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. Author manuscript; available in PMC: 2019 Apr 12.
Published in final edited form as: Nucleosides Nucleotides Nucleic Acids. 2015;34(2):114–129. doi: 10.1080/15257770.2014.965256

Figure 1. UV initiated deprotection and alkaline hydrolysis of 2′-O-caged RNAs containing 2′-O-photolabile groups.

Figure 1.

A: Gel image corresponds to the RNA containing α-methyl-o-nitrobenzyl protecting group. B: Gel image corresponds to the RNA containing o-nitrobenzyl protecting group. Method: A 5′-radiolabeled 30 mer RNA fragment in water (20 μL) was irradiated at 365 nm and 0.5-μL aliquots were taken and diluted in water (3 μL). Alkaline hydrolysis ladders were performed by adding sodium bicarbonate, pH 9, and incubating at 90 °C for 15 min. The resulting ladder of RNA fragments was separated by denaturing PAGE, and deprotection was quantitated by measuring the intensity of the band corresponding to cleavage by the deprotected nucleophile. The first lane in the depicted gel corresponds to deprotected substrate prior to alkaline hydrolysis.