Effect of ENA modification of triplex-forming oligonucleotide on pyrimidine motif triplex formation

We examined the effect of 2'-O,4'-C-ethylene bridged nucleic acid (ENA) backbone modification of triplex-forming oligonucleotide (TFO) on the pyrimidine motif triplex formation at neutral pH, a condition where pyrimidine motif triplexes are unstable. The binding constant of the pyrimidine motif triplex formation at pH 6.8 with ENA-modified TFO was 20 times larger than that observed with unmodified TFO. The number and position of the ENA modification introduced into the TFO did not significantly affect the magnitude of the increase in the binding constant. The consideration of the observed thermodynamic parameters suggested that the increased rigidity itself of the ENA-modified TFO in the free state relative to the unmodified TFO may enable the significant increase in the binding constant at neutral pH. The present results certainly support the idea that the ENA backbone modification of TFO could be a key chemical modification and may eventually lead to progress in therapeutic applications of the antigene strategy in vivo.