Abstract
The ability of non-ionic methoxyethylphosphoramidate (PNHME) α-oligodeoxynucleotides (ODNs), αdT15 and αdCT dodecamer, to form triplexes with their double-stranded DNA targets was evaluated. Thermal stability of the formed complexes was studied by UV thermal denaturation and the data showed that these PNHME α-ODNs formed much more stable triplexes than phosphodiester (PO) β-ODNs did (ΔTm = + 20° C for αdCT PNHME). In addition, FTIR spectroscopy was used to determine the base pairing and the strand orientations of the triplexes formed by αdT15 PNHME compared to phosphodiester ODNs with β or α anomeric configuration. While βdT15 PO failed to form a triplex with a long βdAn•βdTn duplex, the Tm of the Hoogsteen part of the triplex formed by αdT15 PNHME reached 40° C. Moreover αdT15 PNHME displaced the βdT15 strand of a shorter βdA15•βdT15 duplex. The αdCT PNHME and αdT15 PNHME third strands were found antiparallel in contrast to αdT15 PO which is parallel to the purine strand of their duplex target. The uniform preferential Hoogsteen pairing of the nucleotides αdT and αdC combining both replacements might contribute to the improve stability of the triplexes.
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