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. Author manuscript; available in PMC: 2015 Aug 11.
Published in final edited form as: Anal Chem. 2013 Sep 26;85(20):9868–9876. doi: 10.1021/ac4028559

Figure 3. Secondary Structure.

Figure 3

Chromatograms derived for (A) S1-S212a with the violet cluster and for (B) S1-S212a :S2C12a with the blue-green cluster. Absorbances at 260 (dotted lines), 400 (solid line – A), and 490 (solid line – B) nm correspond to the DNA host, the violet cluster, and the blue-green cluster, respectively. Based on the absorbance at 260 nm in (A), the leading peak is native S1-S212a. The lagging peak is the cluster conjugate. Based on the absorbance at 260 nm in (B), the leading peak is due to native duplex S1-S212a:S2C12a, the intermediate peak is the blue-green cluster conjugate, and the lagging peak is the complement S2C12a. (C) Size exclusion chromatograms of blue-green conjugates in which S1-S212a (black and red strands) hybridizes with complements S2C12a, dT10-S2C12a, and dT20-S2C12a (green strands). These produce a blue-green conjugates with a hydrodynamic diameter of Do, Do + α, and Do + β, respectively. Progressively shorter retention times support hybridization of the S212a component and its S2C12a complement.