Journal
CHEMICAL & PHARMACEUTICAL BULLETIN
Volume 65, Issue 10, Pages 982-988Publisher
PHARMACEUTICAL SOC JAPAN
DOI: 10.1248/cpb.c17-00530
Keywords
5-trifluoromethylpyrimidine nucleobase; oligonucleotide; duplex-forming ability; triplex-forming ability
Funding
- Japan Society for the Promotion of Science (JSPS) KAKENHI [JP17K15431, JP17K05943]
- Grants-in-Aid for Scientific Research [17K05943, 17K15431] Funding Source: KAKEN
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A facile synthesis of 2'-deoxy-5-trifluoromethyluridine and 2'-deoxy-5-trifluoromethylcytidine phosphoramidites from commercially available 2'-deoxyuridine and 2'-deoxycytidine was achieved, respectively. The obtained phosphoramidites were incorporated into oligonucleotides, and their binding affinity to double stranded DNA (dsDNA) and single-stranded RNA (ssRNA) was evaluated by UV-melting experiments. The triplex-forming abilities of oligonucleotides including 5-trifluoromethylpyrimidine nucleobases with dsDNA were decreased. Especially, the stability of the triplex containing a trifluoromethylcytosine (C-CF3)-GC base triplet was low, likely due to the low pK(a) of protonated C-CF3 by the electron-withdrawing trifluoromethyl group. A slight decrease in stability of the duplex formed with ssRNA by oligonucleotides including 5-trifluoromethylpyrimidine nucleobases was only observed, suggesting that they might be applicable to various ssRNA-targeted technologies using features of fluorine atoms.
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