Extended Data Fig. 8: Comparison of canonical and reorganized DNA^Myc G-quadruplex.

DNA^Mycǂ denotes the canonical DNA^Myc structure^20,24 whereas DNA^Myc* represents the reorganized DNA^Myc found in the DHX36-DSM–DNA^Myc co-crystal structure. a, Structure of the DNA^Mycǂ top G-quartet (PDB ID: 2N21). b, Structure of the DNA^Myc* top G-quartet. c, Primary sequence alignment of the canonical and reorganized DNA^Myc G-quadruplex. Bold residues participate in formation of a quartet. d, The structure of DNA^Myc G-quadruplex found in our co-crystal structure, represented here by DNA^Myc*. Distances between A1 and T24 as well as G16 and G17, G17 and T18, and T18 and T19 are indicated. Theoretical FRET efficiencies (E) for DNA^Mycǂ and DNA^Myc* were calculated using E = 1/[1 + (r/R₀)⁶] where R₀ = 53 Å for the Cy3–Cy5 pair and r is the distance between Cy3 and Cy5. Since smFRET experiments were performed with a DNA^Myc G-quadruplex containing a 3′ ssDNA extension of nine thymines, we added the distance between two thymines to the theoretical FRET efficiency model assuming an average internucleotide distance of 7.1 Å. As the difference between the hypothetical DNA^Mycǂ previously solved by NMR and DNA^Myc* found in our co-crystal structure is one nucleotide, we modelled rǂ and r* as 50.2 Å and 57.3 Å, respectively. From these parameters, we obtained predicted FRET efficiencies of 0.58 and 0.39 for DNA^Mycǂ and DNA^Myc*, respectively. These predicted FRET efficiencies closely match the experimental oscillating FRET efficiencies of ~0.6 and ~0.4. e, The high FRET state of ~0.85 is observed before DHX36 binding to the DNA^Myc G-quadruplex. f, DHX36 initially binds to DNA^Mycǂ (FRET ~0.6). g, Probably owing to ATP-independent C-terminal domain rotations also observed¹⁶ with Prp43p, the DNA^Myc, G-quadruplex is partially unwound to DNA^Myc* (~0.4). DHX36 then oscillates between DNA^Myc* and DNA^Mycǂ in an ATP-independent repetitive unfolding activity.