What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?

ABSTRACT: We have investigated which aspects of transcription factor DNA interactions are most important to account for the recent in vivo search time measurements for the dimeric lac repressor. We find the best agreement for a sliding model where non-specific binding to DNA is improbable at first contact and the sliding LacI protein binds at high probability when reaching the specific Osym operator. We also find that the contribution of hopping to the overall search speed is negligible although physically unavoidable. The parameters that give the best fit reveal sliding distances, including hopping, close to what has been proposed in the past, i.e. ∼40 bp, but with an unexpectedly high 1D diffusion constant on non-specific DNA sequences. Including a mechanism of inter-segment transfer between dista

SUBMITTER: Mahmutovic A 

PROVIDER: S-EPMC4402528 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature