2′-O,4′-C-methylene bridged nucleic acid (2′,4′-BNA): synthesis and triplex-forming properties

Abstract

For development of ideal antisense and antigene molecules, various chemical modifications of oligonucleotides have been studied. However, despite their importance, there is only limited information available on the triplex-forming ability of the conformationally restricted or locked oligonucleotides. We report herein that 2′-O,4′-C-methylene bridged nucleic acid (2′,4′-BNA) modification of triplex-forming oligonucleotide (TFO) significantly enhances the binding affinity towards target dsDNA. On Tm measurements, the triplex with the 2′,4′-BNA oligonucleotides were found to be stabilized with ΔTm/modification of +4.3 to +5°C at pH 6.6 compared to the triplexes with the unmodified oligonucleotide. By means of gel-retardation assay, the binding constant of the 2′,4′-BNA oligonucleotide at pH 7.0 was at least 300-fold higher than that of the natural oligonucleotide. In addition, the 2′,4′-BNA oligonucleotide clearly showed the inhibition of the NF-κB transcription factor (p50)-target dsDNA binding by forming a stable triplex at pH 7.0.