Extreme instability of pyrimidine motif triplex DNA at physiological pH severely limits its use in an artificial control of gene expression in vivo. Therefore, stabilization of the pyrimidine motif triplex at physiological pH is crucial in improving its therapeutic potential. To this end, Torigoe et al. have investigated the thermodynamic and kinetic effects of a previously reported chemical modification, 2'-O,4'-C-methylene bridged nucleic acid (2',4'- BNA) modification of triplex-forming oligonucleotide (TFO), on pyrimidine motif triplex formation at physiological pH. The thermodynamic analyses showed that the 2',4'-BNA modification of TFO increased the binding constant of the pyrimidine motif triplex formation at neutral pH by ~20 fold. The number and position of the 2',4'-BNA modification introduced into the TFO did not significantly affect the magnitude of the increase in the binding constant. Considering the observed thermodynamic parameters suggested that the increased rigidity of the 2',4'-BNA-modified TFO in the free state relative to the unmodified TFO may enable a significant increase in the binding constant at neutral pH. Kinetic data demonstrated that the observed increase in the binding constant at neutral pH by the 2',4'-BNA modification of TFO resulted from the considerable decrease in the dissociation rate constant. Our results certainly support the idea that the 2',4'-BNA modification of TFO could be a critical chemical modification and may eventually lead to progress in therapeutic applications of the antigene strategy in vivo. pdf at JBC
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