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. 2022 Nov 17;11:e69916. doi: 10.7554/eLife.69916

Figure 3. Evaluation of G-quadruplex formation at mitochondrial Region I.

(A) Bisulphite modification assay on plasmid (pDI1) containing mitochondrial Region I. Vertical bar represents the number of times the respective cytosine in the top and bottom strands of mitochondrial Region I is converted to thymine after deamination when treated with sodium bisulphite, followed by PCR. (B, C) Bisulphite sequencing on the mitochondrial genome for determining the formation of G4 DNA at Region I. Each vertical bar represents the conversion of a cytosine to uracil in the top strand or bottom strand. A total of 59 clones were sequenced from both the top and bottom strands (B). Single strandedness was observed in a DNA fragment of 198 nt containing Region I of the mitochondrial genome following bisulphite modification assay (C). Each row represents cytosines present in a DNA molecule. Each dark circle represents the conversion of cytosine to thymine on the top strand after deamination upon treatment with sodium bisulphite, followed by PCR and DNA sequencing. Of the 59 clones sequenced, the most reactive 25 molecules are shown (C). In all the panels, sequences corresponding to the G-quadruplex forming motif are indicated in a dotted rectangular box (mustard yellow). Refer also Figure 3—figure supplement 1.

Figure 3—source data 1. Sequence of clones after bisulphite treatment in a plasmid containing Region I of mitochondria.
Figure 3—source data 2. Sequence of clones after bisulphite treatment in a region I of mitochondria.

Figure 3.

Figure 3—figure supplement 1. Schematic showing conversion of cytosine to thymine following bisulfite modification assay.

Figure 3—figure supplement 1.

Related to Figure 3. (A, B) Treatment with sodium bisulfite can result in deamination of cytosine, leading to uracil when present on a single-stranded DNA (A). This C to U conversion can lead to C to T change following PCR and sequencing (B). (C) Table showing the summary of clone sequenced from mitochondrial region containing plasmid and mitochondrial genome for bisulfite sequencing for both top and bottom strand.