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. 2017 Sep 13;45(19):11268–11280. doi: 10.1093/nar/gkx823

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© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, 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 3. — (A) Native polyacrylamide gel electrophoresis suggests the formation of intramolecular G-quadruplex structure as indicated by faster migration of genotype B wild-type PQS (GTB-WT-PQS) oligonucleotide compared to the mutated (GTB-MUT-PQS) oligonucleotide and the ssDNA control (25mer). (B) Denaturing polyacrylamide gel electrophoresis showing similar migration rate for the wild-type (GTB-WT-PQS) and the mutated (GTB-MUT-PQS) oligonucleotide in the presence of a denaturant (7 M urea). DMS footprinting of 5′ FAM labelled PQS oligonucleotides namely (C) FAM-N (contains 10 additional bases of the native HBV sequence upstream of the the PQS in the preS2/S promoter) and (D) FAM-T (contains 10 additional stretch of 10 thymine (T) residues upstream of the PQS in the preS2/S promoter). The KCl concentrations used were 600, 100 and 0 mM (no KCl). AG and TC represents sequencing cleavage reactions specific to purine and pyrimidine. The vertical bars next to the sequence of the oligonucleotide represents the G residues protected from DMS methylation due to formation of G-quadruplex structure. Please see Supplementary File S3, Table S1 for sequence of the oligonucleotides.