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. 2012 Dec 5;41(2):1372–1381. doi: 10.1093/nar/gks1208

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© The Author(s) 2012. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.

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Figure 4. — yNhp6A binds bulge_18a DNA in a single kinked state. (A) FRET efficiency histograms for bulge_18a DNA target in the absence and presence of yMhp6A indicating that yNhp6A binds to this DNA target in a single kinked state. (B) Time traces of donor and acceptor emission intensities, and (C) corresponding FRET efficiency time traces showing no DNA target dynamics in the absence of protein but multiple transitions between the low (E_FRET ∼0.17) and high (E_FRET ∼0.25) FRET states in the presence of yNhp6A. (D) FRET efficiency time traces analyzed for a two-state system using a hidden Markov model to determine the average transition rates (v) from low FRET to high FRET states (v₁₂) and from the high FRET to low FRET states (v₂₁). (E) Dwell time distributions for the binding times (τ₁₂) (low FRET states/DNA-only states) are shown at different yNhp6A concentrations. (F) Dwell time distributions for the binding times (τ₂₁) (high FRET states/yNhp6A-bound states) are shown at different yNhp6A concentrations.