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A bridged nucleic acid, 2',4'-BNA COC: synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2',4'-BNA COC monomers and RNA-selective nucleic-acid recognition.

Mitsuoka Y, Kodama T, Ohnishi R, Hari Y, Imanishi T, Obika S - Nucleic Acids Res. (2009)

Bottom Line: Oligonucleotides (BNA(COC)) containing this monomer show high affinity with complementary single-stranded RNA and significant resistance to nuclease degradation.Furthermore, mismatched sequence studies showed that BNA(COC) generally improved the sequence selectivity with Watson-Crick base-pairing compared to the corresponding natural DNA and RNA.A CD spectroscopic analysis indicated that the BNA(COC) formed duplexes with complementary DNA and RNA in a manner similar to natural RNA.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan.

ABSTRACT
Recently, we synthesized pyrimidine derivatives of the 2'-O,4'-C-methylenoxymethylene-bridged nucleic-acid (2',4'-BNA(COC)) monomer, the sugar conformation of which is restricted in N-type conformation by a seven-membered bridged structure. Oligonucleotides (BNA(COC)) containing this monomer show high affinity with complementary single-stranded RNA and significant resistance to nuclease degradation. Here, BNA(COC) consisting of 2',4'-BNA(COC) monomers bearing all four bases, namely thymine, 5-methylcytosine, adenine and guanine was efficiently synthesized and properties of duplexes containing the 2',4'-BNA(COC) monomers were investigated by UV melting experiments and circular dichroism (CD) spectroscopy. The UV melting curve analyses showed that the BNA(COC)/BNA(COC) duplex possessed excellent thermal stability and that the BNA(COC) increased thermal stability with a complementary RNA strand. On the other hand, BNA(COC)/DNA heteroduplexes showed almost the same thermal stability as RNA/DNA heteroduplexes. Furthermore, mismatched sequence studies showed that BNA(COC) generally improved the sequence selectivity with Watson-Crick base-pairing compared to the corresponding natural DNA and RNA. A CD spectroscopic analysis indicated that the BNA(COC) formed duplexes with complementary DNA and RNA in a manner similar to natural RNA.

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Reagents and conditions: (a) silylated O6-(diphenylcarbamoyl)-N2-isobutyrylguanine, TMSOTf, toluene, 80°C, 2 h, 84%; (b) K2CO3, MeOH, 0°C, 40 min, 96%; (c) NBS, DMSO, 60°C, 40 min, 45%; (d) (1) NaNO2, DMSO, 70°C, 19 h, (2) TBAF, THF, rt, 15 h, 62% over two steps; (e) 20% Pd(OH)2-C, H2, MeOH, rt, 40 h, 85%; (f) DMTrCl, pyridine, rt, 9 h, 95%; (g) (iPr2N)2POCH2CH2CN, DCI, MeCN-THF, rt, 25 h, 64%.
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Figure 9: Reagents and conditions: (a) silylated O6-(diphenylcarbamoyl)-N2-isobutyrylguanine, TMSOTf, toluene, 80°C, 2 h, 84%; (b) K2CO3, MeOH, 0°C, 40 min, 96%; (c) NBS, DMSO, 60°C, 40 min, 45%; (d) (1) NaNO2, DMSO, 70°C, 19 h, (2) TBAF, THF, rt, 15 h, 62% over two steps; (e) 20% Pd(OH)2-C, H2, MeOH, rt, 40 h, 85%; (f) DMTrCl, pyridine, rt, 9 h, 95%; (g) (iPr2N)2POCH2CH2CN, DCI, MeCN-THF, rt, 25 h, 64%.

Mentions: As shown in Scheme 5, an amidite 24 was synthesized by using a common intermediate 4 as the starting material. To circumvent the formation of an N7/N9-diastereo-mixture during nucleosidation of 4, we chose O6-(diphenylcarbamoyl)-N2-isobutyrylguanine as the base moiety (36) to give 18 in 84% yield. After removal of the acetyl groups of 18, the bridge structure formation was accomplished by the same reaction conditions as for the synthesis of the adenine congener to afford 20 in a moderate yield. The O6-diphenylcarbamoyl group was removed by treatment with sodium nitrite (37) and subsequent desilylation by TBAF leading to 21. Hydrogenolysis of 21 with palladium hydroxide on carbon afforded the desired 2′,4′-BNACOC-Gi-Bu monomer 22. Finally, dimethoxytritylation of 22 with 4,4′-dimethoxytrityl chloride followed by phosphitylation gave the phosphoroamidite 24.


