Base-pair recognition ability of hydroxyphenyl nucleobases in parallel triplex DNA

Abstract Oligonucleotides containing 2′-deoxyribonucleotides bearing hydroxyphenyl nucleobases or their 2′,4′-BNA-modified analogs were synthesized, and the triplex-forming ability of their oligonucleotides with double-stranded DNA targets was evaluated by UV melting experiments. Results showed that 2′-deoxyribonucleotide bearing 2′-hydroxyphenyl nucleobase could be recognized by a dUA base pair while no affinity to a TA base pair was observed. The ,4′-BNA modification led to a further increase in the binding affinity to a dUA base pair. The ,4′-BNA bearing 3-hydroxyphenyl nucleobase showed moderate binding affinity to a TA base pair, but without selectivity.