Promotion of triplex formation by a fixed N-form sugar puckering: thermodynamic and kinetic studies

We analyzed the effect of a fixed N-form sugar puckering of TFO (triplex-forming oligonucleotide) on the pyrimidine motif triplex formation at neutral pH, a condition where pyrimidine motif triplexes are unstable. Both thermodynamic and kinetic analyses revealed that the binding constant of the pyrimidine motif triplex formation at pH 6.8 with modified TFO containing the fixed N-form sugar puckering was about 20-times larger than that observed with unmodified TFO. Kinetic data also demonstrated that the observed increase in the binding constant at neutral pH by the fixed N-form sugar puckering resulted from the considerable decrease in the dissociation rate constant. Our results certainly support the idea that the fixed N-form sugar puckering of TFO could be a key modification and may eventually lead to progress in therapeutic applications of the antigene strategy in vivo.