Synthesis of 2′-O-(thymin-1-yl)methyluridine and its incorporation into secondary nucleic acid structures

A double-headed nucleoside wherein an additional thymine is attached to the 2'-O-position of uridine via a methylene linker is prepared and incorporated into oligonucleotides. With single incorporations of the modified nucleotide monomer, these oligonucleotides form duplexes with the complementary DNA sequences which are thermally less stable as compared to the unmodified duplexes. However, stabilization of bulged duplexes or three way junctions is observed. A cross-strand interaction between two additional thymines is also seen in a DNA-duplex, when specifically introduced in a so-called (+1)-zipper motif, however, much weaker than obtained with the corresponding analogue with the methylene linker directly attached to the 2'-C-position. This demonstrates that the ability to act as a compressed dinucleotide is unique for the latter and due to its perfect preorganization of the additional base in the duplex core.