Shape matters!

Have you ever wondered why DNA is a helical molecule? Although the shape of this ultimate information carrier is maybe an inevitable consequence of stacking single monomer units into a polymer, the shape also has an important effect on the time it takes for DNA binding proteins to find their targets. By solving the reaction-diffusion equations for DNA-like geometries, and complementing with simulations when necessary, we show that the helical structure can make binding to the DNA more than twice as fast compared to binding a straight molecule.

Rule'em all

Figure: Reaction-diffusion equation and boundary conditions for example geometry. Only when the reactive patch on the sphere (gray) is in contact with the reactive patch on the cylinder do they react with rate kappa. The sphere moves around the cylinder with translational diffusion rate D. When the sphere reaches a distance Rc away from the cylinder it is equally likely to bind another DNA segment.

Check out the publication in MSB