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. 2007 Apr 11;35(9):2833–2845. doi: 10.1093/nar/gkm134

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© 2007 The Author(s)

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) 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. — Calculation of the angle between helix I and U6 ISL using the acceptor normalization method. (A) The metal-ion-binding site on arm Y cannot be determined without knowing the angle between arms X and Y. As shown, the distance between Cy3 and a site-bound Tb(III) ion (dashed line from Cy3 to star) will correspond to different sites on arm Y if the angle between arms X and Y is unknown. (B) ‘Acceptor normalization method’ normalization process. Normalized Cy5 fluorescence, which is the acceptor intensity, is calculated from normalized Cy3–Cy5 emission spectra minus normalized Cy3 scan.