Oligo(2'-O-methyl)ribonucleotides. Effective probes for duplex DNA.
To find novel probes for duplex DNA, we prepared four types of triplexes containing a homopurine-homopyrimidine 15-mer duplex DNA, and examined their thermal stabilities (Tm values). The single strand used for triplex formation were a DNA 15-mer having a defined C-T mixed sequence, and its sugar-modified analogs, namely 2'-fluoro DNA, RNA, and 2'-O-methyl RNA. The 2'-O-methyl RNA and the RNA-containing triplexes were similar in their enhanced stabilities at pH 6.1 and, amongst the four triplexes, the 2'-O-methyl was the most stable at pH 5.0. Furthermore, an experiment using a 34-mer duplex DNA suggested that the 2'-O-methyl RNA-triplex was destabilized, mostly as a result of the incorporation of a mismatched triplet, as compared to the DNA triplex counterpart. Thus, 2'-O-methyl RNA can serve as an effective probe for duplex DNA.
Shimizu
M
M
Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
Konishi
A
A
Shimada
Y
Y
Inoue
H
H
Ohtsuka
E
E
D001483:Base Sequence; D003562:Cytidine / Q000031:analogs & derivatives*; D004247:DNA / Q000737:chemistry*; D004355:Drug Stability; D004591:Electrophoresis, Polyacrylamide Gel; D006358:Hot Temperature; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D015347:RNA Probes / Q000737:chemistry*; D014529:Uridine / Q000031:analogs & derivatives*
D015347:RNA Probes; C052202:2'-O-methyluridine; C052203:2'-O-methylcytidine; D003562:Cytidine; D004247:DNA; D014529:Uridine