Introducing structural diversity in oligonucleotides via photolabile, convertible C5-substituted nucleotides

Chemically synthesized oligonucleotides are functionalized at defined sites while in their protected form on solid-phase supports via the incorporatio n of nucleotides containing masked alkyl carboxylic acids or alkylamines. T he reactive functional groups are selectively revealed upon 365 nm irradiat ion of the appropriate o-nitrobenzyl based protecting group. For the photol abile nucleotide that reveals alkylamines, a combination of analytical meth ods revealed that very high yields (greater than or equal to 94%) of the ol igonucleotide containing a single reactive functional group were obtained b y using photolysis conditions that do not damage the biopolymer. Either fun ctionalized nucleotide is efficiently coupled to the corresponding reaction partner via PyBOP mediated amide bond formation. Isolated yields of the co njugated oligonucleotides are greater than or equal to 90%. This method is compatible with introducing multiple modified sites sequentially and is ame nable to the synthesis of libraries of oligonucleotides in a combinatorial fashion containing nonnative nucleotides while bound to their solid support s.