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. 2011 Nov 25;40(6):2494–2505. doi: 10.1093/nar/gkr1095

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© The Author(s) 2011. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — Determination of binding affinities of XPC-RAD23B binding to dG-ALII and dG-AAF containing oligonucleotides. (A) Lesion-containing 44-mer oligonucleotides (4 nM) were annealed to a complement containing a 5′ Cy5 fluorescent label and incubated with different concentrations (0–125 nM) of XPC-RAD23B for 30 min. The reactions were analyzed on a 5% native polyacrylamide gel and visualized on a Typhoon imaging system. Two representative gels using C209-ALII and C209-ALII with mismatch are shown. (B) Determination of K_d values: the percentage of bound (DNA+XPC-RAD23B) and non-bound fractions (DNA) were determined using Image Quant TL. K_d were calculated from at least three independent experiments and the data analyzed using sigma plot. Standard deviations are indicated by error bars.