A cautionary note on the use of blot hybridization for RNA size determination

The ease with which RNA blot hybridization analysis can be performed makes it among the most widely used analytical tools in molecular biology. Hybridization with a labeled probe, subsequent to size fractionation and immobilization on a filter, allows one to approximate both the size and abundance of a given RNA in a single experiment. This communication demonstrates that dramatic differences in the electrophoretic mobility of the yeast GCN2 transcript are observed when size fractionation on formaldehyde gels is compared to fractionation of glyoxalated RNA. Both routinely used systems are considered to be fully denaturing. The anomalous mobilities therefore pose a potential problem when size determination is performed using a single gel system.