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Excess of RelQ over mRNA masks the inhibitory effect of mRNA on 3H ppGpp. In contrast to enzymatic assays in which mRNA(MF) is added in excess over RelQ [0.2 μM RelQ vs. 2 μM mRNA(MF)] (A), in EMSA experiments RelQ is added to the reaction mixture in excess over mRNA(MF) [2 μM RelQ vs. 0.15 μM mRNA(MF)] (B). This results in inefficient inhibition of RelQ’s enzymatic activity under EMSA conditions and accumulation of in situ-produced ppGpp.
