Figure 2.

Validation of the single-molecule real-time (SMRT) method for mapping PT modifications in genomes. To validate the SMRT method, experiments were performed using (A) oligodeoxynucleotides containing S_p and R_p configuration PT modifications and (B) a pBluescript SK⁺ plasmid grown in Salmonella enterica serovar Cerro 87 and a dndD knockout strain as a control. (A) Upper and lower panels show the kinetic signals for SMRT sequencing of oligodeoxynucleotides containing PT in the R_p and S_p configurations, respectively. (B) Circos plot of kinetic signals of pBluescript plasmids grown in Salmonella enterica serovar Cerro 87 (±DndD). The inner and outer circles denote IPD ratios for the forward and reverse DNA strands, respectively. Tick marks denote all occurrences of the 5′-GAAC-3′/3′-CTTG-5′ sequence across the plasmid (for IPD ratios at these locations see Supplementary Table 1). The lower panel shows examples for kinetic signals at two locations on the plasmid.