Synthesis of Site-Specifically Phosphate-Caged siRNAs

Photolabile small interfering RNA (siRNA) oligonucleotide duplexes are becoming a powerful tool for photoregulation of gene expression through an RNA interference (RNAi) mechanism. Terminal or statistical labeling of siRNAs has been previously achieved. Recently, we have shown a new strategy for site-specific incorporation of a photolabile group (1-(2-nitrophenyl)ethyl [NPE]) at any phosphate position of siRNA strands for photomodulation of their gene-silencing activity. In this unit, we first describe in detail the syntheses of four new NPE protected nucleoside phosphoramidites (dA 0, dG 0, dC 0, dT 0) and 2-cyanoethyl-1-(2-nitrophenyl)ethyl-N,N'-diisopropylphosphoramidite (N 0). They are then site specifically incorporated into any position of RNA oligonucleotides according to standard phosphoramidite chemistry. Phosphate-caged siRNA duplexes are then prepared by hybridization of single-stranded RNAs containing the 1-(2-nitrophenyl)ethyl caging moiety on the phosphate group with their complementary RNA.