AI Article Synopsis
- Researchers successfully synthesized new phosphoramidites from common nucleosides, specifically 2'-deoxy-5-trifluoromethyluridine and 2'-deoxy-5-trifluoromethylcytidine.
- They tested how well these new compounds bind to double-stranded DNA and single-stranded RNA using UV-melting experiments.
- Findings showed that while the new oligonucleotides had decreased ability to form stable triplexes with DNA, they might still be useful in targeting single-stranded RNA due to the unique properties of the fluorine atoms.
Article Abstract
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)-GC base triplet was low, likely due to the low pK of protonated C 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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| http://dx.doi.org/10.1248/cpb.c17-00530 | DOI Listing |
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