Supplementary Figure 5: Characteristics of A-form DNA are well resolved and base pairing between distant donor DNA regions is required for strand transfer activity.

a, Ideal A-form DNA fitted into donor DNA reconstruction, depicting widened minor groove, base pair tilt, axial rise and helical axis dislocation relative to base pairs. A single donor DNA is depicted for clarity. The reconstruction is colored green and yellow, for transferred strand and non-transferred strand, respectively. Relevant regions of DNA are indicated. b, Atomic model of donor DNA depicting A-form DNA characteristics. Views are as in a, except only relevant regions the donor DNA atomic model are depicted. c, Schematic of the secondary structure of a donor DNA terminal inverted repeat (left). Watson-Crick base pairing is indicated by solid lines. Non-canonical base pairing is indicated by dots, or dotted lines. Nucleotides of the transferred strand are numbered -1 to -31, starting at the 3′ terminal guanosine. Distant noncanonical A-form helical base pairing between the transferred and non-transferred strand is highlighted (dashed red box). Agarose gel of a strand transfer assay with 5′-radiolabeled mutant and rescue donor DNAs (right). Assays were largely performed as previously described (Beall, E. L., et al., EMBO J. 17, 2122–2136, 1998). The base pairs are shown above each lane, with the substituted bases highlighted in red (mutant, lanes 2 - 8). Compensatory substitutions in the non-transferred strand are shown above each lane, with substitutions to restore base pairing highlighted in blue (rescue, lanes 10 - 16). The expected positions of single-ended integration (SET) and double-ended integration (DET), as well as free donor DNA (Probe), are indicated. wt, wild type donor DNA.