The antiparallel triplex DNA is formed by the interaction between purine-rich triplex forming oligonucleotides (TFOs) and the homo-purine region within a duplex DNA. The formation of such a structure with the genome DNA promises to control the gene expression in a living cell. In this study, in an attempt to enhance the stability of the triplex DNAs, we have designed the N 2 -arylated deoxyguanosine derivatives. Among these analogues, we found that the TFOs containing N 2 -phenyl-2′-deoxyguanosine (PhdG) showed a stable and selective triplex DNA formation with the GC base pair as compared to the natural dG/GC triplet. However, the multiple incorporation of PhdG into the TFOs hampered the stable triplex DNA, instead, showed a tendency to form a higher order structure. Therefore, we concluded that the stable and selective triplex DNA formation is expected by the replacement of dG by PhdG in the purine-rich TFO sequence. Key words N2 -arylated deoxyguanosine; triplex forming oligonucleotide; triplex DNA By forming the triplex DNA versus the duplex DNA, it is possible to control the gene expression, gene recombination, gene repair, etc. Therefore, the site specific and stable triplex DNA formation for the target duplex DNA is anticipated to become an important method for the gene targeting technologies and therapies as an antigene method.1-5) The triplex DNA is formed by the interaction between the triplex forming oligonucleotides (TFOs) and the homopurine region within the duplex DNA.6) Triplex DNAs are classified into two types according to the orientation of the phosphate backbone of the TFOs. The antiparallel type triplex DNA is formed under neutral conditions, in which the TFOs composed of deoxyguanosine (dG) and deoxyadenosine (dA) form two hydrogen bonds in the guanine base of the GC base pair and the adenine base of the AT base pair of the duplex DNA, respectively, in an antiparallel orientation regarding the homopurine strand of the duplex DNA (Fig. 1A). On the other hand, the TFOs composed of deoxycytosine (dC) and thymidine (T) forms two hydrogen bond in the guanine base and adenine base of the homopurine strand in a parallel orientation, respectively. As the protonated cytidine is included in the parallel type triplex, its formation requires acidic conditions (Fig. 1B). To date, we have developed the artificial nucleoside analogues to form the nonnatural and antiparallel type triplex DNA for the duplex DNA containing the CG and TA base pair to expand the triplex recognition code.7-12) However, improvement of the stability of the antiparallel type triplex DNA by an artificial nucleic acid is a still challenging issue.The stacking interaction has been shown to be more effective with the triplex DNA than with the duplex DNA. For example, adriamycin and actinomycin, having a high aromaticity, are known to interact with the duplex DNA, but have a rather high binding ability to the triplex DNA.13) Moreover, the duplex DNA containing N 2 -phenyldeoxyguanosine (PhdG) showed a slightly higher thermal melting temp...

This paper reports the preparation of 14-mer triplex-forming oligonucleotides (TFOs) containing a 2-Omethyl-1-β-phenyl-α-propargyl-ribose unit, which was conjugated with azide-modified molecules via a click reaction. Modification of these TFOs with pyrene assisted triplex formation, improving the stability of the triplex DNA and the anti-proliferative effects against A549 cells.

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