against a double-stranded DNA was also better than that of 2',4'-BNA. 2',4'-BNA(NC) exhibited higher RNA selectivity than 2',4'-BNA.

Bridged-Ring Compounds↗
PubMed2006

Antisense activity of 2',4'-BNA targeted to bcl-xL gene in HepG2 cell.

Introduction of the 2',4'-BNA monomer into oligonucleotides significantly enhanced binding affinity toward ssRNA and resistance to nuclease degradation. Here, we evaluated the antisense activity of 2',4'-BNA oligonucleotides against bcl-xL in HepG2 cells. Our data revealed that 2',4'-BNA antisense oligonucleotides remarkably inhibited the expression of bcl-xL in HepG2 cells compared to the natural DNA antisense oligonucleotide. The inhibitory effect of 2',4'-BNA antisense oligonucleotide was dose-dependent and highly sequence-specific.

Bridged-Ring Compounds↗
PubMed2005

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.

Animals↗
PubMed2005

Promotion of stable triplex formation by partial incorporation of 2',5'-phosphodiester linkages into triplex-forming oligonucleotides.

Pentadecamer homopyrimidine oligonucleotides containing three or more 2',5'-phosphodiester linkages in different modes were prepared and used to evaluate the ability as a triplex-forming oligonucleotide (TFO), and it was found that discontinuous replacement of the 3',5'-phosphodiester linkages in TFO by 2',5'-linkages significantly stabilizes parallel-motif triplexes.

Base Sequence↗
PubMed2005

Presence of 2',5'-linkages in a homopyrimidine DNA oligonucleotide promotes stable triplex formation under physiological conditions.

We prepared 15-mer homopyrimidine oligonucleotides containing three or four 2',5'-linked DNA units, and their ability as a triplex-forming oligonucleotide (TFO) was analyzed in detail UV melting experiments showed that replacement of a 3',5'-linkage by a 2',5'-linkage at every third or fourth residue in TFO significantly promoted stable triplex formation under physiological conditions.

Base Composition↗
PubMed2005

Synthesis and properties of a novel bridged nucleic acid analogue, 5'-amino-3',5'-BNA.

An oligonucleotide P3'-->N5' phosphoramidate (5'-amino-DNA) attracts much attention because of its potential for application to DNA sequencing; however, its ability to hybridize with complementary strands is low. To overcome this drawback of the 5-amino-DNA, we have designed and successfully synthesized a novel nucleic acid analogue having a P3'-->N5' phosphoramidate linkage and a constrained sugar moiety, 5'-amino-3'-C,5'-N-methylene bridged nucleic acid (5'-amino-3',5'-BNA). The binding affinity of the 5'-amino-3',5'-BNA towards complementary DNA and RNA strands was investigated by UV melting experiments. The melting temperature (Tm) of the duplex comprising the 5'-amino-3',5'-BNA and its complementary strand was much higher than that of the duplex containing the corresponding 5-amino-DNA.

Bridged Bicyclo Compounds, Heterocyclic↗
PubMed2005

Promotion of acid-mediated cleavage of oligonucleotide P3'->N5' phosphoroamidates by triplex formation: a novel approach to sequence-specific DNA detection.

The 5'-amino-2',4'-BNA, bearing a locked N-type sugar conformation and a P3'-->N5' phosphoramidate linkage, was found to be rapidly cleaved by acid-mediated hydrolysis when they formed a triplex with the target dsDNA. The fluorophore and quencher moieties were introduced into the 5'-amino-2',4'-BNA-modified oligonucleotide which was used as a novel and innovative DNA detection probe.

DNA↗
PubMed2005

Synthesis and triplex-forming properties of 2',4'-BNA derivatives bearing pyridines as an unnatural nucleobase.

Triplex-forming oligonucleotide (TFO) could serve as a potential tool to regulate gene expression. However, stability of the triplex is relatively low, and the sequence of the target dsDNA is severely regulated. In an attempt to overcome these problems, we have designed and synthesized 2',4'-BNA monomers bearing a 6-aminopyridin-3-yl (aPy(B)) and pyridin-2-yl group (Py(B)) as a nucleobase. These monomers were successfully incorporated into natural TFOs, and the triplex-forming property of the modified TFOs was evaluated by UV melting experiments.

