Highly stable DNA triplexes formed with cationic phosphoramidate pyrimidine alpha-oligonucleotides.
The ability of cationic phosphoramidate pyrimidine alpha-oligonucleotides (ONs) to form triplexes with DNA duplexes was investigated by UV melting experiments, circular dichroism spectroscopy and gel mobility shift experiments. Replacement of the phosphodiester linkages in alpha-ONs with positively charged phosphoramidate linkages results in more efficient triplex formation, the triplex stability increasing with the number of positive charges. At a neutral pH and in the absence of magnesium ions, it was found that a fully cationic phosphoramidate alpha-TFO (triplex-forming oligonucleotide) forms a highly stable triplex that melts at a higher temperature than the duplex target. No hysteresis between the annealing and melting curves was noticed; this indicates fast association. Moreover, the recognition of a DNA duplex with a cationic alpha-TFO through Hoogsteen base pairing is highly sequence-specific. To the best of our knowledge, this is the first report of stable triplexes in the pyrimidine motif formed by cationic alpha-oligonucleotides and duplex targets.
Michel
Thibaut
T
LCOBS, UMR 5625 CNRS-UMII, CC 008, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France.
Debart
Françoise
F
Heitz
Frédéric
F
Vasseur
Jean-Jacques
JJ
D000577:Amides / Q000737:chemistry*; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D010756:Phosphoric Acids / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry*; D013696:Temperature; D014466:Ultraviolet Rays
D000577:Amides; D009841:Oligonucleotides; D010756:Phosphoric Acids; D011743:Pyrimidines; C051802:triplex DNA; D004247:DNA; C011067:phosphoramidic acid