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. 2014 Dec 8;9(12):e114580. doi: 10.1371/journal.pone.0114580

Figure 4. Permanganate reactivity of pyrimidine bases in the protein-DNA complexes.

Figure 4

Sequences at the top of the panels schematically depict the ‘cognate’ and the ‘non-cognate’ thymine-substituted substrates, the asterisk marks the 33P radiolabel. Base pairs important for specific binding are in black boxes. Positions of the mispaired thymine and the 5-methylcytosine are marked with red arrows. (A) Thymine oxidation by KMnO4 with or without LpnPI-N. ‘M’, the A+G markers of the radiolabeled ‘cognate’ and ‘non-cognate’ strands; ‘ss’, oxidation of the single-strand oligonucleotides; ‘ds’, double-stranded 16-T (cognate) and 16-T-N (noncognate) oligoduplexes without the protein; ‘L’, 16-T and 16-T-N oligoduplexes + LpnPI-N. Density profiles of individual lanes are shown: cognate DNA (blue), cognate DNA + LpnPI-N (red), non-cognate DNA (green), and non-cognate DNA + LpnPI-N (magenta). (B) Thymine oxidation by KMnO4 in the presence of YkrI and BmeDI. ‘M’, the A+G markers of the radiolabeled ‘cognate’ and ‘non-cognate’ strands; ‘ss’, oxidation of the single-strand oligonucleotides; ‘ds’, 39-T/H (cognate) and 39-T (noncognate) oligoduplexes without the protein; ‘Y’, 39-T/H and 39-T oligoduplexes + YkrI; ‘B’, 39-T/H and 39-T oligoduplexes + BmeDI. Density profiles: cognate DNA (blue), cognate DNA + BmeDI and YkrI (orange and red, respectively), non-cognate DNA (green), non-cognate DNA + BmeDI and YkrI (magenta and cyan, respectively). (C) 5-methylcytosine oxidation by KMnO4 at pH 4.3 with or without LpnPI-N. ‘M’, the A+G markers of the radiolabeled ‘cognate’ and ‘non-cognate’ strands; ‘ds’, double-stranded 30-M (cognate) and 39-M/H (noncognate) oligoduplexes without the protein; ‘L’, 30-M and 39-M/H oligoduplexes + LpnPI-N. Density profiles of individual lanes are colored as in panel (A).