Locked Nucleic Acid Synthesis

Methods and protocols for automated synthesis and purification of locked nucleic acid (LNA), a class of oligonucleotides obeying the Watson-Crick base-pairing rules but displaying unprecedented binding affinities toward complementary deoxyribonucleic acid (cDNA) and ribonucleic acid (RNA), is described. LNA and LNA-DNA chimeras containing phosphordiester or phosphorothioate linkages, or a mixture thereof, can be assembled by standard DNA synthesizers using 2-cyanoethyl DNA phosphoramidites and 2-cyanoethyl LNA phosphoramidites. Compared to the standard protocols used for DNA synthesis, slightly longer coupling time and oxidation time are needed for efficient oligomerization of LNA phosphoramidites. When the LNA has been assembled, it is removed from the solid support as the 5′-end-O dimethoxytrityl (DMT) protected LNA oligomer by treatment with concentrated aqueous ammonia that also removes the phosphate and nucleobase protecting groups. The crude DMT protected LNA product can be purified using, for example, reversed-phase chromatography.