Branched oligonucleotides with symmetric arms 6-15 which may contain biotin as a second recognition code were prepared. These molecules are designed to be used for the directed assembly of nanomaterials. The branched structure of the desired oligonucleotides was confirmed by mass spectrometry on small branched oliognucleotides, by gel electrophoresis and by hybridization with complementary oligonucleotide-nanoparticle conjugates followed by visualization of the complexes by transmission electron microscopy.

The synthesis of several branched oligonucleotides, i.e., of the parallel hairpins 5 ± 8 and the Y-shaped 9 is described, together with their use in the formation of pyrimidine ¥ pyrimidine ¥ purine triple helices. Special attention was paid to the optimization of the assembly of the second strand from asymmetric branching molecules. The presence of 8-aminoadenine moieties in the WatsonÀCrick purine strand and 2'-O-methyl-RNA in the Hoogsteen pyrimidine strand produced strong stabilization of the triplex.

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The synthesis and properties of triplex-forming DNA clamps carrying 8-aminopurines are described. The stability of triple helices is enhanced by replacing purine bases with 8-aminopurine residues. These enhanced binding properties are used for the specific capture of polypyrimidine RNA/DNA sequences of interest.