Base Pairing↗
PubMed2005

Effects of the 2',4'-BNA modification on the sequence specificity of molecular beacons.

Molecular beacons (MBs) are stem-loop hairpin oligonucleotide probes with an internally quenched fluorophore. These probes recognize their targets with higher specificity than conventional linear probes. To further enhance sequence-specificity of MBs, we have designed and synthesized MBs having 2',4'-BNA modification. Thermodynamic analysis revealed that the MBs with the 2',4'-BNA-modified stem region have high sequence-specificity. In addition, the 2',4'-BNA modification in the loop region was also found to be efficient for discrimination of one base mismatch.

Base Pair Mismatch↗
PubMed2005

Antigene-block strategy: effective regulation of gene expression by 2',4'-BNA-modified TFOs with an additional stem-loop structure.

Antigene strategy is promising technology to regulate gene expression. We have previously reported that 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) modification of triplex-forming oligonucleotides (TFOs) significantly enhanced the binding affinity towards the target dsDNA. In spite of its usefulness, the TFO-binding site may not completely overlay the protein-binding site because of the limitation of TFOs targeting sequences. To overcome this problem, we developed an antigene-based new methodology called "antigene-block" strategy. In this methodology, the TFOs bearing a bulky hairpin tail are used for efficient inhibition of protein-DNA interaction. The antigene-block TFOs having 2',4'-BNA modifications formed stable triplexes with the homopurine-homopyrimidine sequence which partially overlap the transcription factor NF-kappaB binding site. In addition, the antigene-block TFOs significantly reduced the expression level of the target-gene in living cells, while conventional 2',4'-BNA-modified or unmodified TFOs showed no effect on the target-gene expression.

Animals↗
PubMed2005

Synthesis and properties of 2',4'-BNA(NC), a second generation BNA.

We have recently designed and synthesized a novel bridged nucleic acid analogue 2',4'-BNA(NC), bearing an N-O bridged structure, which furnished both higher duplex and triplex-forming abilities and sequence selectivity towards complementary RNA and/or DNA, respectively, and showed excellent resistance against nuclease degradation. Duplex and triplex-forming abilities were slightly higher or similar to those of 2',4'-BNA and nuclease resistance was as high as that of S-oligo.

Bridged-Ring Compounds↗
PubMed2005

Synthesis and triplex-forming ability of 2',4'-BNAs bearing imidazoles as a nucleobase.

To expand the sequence of double-stranded DNA (dsDNA) targets in a triplex formation, 2',4'-BNAs (2'-O,4'-C-methylene bridged nucleic acids) having imidazoles as a nucleobase were synthesized and incorporated into oligonucleotides. Triplex-forming ability of the modified oligonucleotides was evaluated by using melting temperature (Tm) measurements.

Chromatography, High Pressure Liquid↗
PubMed2004

Synergistic stabilization of triplex by combination of comb-type cationic copolymer and 2',4'-BNA.

We examined the effect of the combination of the two triplex-stabilizing factors, poly(L-lysine)-graft-dextran (PLL-g-Dex) copolymer and 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) backbone modification of triplex-forming oligonucleotide (TFO), on the pyrimidine motif triplex formation at neutral pH, a condition where pyrimidine motif triplexes are unstable. The combination of both stabilizing factors that was the triplex involving the 2',4'-BNA TFO in the presence of the copolymer synergistically increased the thermal stability of the pyrimidine motif triplex at neutral pH. The present results certainly support the idea that the combination of the stabilizing factors can be a key method for triplex stabilization and may lead to progress in therapeutic applications of the antigene strategy in vivo.

DNA↗
PubMed2004

2',4'-BNA derivatives bearing an unnatural nucleobase: synthesis and application to triplex-forming oligonucleotides.

Recognition of dsDNA by a triplex-forming oligonucleotide (TFO) is limited to homopurine x homopyrimidine sequences. Therefore, it is necessary to develop novel nucleoside analogues which recognize pyrimidine x purine basepairs (C x G or T x A). We have designed and synthesized novel 2',4'-BNA/LNA monomers bearing 3-hydroxybenzene and indole as a nucleobase (3HB(B) and In(B)), and these nucleoside analogues have been introduced into TFOs. On melting temperature (Tm) measurements, 3HB(B) and In(B) were found to interact with T x A base pair interruption with moderate binding affinity.

Base Sequence↗