Triplex- and duplex-forming abilities of oligonucleotides containing 2′-deoxy-5-trifluoromethyluridine and 2′-deoxy-5-trifluoromethylcytidine
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 (CF3C)-GC base triplet was low, likely due to the low pKa of protonated CF3C by the electron-withdrawing trifluoromethyl group. A slight decrease in stability of the duplex formed with ssRNA by oligonucleotides including 5-tri-fluoromethylpyrimidine nucleobases was only observed, suggesting that they might be applicable to various ssRNA-targeted technologies using features of fluorine atoms.
Incorporation of 2′-deoxy-5-(trifluoromethyl)uridine and 5-cyano-2′-deoxyuridine into DNA
In an attempt to synthesize DNA containing 2′-deoxy-5-(trifluoromethyl)uridine (1) using previously published protocols, we found that the trifluoromethyl group converted into a cyano group, resulting in DNA containing 5-cyano-2′-deoxyuridine (3). We show
Markley, John C.,Chirakul, Panadda,Sologub, Dina,Sigurdsson, Snorri Th.
Modified Oligonucleotides and Applications Thereof
Disclosed, among other things, are primers containing certain modified nucleobases in the 3′ terminal region of the primers that provide reduced formation of primer-dimers during amplification reactions, and various methods of use thereof.
-
Page/Page column 12-13
(2011/06/26)
Improved synthesis of 5-hydroxymethyl-2′-deoxycytidine phosphoramidite using a 2′-deoxyuridine to 2′-deoxycytidine conversion without temporary protecting groups
5-Hydroxymethylcytosine has recently been characterized as the 'sixth base' in human DNA. To enable research on this DNA modification, we report an improved method for the synthesis of 5-hydroxymethyl-2′-deoxycytidine (5-HOMedC) phosphoramidite for site-specific incorporation into oligonucleotides. To minimize manipulations we employed a temporary protecting group-free 2′-deoxyuridine to 2′-deoxycytidine conversion procedure that utilizes phase transfer catalysis. The desired 5-HOMedC phosphoramidite is obtained in six steps and 24% overall yield from 2′-deoxyuridine.
Hansen, Anders S.,Thalhammer, Armin,El-Sagheer, Afaf H.,Brown, Tom,Schofield, Christopher J.
p. 1181 - 1184
(2011/04/16)
Synthesis, Annealing Properties, 19F NMR Characterization, and Detection Limits of a Trifluorothymidine-Labeled Antisense Oligodeoxyribonucleotide 21 mer
The synthesis and characterization are described of trifluorothymidine groups incorporated into an antisense 21 mer designed to target gene sequences that encode serine proteases in T-lymphocytes. 1H NMR titration studies on 3',5'-O-TPDS-trifluorothymidin
Gmeiner, William H.,Pon, Richard T.,Lown, J. William
p. 3602 - 3608
(2007/10/02)
More Articles about upstream products of 133128-06-0