FTIR and UV spectroscopy studies of triplex formation between pyrimidine methoxyethylphosphoramidates alpha-oligodeoxynucleotides and ds DNA targets.
The ability of non-ionic methoxyethylphosphoramidate (PNHME) alpha-oligodeoxynucleotides (ODNs), alpha dT(15) and alpha dCT 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 alpha-ODNs formed much more stable triplexes than phosphodiester (PO) beta-ODNs did (Delta Tm = + 20 degrees C for alpha dCT PNHME). In addition, FTIR spectroscopy was used to determine the base pairing and the strand orientations of the triplexes formed by alpha dT(15) PNHME compared to phosphodiester ODNs with beta or alpha anomeric configuration. While beta dT(15) PO failed to form a triplex with a long beta dA(n) x beta dT(n) duplex, the Tm of the Hoogsteen part of the triplex formed by alpha dT(15) PNHME reached 40 degrees C. Moreover alpha dT(15) PNHME displaced the beta dT(15) strand of a shorter beta dA(15) x beta dT(15) duplex. The alpha dCT PNHME and alpha dT(15) PNHME third strands were found antiparallel in contrast to alpha dT(15) PO which is parallel to the purine strand of their duplex target. The uniform preferential Hoogsteen pairing of the nucleotides alpha dT and alpha dC combining both replacements might contribute to the improve stability of the triplexes.
Sun
Bei-Wen
BW
Laboratoire de Spectroscopie Biomoléculaire, UFR de Médecine, UMR 7033 CNRS, Université Paris-Nord, F-93017 Bobigny Cedex, France.
Geinguenaud
Frédéric
F
Taillandier
Eliane
E
Laurent
Magali
M
Debart
Françoise
F
Vasseur
Jean-Jacques
JJ
D000577:Amides / Q000378:metabolism*; D004247:DNA / Q000378:metabolism*; D006358:Hot Temperature; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000378:metabolism*; D010756:Phosphoric Acids / Q000378:metabolism*; D011743:Pyrimidines / Q000378:metabolism*; D013056:Spectrophotometry, Ultraviolet; D017550:Spectroscopy, Fourier Transform Infrared
D000577:Amides; D009838:Oligodeoxyribonucleotides; D010756:Phosphoric Acids; D011743:Pyrimidines; D004247:DNA; C011067:phosphoramidic acid