Chemical purity of RNA samples is critical for high-precision studies of RNA folding and catalytic behavior, but such purity may be compromised by photodamage accrued during ultraviolet (UV) visualization of gel-purified samples. Here, we quantitatively assess the breadth and extent of such damage by using reverse transcription followed by single-nucleotide-resolution capillary electrophoresis. We detected UV-induced lesions across a dozen natural and artificial RNAs including riboswitch domains, other non-coding RNAs, and artificial sequences; across multiple sequence contexts, dominantly at but not limited to pyrimidine doublets; and from multiple lamps that are recommended for UV shadowing in the literature. Most strikingly, irradiation time-courses reveal detectable damage within a few seconds of exposure, and these data can be quantitatively fit to a skin effect model that accounts for the increased exposure of molecules near the top of irradiated gel slices. The results indicate that 200-nucleotide RNAs subjected to 20 seconds or less of UV shadowing can incur damage to 20% of molecules, and the molecule-by-molecule distribution of these lesions is more heterogeneous than a Poisson distribution. Photodamage from UV shadowing is thus likely a widespread but unappreciated cause of artifactual heterogeneity in quantitative and single-molecule-resolution RNA biophysical measurements.
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