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. 2008 Apr 29;6(4):e96. doi: 10.1371/journal.pbio.0060096

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© 2008 Wilkinson et al.

This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.

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(A) SHAPE reactivities as a function of nucleotide position for ex virio (red), in virio (green), and AT-2-treated (blue) states.

(B) Difference plot illustrating the effect of AT-2 treatment on SHAPE reactivity relative to in virio genomic RNA. Sites of enhanced SHAPE reactivity upon compromising nucleocapsid zinc knuckle structures by AT-2 treatment are reported as positive peaks. Individual nucleotides showing large changes in reactivity are indicated with upward-pointing arrowheads and correspond to the same symbols shown in Figure 4A. Primary and secondary sites are emphasized with double (**) and single asterisks (*) , respectively. Reactivity differences are smoothed over a 5-nt window.