Thio‐ and seleno‐α,β‐ and α,β,γ‐D‐CNA (constrained nucleic acid) dinucleotides in which two or three torsion angles of the sugar/phosphate backbone are controlled within a dioxaphosphorinane structure have been prepared. Their structural determination was carried out by means of NMR spectroscopy to show only slight variation on the torsion‐angle control in comparison with their oxo analogues. Unexpected selenium migration has been pointed out from selenophosphotriester moiety to phosphoramidite group, but this drawback can be overcome using H‐phosphonate chemistry.

Construction and physico-chemical behavior of DNA three way junction (3WJ) functionalized by protein-like residues (imidazole, alcohol and carboxylic acid) at unpaired positions at the core is described. One 5 -C(S)-propargyl-thymidine nucleotide was specifically incorporated on each strand to react through a post synthetic CuACC reaction with either protected imidazolyl-, hydroxyl-or carboxyl-azide. Structural impacts of 5 -C(S)-functionalization were investigated to evaluate how 3WJ flexibility/stability is affected.