Fig. 3: Structural analysis of DNA conformation using a computational approach.

a Workflow for determining the kinking angles of DNA bound to different PARP-1 fragments. For an ensemble of possible DNA conformations, the expected FRET efficiencies are simulated, taking experimental data into account, i.e. Förser radius, fluorescence lifetime and time-resolved anisotropy. From the ensemble of conformations, structures are selected for which the simulated FRET efficiency is in agreement with the measured efficiency within the given uncertainties. E_exp: experimental FRET efficiency; E_sim: simulated FRET efficiency; τ: lifetime; ρ: rotational correlation time; r_∞: residual anisotropy. b Model structure for the straight DNA ligand modeled in B-form. The bases to which donor and acceptor are attached are highlighted in cyan and red, respectively. The corresponding computed accessible volumes (AV) are shown by meshes in the respective colors. c Example of a structure taken from the computed ensemble of sterically possible DNA structures; the bases to which the dyes are attached are highlighted in cyan (donor) and red (acceptor), respectively. The transparent sphere represents the flexible DNA backbone in the linker region connecting the two stems. d Ensemble of computed model structures for the DNA ligand alone. Structures are superposed using the 3′ stem of the DNA, and the 5′ stem is allowed to adopt any sterically possible orientation relative to the 3′ stem. For visual clarity, only 100 randomly chosen structures are shown, extracted from the full set of 1000 calculated structures. e Histogram of simulated FRET efficiencies for all 1000 structures of the DNA ensemble represented in d. f Representation of all simulated DNA structures in a spherical coordinate system. All structures are aligned with respect to the 3′ stem. The axis of the 3′ stem is represented by a black line. The grey dots indicate the position of the tip of the 5′ stem for each DNA structure.