2',4'-BNA bearing a 2-pyridine nucleobase for CG base pair recognition in the parallel motif triplex DNA.

We succeeded in the synthesis of triplex-forming oligonucleotides (TFOs) that contain a deoxyribonucleotide (Py) bearing a 2-pyridine nucleobase or the 2',4'-BNA congener (Py(B)). By UV melting experiments, it was found that 2-pyridine was a very promising nucleobase for the sequence-selective recognition of a CG base pair within double-stranded DNA (dsDNA) in a parallel motif triplex. Moreover, Py(B) in TFOs showed stronger affinity to a CG base pair than Py with further increase in the selectivity. Using TFO including multiple Py(B) units, triplex formation with dsDNA containing three CG base pairs was observed.

Recognition of T.A interruption by 2',4'-BNAs bearing heteroaromatic nucleobases through parallel motif triplex formation.

2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) monomers bearing novel unnatural nucleobases, 4-(3-benzamidophenyl)-2-pyridone and 2-(N-methylbenzamido)thiazole, were synthesized and successfully incorporated into oligonucleotides. UV melting experiments showed that the corresponding oligonucleotide derivatives formed stable triplexes with dsDNA targets even in the presence of a T.A interruption.

Synthesis and triplex-forming ability of 2',4'-BNAs bearing imidazoles as a nucleobase.

To expand the sequence of double-stranded DNA (dsDNA) targets in a triplex formation, 2',4'-BNAs (2'-O,4'-C-methylene bridged nucleic acids) having imidazoles as a nucleobase were synthesized and incorporated into oligonucleotides. Triplex-forming ability of the modified oligonucleotides was evaluated by using melting temperature (Tm) measurements.

Synthesis and triplex-forming properties of 2',4'-BNA derivatives bearing pyridines as an unnatural nucleobase.

Triplex-forming oligonucleotide (TFO) could serve as a potential tool to regulate gene expression. However, stability of the triplex is relatively low, and the sequence of the target dsDNA is severely regulated. In an attempt to overcome these problems, we have designed and synthesized 2',4'-BNA monomers bearing a 6-aminopyridin-3-yl (aPy(B)) and pyridin-2-yl group (Py(B)) as a nucleobase. These monomers were successfully incorporated into natural TFOs, and the triplex-forming property of the modified TFOs was evaluated by UV melting experiments.

2',4'-BNA derivatives bearing an unnatural nucleobase: synthesis and application to triplex-forming oligonucleotides.

Recognition of dsDNA by a triplex-forming oligonucleotide (TFO) is limited to homopurine x homopyrimidine sequences. Therefore, it is necessary to develop novel nucleoside analogues which recognize pyrimidine x purine basepairs (C x G or T x A). We have designed and synthesized novel 2',4'-BNA/LNA monomers bearing 3-hydroxybenzene and indole as a nucleobase (3HB(B) and In(B)), and these nucleoside analogues have been introduced into TFOs. On melting temperature (Tm) measurements, 3HB(B) and In(B) were found to interact with T x A base pair interruption with moderate binding affinity.