DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid  Edmond Chow, Jeffrey Skolnick  Biophysical Journal  Volume 112, Issue 11, Pages 2261-2270 (June 2017) DOI: 10.1016/j.bpj.2017.04.049 Copyright © 2017 Biophysical Society Terms and Conditions

Figure 1 Given here is the initial configuration of the LacI-DNA system with 6913 total particles, with DNA beads drawn as a chain. (A) The system is drawn within its periodic simulation box. (B) The same system is drawn, showing that the DNA beads form a continuous chain. The portions of DNA outside the box also exist as periodic images within the box, which are not drawn. (C) Both previous figures are superimposed. (D) Portions of the DNA system have been cut away to show the LacI sphere crowded in its DNA environment. To see this figure in color, go online. Biophysical Journal 2017 112, 2261-2270DOI: (10.1016/j.bpj.2017.04.049) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 2 (Left) Given here is the MSD for the large LacI-DNA system for BD simulations without HI. The results for LacI and DNA beads are shown separately. (Right) Here, the log-log plot shows data for long time intervals. To see this figure in color, go online. Biophysical Journal 2017 112, 2261-2270DOI: (10.1016/j.bpj.2017.04.049) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 3 Given here is an index of the closest DNA bead to LacI over time for the small 256 DNA bead model. To see this figure in color, go online. Biophysical Journal 2017 112, 2261-2270DOI: (10.1016/j.bpj.2017.04.049) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 4 Shown here is the trajectory of LacI in the small 256-DNA bead model projected on the x-y and the x-z planes between times 2400 and 2600. LacI transitions from one cage to another at time 2495. The trajectories before and after the transition are colored red and blue, respectively. The motion of LacI is evidently confined before and after the transition. To see this figure in color, go online. Biophysical Journal 2017 112, 2261-2270DOI: (10.1016/j.bpj.2017.04.049) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 5 (Left) Given here is the MSD for the small LacI-DNA system for BD simulations with the FD approximation (without HI) and for SD simulations. The results for LacI and DNA beads are shown separately. (Right) The log-log plot shows data for long time intervals. To see this figure in color, go online. Biophysical Journal 2017 112, 2261-2270DOI: (10.1016/j.bpj.2017.04.049) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 6 Here we give the cumulative number of contacts that LacI makes with DNA beads for the large LacI-DNA system. When LacI is nonspecifically bound to a specific site on the DNA (the 1D diffusion case), the cumulative number of contacts is significant compared to the 3D diffusion case and also grows over time. To see this figure in color, go online. Biophysical Journal 2017 112, 2261-2270DOI: (10.1016/j.bpj.2017.04.049) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 7 For LacI hopping on DNA in the small LacI-DNA system, we show here the index of the closest DNA bead to LacI over time, in a simulation using the FD approximation. The red highlighted points indicate the facing bead on the DNA segment along which the LacI is hopping. To see this figure in color, go online. Biophysical Journal 2017 112, 2261-2270DOI: (10.1016/j.bpj.2017.04.049) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 8 (A) Shown here are 6912 DNA beads arranged along a closed space-filling curve where straight segments are not shorter than twice the persistence length. Red to white to blue coloration varies along the curve. This configuration is placed in a periodic simulation box that is slowly reduced in volume until the desired DNA volume fraction is reached. (B) Shown here is the initial DNA configuration for simulation after the simulation box volume has been reduced. Colors suggest a territorial structure. (C) Given here is the DNA configuration at time 10,000 of simulation with 3D LacI diffusion and mobile DNA. (D) Shown here is the DNA bead contact frequency (proportional to probability in our case) for the initial configuration. Two DNA beads are considered as being in contact if they are within four DNA bead radii of each other. The solid line corresponds to a power-law scaling exponent of γ = 1.5. The value for γ for the configuration at time 10,000 is nearly identical. To see this figure in color, go online. Biophysical Journal 2017 112, 2261-2270DOI: (10.1016/j.bpj.2017.04.049) Copyright © 2017 Biophysical Society Terms and Conditions