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. Author manuscript; available in PMC: 2014 Feb 27.
Published in final edited form as: J Am Chem Soc. 2013 Feb 11;135(8):3136–3143. doi: 10.1021/ja310742m

Figure 3.

Figure 3

The microfluidic assay can measure Kd for riboswitches with rapid interconversion rates. Riboswitch mobility can be used to extract Kd values that are equivalent to those measured by traditional in-line probing assays. μMSA (left) and slab gel (right) results for the SAM-I Bs riboswitch aptamer with (A) TB buffer + 1 mM Mg2+ and (B) TB buffer + 10 mM Mg2+. On-chip RNA mobility values (relative to internal standard) are given as × 10−5 cm2/Vs. 0 nM SAM sample was used to determine Kd but plotted at 0.1 nM for on-chip data to allow for logarithmic axis. Solid traces are best-fit 3-parameter logistic curves at the Kd shown. Error bars for on-chip data are standard deviation of quadruplicate runs. Error bars for in-line probing assays shown are the standard deviation of values for the sites of modulation analyzed from a single slab gel.