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What is the recommendation for analyzing 2'-deprotected RNA oligos with significant secondary structure?
Most RNA oligos with secondary structure may be analyzed by heating the sample to 90°C for 3 minutes prior to loading onto a denaturing gel. This treatment should denature any secondary structures and result in the RNA forming a single band on the gel. It is also critical that the gel be pre-heated before the sample is loaded. Even under strong denaturing conditions, some bands representing alternative structures may still be visible on a denaturing gel.