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. 2015 Nov 2;5:15952. doi: 10.1038/srep15952

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Copyright © 2015, Macmillan Publishers Limited

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oc, open circular molecules; ccc, covalently closed circular molecules; lin, linear molecules; DpnI, the fragments of DpnI-digested unreplicated genomes. Black arrowheads mark the HPV18 genomes in ccc form, and white arrowheads mark the HPV18 genomes in oc form. The numbers before the abbreviations denote the number of monomeric genome copies within the molecule. The direction of the gel electrophoresis in the first (1D) and second (2D) dimension is indicated in the top left (a–c) or right (d) corner throughout the panel. (a) 2D N/N AGE analysis of DpnI-treated, uncut HPV18wt episomes extracted from U2OS cells 2 to 9 days post-transfection. (b) 2D N/N AGE analysis of the nicking enzyme Nb.Mva1269I-treated HPV18wt episomes extracted from U2OS cells 5 days post-transfection and a schematic depiction of the expected migration patterns of circular molecules following 2D N/N AGE³¹,³⁹. The direction for the increase of molecular weight and structural complexity is indicated along the top and right edges of the scheme. (c) 2D N/N AGE analysis of uncut RIs arising during the initial amplification replication of HPV18E8ˉ episomes. Bold arrows, putative theta RIs; thin arrow, diffuse putative RIs. (d) A schematic depiction of the expected migration patterns of bidirectional theta (θRIs) and rolling-circle RIs (σRIs)³¹,³⁹. The direction for the increase of molecular weight and structural complexity is indicated along the top and right edges of the scheme.