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Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs.

Ohkubo A, Yamada K, Ito Y, Yoshimura K, Miyauchi K, Kanamori T, Masaki Y, Seio K, Yuasa H, Sekine M - Nucleic Acids Res. (2015)

Bottom Line: Further, we observed that N-acetyl-2,7-diamino-1,8-naphtyridine ((DA)Nac) has a higher binding and base recognition abilities for a T-A base pair compared with that of dG and the other DNA derivatives.On the basis of this knowledge, we successfully synthesized a fully modified TFO containing (DA)Nac, d(g)C, 2'-OMe-2-thiothymidine (2'-OMe (s)T) and 2'-OMe-8-thioxoadenosine (2'-OMe (s)A) with high binding and base recognition abilities.To the best of our knowledge, this is the first report in which a fully modified TFO accurately recognizes a complementary DNA duplex having a mixed sequence under neutral conditions.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan aohkubo@bio.titech.ac.jp.

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Synthesis of 2’-OMesA phosphoramidite units 26.
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Figure 14: Synthesis of 2’-OMesA phosphoramidite units 26.

Mentions: Finally, synthesis of the fully modified TFO 10 containing DANac, dgC, 2’-OMesT and 2’-OMesA was carried out to measure the binding and base recognition of the fully modified TFO to HP DNAs 5–13 with the mixed sequences. Although we previously reported synthesis of the 2’-OMesA containing a benzoyl group as a protecting group, it was observed that the DANac moieties were decomposed under the conditions for deprotection of the N-benzoyl group (treatment with 28% NH4OH for 8 h). Therefore, a phenoxyacetyl group, which can be easily cleaved under mild conditions compared with a benzoyl group, was introduced into the amino group of 2’-O-methyl-8-(2-trimethylsilylethylthio)adenosine 23 in the presence of trimethylsilyl chloride, as shown in Scheme 6. After tritylation of the 5’-hydroxy group, the 3’-phosphitylation was carried out to give the 2’-OMesA phosphoramidite unit 26.


Synthesis and triplex-forming properties of oligonucleotides capable of recognizing corresponding DNA duplexes containing four base pairs.

Ohkubo A, Yamada K, Ito Y, Yoshimura K, Miyauchi K, Kanamori T, Masaki Y, Seio K, Yuasa H, Sekine M - Nucleic Acids Res. (2015)

Synthesis of 2’-OMesA phosphoramidite units 26.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4499124&req=5

Figure 14: Synthesis of 2’-OMesA phosphoramidite units 26.
Mentions: Finally, synthesis of the fully modified TFO 10 containing DANac, dgC, 2’-OMesT and 2’-OMesA was carried out to measure the binding and base recognition of the fully modified TFO to HP DNAs 5–13 with the mixed sequences. Although we previously reported synthesis of the 2’-OMesA containing a benzoyl group as a protecting group, it was observed that the DANac moieties were decomposed under the conditions for deprotection of the N-benzoyl group (treatment with 28% NH4OH for 8 h). Therefore, a phenoxyacetyl group, which can be easily cleaved under mild conditions compared with a benzoyl group, was introduced into the amino group of 2’-O-methyl-8-(2-trimethylsilylethylthio)adenosine 23 in the presence of trimethylsilyl chloride, as shown in Scheme 6. After tritylation of the 5’-hydroxy group, the 3’-phosphitylation was carried out to give the 2’-OMesA phosphoramidite unit 26.

Bottom Line: Further, we observed that N-acetyl-2,7-diamino-1,8-naphtyridine ((DA)Nac) has a higher binding and base recognition abilities for a T-A base pair compared with that of dG and the other DNA derivatives.On the basis of this knowledge, we successfully synthesized a fully modified TFO containing (DA)Nac, d(g)C, 2'-OMe-2-thiothymidine (2'-OMe (s)T) and 2'-OMe-8-thioxoadenosine (2'-OMe (s)A) with high binding and base recognition abilities.To the best of our knowledge, this is the first report in which a fully modified TFO accurately recognizes a complementary DNA duplex having a mixed sequence under neutral conditions.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan aohkubo@bio.titech.ac.jp.

Show MeSH