Single Molecule Measurements of Repressor Protein 1D Diffusion on DNA

Abstract

We used single-molecule imaging techniques and measured the one-dimensional diffusion of LacI repressor proteins along elongated DNA to address the long-standing puzzle of why some proteins find their targets faster than allowed by 3D diffusion. Our analysis of the LacI transcription factor’s diffusion yielded four main results: (1) LacI diffuses along nonspecific sequences of DNA in the form of 1D Brownian motion; (2) the observed 1D diffusion coefficients $D_1$ vary over an unexpectedly large range, from $2.3\times {10}^{-12}{\mathrm{cm}}^2/\mathrm{s}$ to $1.3\times {10}^{-9}{\mathrm{cm}}^2/\mathrm{s}$; (3) the lengths of DNA covered by these 1D diffusions vary from 120 nm to 2920 nm; and (4) the mean values of $D_1$ and the diffusional lengths indeed predict a LacI target binding rate 90 times faster than the 3D diffusion limit.