One-dimensional diffusion of TrpR along DNA enhances its affinity for the operator by chemical ratchet mechanism.

ABSTRACT: Several DNA-binding proteins show the affinities for their specific DNA sites that positively depend on the length of DNA harboring the sites, i. e. antenna effect. DNA looping can cause the effect for proteins with two or more DNA binding sites, i. e. the looping mechanism. One-dimensional diffusion also has been suggested to cause the effect for proteins with single DNA sites, the diffusion mechanism, which could violate detailed balance. We addressed which mechanism is possible for E. coli TrpR showing 10⁴-fold antenna effect with a single DNA binding site. When a trpO-harboring DNA fragment was connected to a nonspecific DNA with biotin-avidin connection, the otherwise sevenfold antenna effect disappeared. This result denies the looping mechanism with an unknown second DNA b

SUBMITTER: Kinebuchi T 

PROVIDER: S-EPMC7896080 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature