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 $2.3\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}12}\text{ }\text{ }{\mathrm{cm}}^{2}/\mathrm{s}$ to $1.3\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}9}\text{ }\text{ }{\mathrm{cm}}^{2}/\mathrm{s}$; (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.