Fig. 3: UvrD sequesters unwound DNA by looping.

a Snapshot of MD simulation of UvrD-DNA fork complex showing DNA loop formation. Simulations are based on a crystal structure of UvrD (PDB accession number 2IS2) bound to a ss-dsDNA junction with extended 3′ and 5′ tails. Both 3′ (orange dashed box), and 5′ (gray dashed box) loops are shown. b Representative conformations showing how the 3′ (orange dashed box) and 5′ (gray dashed box) loops are anchored to the protein surface and released. The primary anchor residues for 3′ and 5′ loops are R213 and R619, respectively. Before the release, nt 4 is in contact with the anchor residue; the 3-nt release is achieved by forming a new contact between nt 1 and the anchor residue. Black dashed circles highlight contact points between the anchor residue and nt 1 or 4. Backbone atoms of DNA phosphate groups and backbone carbon atoms near the contact points are shown in ball-and-stick representation (brown = phosphorous, red = oxygen, cyan = carbon). c Distributions of 3′ (orange) and 5′ (gray) loop size changes. d Scatter plot comparing the step sizes predicted from simulated loop release to the individual experimental unwinding step size measurements (blue dots) at 0.5 µM ATP, and plot of average step size for both distributions (blue diamonds). Error bars represent standard deviation. Total number of steps displayed: N = 394 (experimental) and 500 (theoretical). Only integer and half-integer values are possible for the simulated step sizes, as they are calculated from distributions in (c), assuming loops released from the 3′ and 5′ ends are independent. Source data are provided as a Source Data file.