(576a) Role of Nucleoid Associated Proteins in Stabilizing DNA Supercoils

Nucleoid associated proteins (NAPs) play an important role in prokaryotic cells by manipulating the shape and structure of the DNA. These NAPs act by locally bending or twisting DNA, and there are indications that NAPs bind preferentially to DNA that is already bent or twisted. We hypothesize that these binding behaviors strongly impact the stability and structure of DNA.

We use coarse-grained simulation of NAPs and DNA that allow us to achieve the time and length scales where DNA supercoiling occurs. Supercoiling can induce large-scale writhed structures where the dsDNA strand crosses over itself, which is a result of relaxing over- or under-wound DNA by inducing higher degrees of bending and writhe. We allow NAPs to be preferentially bound to a bent DNA site via the binding and unbinding energy of the simulated NAPs. Upon binding, these NAPs cause the local equilibrium bending angle to change, causing kinks in the DNA strand. We are able to reproduce experimental observations, such as the extension of a DNA molecule as a function of force, linking number, and NAP concentration. Due to the protein’s preference for binding to bent DNA, NAPs localize along the contour of the supercoil, and the induced bend in the DNA stabilizes the writhed structures that can form within the nucleoid.