Fig. 6

Interactions between RNAs and HEL. a EMSA with HEL and 5ʹ-³²P-labeled RNA: R32 (32-nt), R42 (42-nt), R56 (56-nt) (2.5 nM). Increasing amounts of HEL (2.97, 5.94, 11.86, 23.75, 47.5, 95 µM) are represented by a triangle. Reaction mixtures were incubated at 37 °C for 15 min. C- indicates a control sample with no protein. b Native PAGE analysis of mixtures of 5ʹ-³²P-labeled R42 (2.5 nM) and increasing amounts of HEL (5.94, 23.75, 95 µM). After a 15 min incubation at 37 °C, sodium dodecyl sulfate (SDS) to a final concentration of 1% was added to denature protein. C- indicates a control sample with no protein. + ATP indicates reaction mixtures with 1 mM ATP. -ATP indicates reaction mixtures without ATP. c Secondary structure of R42 generated using the RNAstructure Fold online tool (Mathews Lab) [51]. The free energy value expressed in kcal/mol is shown at the bottom. Nucleotides are numbered starting from the 5'-end. d EMSA with HEL and 5ʹ-³²P-labeled (CU)₂₁ (42-nt) (2.5 nM). Increasing amounts of HEL (2.97, 5.94, 11.86, 23.75, 47.5, 95 µM) are represented by a triangle. Reaction mixtures were incubated at 37 °C for 15 min. C- indicates a control sample with no protein