Extended Data Fig. 5: Topological features of hexameric sequences and the CDMs.

a, The relationship between different hexanucleotide sequences (log2 ratio standardized to 1; mean of 4 independent experiments) and the values of predicted DNA shape parameters. CDMs are noted, demonstrating notable enrichment. For propeller twist (ProT), the mean of the values are computed for the 3rd and 4th nucleotide of the motif; for roll and helical twists (HelT), the mean of the values are computed for base-pair steps 2 to 4 in each hexamer. Error bars denote the 95% CI around mean scaled log2 ratios for each hexanucleotide sequence, n=4. b, The distance between the cyclopropanes (Å) of colibactin by running a molecular dynamics simulation of free colibactin in water, n=1. The horizontal red line identifies the average values of this distance (12.8 Å). c, The correlations of hexanucleotide motif enrichment (mean log2 ratio) with DNA shape parameters (left - 3 columns) and central dinucleotides (rightmost column), depending on the presence and distance of adenines on opposite strands, n=4 independent experiments. The presence and distance of adenines are classified in the following groups (from top to bottom, all sequences in 5’-3’ direction): A-T at 3 nt distance, A-T at 4 nt distance, A-T at 3 and 4 nt distance, T-A at 3 nt distance, T-A at 4 nt distance, T-A at 3 and 4 nt distance, no A-T/T-A at 3 or 4 nt distance. Lines in the left three columns are mean log2 ratios smoothed by local regression, method LOESS (locally estimated scatterplot smoothing).