Figure 2: Molecular characteristics of G4 DNA-induced deletions.

(a) Position of the 3′ junctions with respect to the cognate G4 motif (boxed). Triangles indicate junctions of separately isolated deletion alleles. For each motif, the minimal 5′ sequence that complies to the G4 motif consensus is shown in pink to visually emphasize the notion that almost all junctions (94%) map 3′ of a possible G4 structure. (b) Illustration defining single-nucleotide homology. The chance that the outermost nucleotide on one deletion junction is identical to the first deleted base at the other junctions was calculated as well as empirically determined to be 47% (Supplementary Fig. 1). (c) Pie charts displaying the overrepresentation of single-nucleotide homology for G4 DNA-induced simple deletions (in blue). (d) Templated insertions coinciding with G4 DNA-induced deletion formation. On the left this phenomenon is graphically represented. The right panel displays seven examples. Matching sequences are underlined. Lines 1–4 are simple inserts templated on the 5′ flank. Lines 5 and 6 represent cases where the same flank is used twice as a template. Line 7 represents a case where both the 5′ and 3′ flanks contribute to the insert but also illustrates that the flank 3′ to the G-tract can serve as a template (see Supplementary Figs 2 and 4 for more cases).