Synthesis and Conformational Analysis of Synthetic DNA Fragments

It is now well recognized that the synthesis of DNA fragments with a defined sequence and length can be performed most successfully via 3′–5′-phosphotriester intermediates. The approaches devised for the introduction of 3′–5′-internucleotide phosphotriester linkages can be divided into two main classes: a direct approach and a transient approach. In the direct approach (Reese 1978; de Rooij 1979b), a 3′-phosphodiester d-nucleoside derivative (e.g., 1; R1 = 2-chlorophenyl; R2 = levulinoyl) is condensed in the presence of an activating agent (e.g., 4) with a properly protected d-nucleoside having a free 5′-hydroxyl function, to give a fully protected dimer (e.g., 13a in Scheme 3). In the transient approach (Mateucci and Caruthers 1981), a 3′-phosphite derivative (e.g., 2; R2 = 4,4′-dimethoxytrityl [DMTR]) is condensed in the presence of tetrazole (5) with a properly protected d-nucleoside having a free 5′-hydroxyl function, to give a transient 3′–5′-phosphite intermediate, which is oxidized into a stable phosphotriester...