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. 2011 Dec 1;6(12):e27751. doi: 10.1371/journal.pone.0027751

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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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The indicated numbering is as used throughout the manuscript. The Y-mer strand Y4 has non-wild type bases at positions 20 and 21 in order to increase the stability of this arm of the substrate. DNA strands in the Y-mer substrate are colored for identification as in Figures 3 – 6 . The host portion of strand Y4 is colored in lighter shade of blue to distinguish the host sequence from the viral sequence after covalent joining to viral DNA. In linear and Ymer DNAs, the conserved adenine preceding the scissile phosphate is shown in bold.