A directional nucleation-zipping mechanism for triple helix formation.
A detailed kinetic study of triple helix formation was performed by surface plasmon resonance. Three systems were investigated involving 15mer pyrimidine oligonucleotides as third strands. Rate constants and activation energies were validated by comparison with thermodynamic values calculated from UV-melting analysis. Replacement of a T.A base pair by a C.G pair at either the 5' or the 3' end of the target sequence allowed us to assess mismatch effects and to delineate the mechanism of triple helix formation. Our data show that the association rate constant is governed by the sequence of base triplets on the 5' side of the triplex (referred to as the 5' side of the target oligopurine strand) and provides evidence that the reaction pathway for triple helix formation in the pyrimidine motif proceeds from the 5' end to the 3' end of the triplex according to the nucleation-zipping model. It seems that this is a general feature for all triple helices formation, probably due to the right-handedness of the DNA double helix that provides a stronger base stacking at the 5' than at the 3' duplex-triplex junction. Understanding the mechanism of triple helix formation is not only of fundamental interest, but may also help in designing better triple helix-forming oligonucleotides for gene targeting and control of gene expression.
Alberti
Patrizia
P
Laboratoire de Biophysique, USM0503 Muséum National d'Histoire Naturelle, UMR8646 CNRS-MNHN, U565 INSERM, 43 rue Cuvier 75231 Paris cedex 05, France.
Arimondo
Paola B
PB
Mergny
Jean-Louis
JL
Garestier
Thérèse
T
Hélène
Claude
C
Sun
Jian-Sheng
JS
D004247:DNA / Q000737:chemistry* / Q000187:drug effects; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D015636:Magnesium Chloride / Q000494:pharmacology; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000737:chemistry; D009994:Osmolar Concentration; D012965:Sodium Chloride / Q000494:pharmacology; D020349:Surface Plasmon Resonance; D013696:Temperature
D009841:Oligonucleotides; C051802:triplex DNA; D015636:Magnesium Chloride; D012965:Sodium Chloride; D004247:DNA