FIGURE 4.

Illustration of DNA scanning by facilitated diffusion. (A) Sketch of DNA showing the negatively charged region of DNA important for facilitated diffusion of A3 enzymes. (B–D) Enzyme in sketches is shown as a dimer, although the oligomerization state may vary with different A3 enzymes. (B) Sketch depicting a 1-dimensional DNA scanning path by sliding. Dotted line indicates path of enzyme (orange). Sliding enables an in depth search of local areas of a substrate. (C) Sketch depicting a 3-dimensional DNA scanning path by jumping. Jumping enables larger translocations on DNA substrates, but lacks a local search process. The microdissociations of the enzyme from the DNA that occur when the enzyme jumps does not leave the negatively charged domain of the DNA so the enzyme has a higher likelihood of reassociating with the same DNA substrate than diffusion into the bulk solution. (D) Sketch depicting a 3-dimensional DNA scanning path by intersegmental transfer. Intersegmental transfer enables larger translocations on DNA substrates, but lacks a local search process. An enzyme with two DNA-binding domains binds two regions of DNA simultaneously before dissociating from one region to move to another.