A bridged nucleic acid, 2',4'-BNA COC: synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2',4'-BNA COC monomers and RNA-selective nucleic-acid recognition.

Mitsuoka Y, Kodama T, Ohnishi R, Hari Y, Imanishi T, Obika S - Nucleic Acids Res. (2009)

Reagents and conditions: (a) silylated O6-(diphenylcarbamoyl)-N2-isobutyrylguanine, TMSOTf, toluene, 80°C, 2 h, 84%; (b) K2CO3, MeOH, 0°C, 40 min, 96%; (c) NBS, DMSO, 60°C, 40 min, 45%; (d) (1) NaNO2, DMSO, 70°C, 19 h, (2) TBAF, THF, rt, 15 h, 62% over two steps; (e) 20% Pd(OH)2-C, H2, MeOH, rt, 40 h, 85%; (f) DMTrCl, pyridine, rt, 9 h, 95%; (g) (iPr2N)2POCH2CH2CN, DCI, MeCN-THF, rt, 25 h, 64%.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651773&req=5

Figure 9: Reagents and conditions: (a) silylated O6-(diphenylcarbamoyl)-N2-isobutyrylguanine, TMSOTf, toluene, 80°C, 2 h, 84%; (b) K2CO3, MeOH, 0°C, 40 min, 96%; (c) NBS, DMSO, 60°C, 40 min, 45%; (d) (1) NaNO2, DMSO, 70°C, 19 h, (2) TBAF, THF, rt, 15 h, 62% over two steps; (e) 20% Pd(OH)2-C, H2, MeOH, rt, 40 h, 85%; (f) DMTrCl, pyridine, rt, 9 h, 95%; (g) (iPr2N)2POCH2CH2CN, DCI, MeCN-THF, rt, 25 h, 64%.
Mentions: As shown in Scheme 5, an amidite 24 was synthesized by using a common intermediate 4 as the starting material. To circumvent the formation of an N7/N9-diastereo-mixture during nucleosidation of 4, we chose O6-(diphenylcarbamoyl)-N2-isobutyrylguanine as the base moiety (36) to give 18 in 84% yield. After removal of the acetyl groups of 18, the bridge structure formation was accomplished by the same reaction conditions as for the synthesis of the adenine congener to afford 20 in a moderate yield. The O6-diphenylcarbamoyl group was removed by treatment with sodium nitrite (37) and subsequent desilylation by TBAF leading to 21. Hydrogenolysis of 21 with palladium hydroxide on carbon afforded the desired 2′,4′-BNACOC-Gi-Bu monomer 22. Finally, dimethoxytritylation of 22 with 4,4′-dimethoxytrityl chloride followed by phosphitylation gave the phosphoroamidite 24.

Bottom Line: Oligonucleotides (BNA(COC)) containing this monomer show high affinity with complementary single-stranded RNA and significant resistance to nuclease degradation.Furthermore, mismatched sequence studies showed that BNA(COC) generally improved the sequence selectivity with Watson-Crick base-pairing compared to the corresponding natural DNA and RNA.A CD spectroscopic analysis indicated that the BNA(COC) formed duplexes with complementary DNA and RNA in a manner similar to natural RNA.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan.

ABSTRACT
Recently, we synthesized pyrimidine derivatives of the 2'-O,4'-C-methylenoxymethylene-bridged nucleic-acid (2',4'-BNA(COC)) monomer, the sugar conformation of which is restricted in N-type conformation by a seven-membered bridged structure. Oligonucleotides (BNA(COC)) containing this monomer show high affinity with complementary single-stranded RNA and significant resistance to nuclease degradation. Here, BNA(COC) consisting of 2',4'-BNA(COC) monomers bearing all four bases, namely thymine, 5-methylcytosine, adenine and guanine was efficiently synthesized and properties of duplexes containing the 2',4'-BNA(COC) monomers were investigated by UV melting experiments and circular dichroism (CD) spectroscopy. The UV melting curve analyses showed that the BNA(COC)/BNA(COC) duplex possessed excellent thermal stability and that the BNA(COC) increased thermal stability with a complementary RNA strand. On the other hand, BNA(COC)/DNA heteroduplexes showed almost the same thermal stability as RNA/DNA heteroduplexes. Furthermore, mismatched sequence studies showed that BNA(COC) generally improved the sequence selectivity with Watson-Crick base-pairing compared to the corresponding natural DNA and RNA. A CD spectroscopic analysis indicated that the BNA(COC) formed duplexes with complementary DNA and RNA in a manner similar to natural RNA.

Show MeSH
Related in: MedlinePlus