Assay of Random RNA Oligomerisation in Buffers with High Concentrations of Divalent Metal Ions

Abstract

Certain conditions, such as high concentrations of divalent metal ions in the reaction buffer or low pH, can cause aggregation and precipitation of RNA species with complementary sequences. If oligomerisation has gone unnoticed, some sequences from the pool of random RNA may be underrepresented or even lost at the very beginning of the selection experiment. Two simple assays for RNA oligomerisation are suggested. One is based on electrophoresis in non‐denaturing gels, and the other uses gel‐filtration.