Synthesis of photolabile 5′-O-phosphoramidites for the photolithographic production of microarrays of inversely oriented oligonucleotides

The photolabile 3 ' -O-{[2-(2-nitrophenyl)propoxy]carbonyl}-protected 5 ' -phosphoramidites (16-18) were synthesized (see Scheme) for an alternative mode of light-directed production of oligonucleotide arrays. Because of the characteristics of these monomeric building blocks, photolithographic in situ DNA synthesis occurred in 5 ' --> 3 ' direction, in agreement with the orientation of enzymatic synthesis. Synthesis yields were as good as those of conventional reactions. The resulting oligonucleotides are attached to the: surface via their 5 ' -termini, while the 3 ' -hydroxy groups are available as substrates for enzymatic reactions such as primer extension upon hybridization of a DNA template (see Fig. 2). The production of such oligonucleotide chips adds new procedural avenues to the growing number of applications of DNA microarrays.