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. Author manuscript; available in PMC: 2013 Nov 23.
Published in final edited form as: J Mol Biol. 2012 Sep 18;424(1-2):54–67. doi: 10.1016/j.jmb.2012.09.012

Figure 3.

Figure 3

Probing the thermodynamics of expanded RA variant constructs based on tectoRNA assembly attenuation. (a) Schematic illustrating the experimental design strategy used to test RA variants in an expanded context. The third helix (helix Z) was added 3′ of the RA motif to either mimic the AAAG_P3_P8 junction from group IC1 and ID introns or the H3-H4-H18 region of bacterial 16S rRNA. (b) Expanded RA variants tested and their resulting Kd values. (c) Sample native PAGE (1x TB, 15 mM Mg2+) gel-shift assays used to determine relative equilibrium dissociation constant (Kd) at 10°C (left) and corresponding apparent free energy variation of attenuation (ΔΔGAT), referenced to the minimal AAAU construct (right) (see also Figure 2).