Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion

Nucleic Acids Res. 2006 Jul 11;34(12):3409-20. doi: 10.1093/nar/gkl393. Print 2006.

Abstract

The tethered particle motion (TPM) allows the direct detection of activity of a variety of biomolecules at the single molecule level. First pioneered for RNA polymerase, it has recently been applied also to other enzymes. In this work we employ TPM for a systematic investigation of the kinetics of DNA looping by wild-type Lac repressor (wt-LacI) and by hinge mutants Q60G and Q60 + 1. We implement a novel method for TPM data analysis to reliably measure the kinetics of loop formation and disruption and to quantify the effects of the protein hinge flexibility and of DNA loop strain on such kinetics. We demonstrate that the flexibility of the protein hinge has a profound effect on the lifetime of the looped state. Our measurements also show that the DNA bending energy plays a minor role on loop disruption kinetics, while a strong effect is seen on the kinetics of loop formation. These observations substantiate the growing number of theoretical studies aimed at characterizing the effects of DNA flexibility, tension and torsion on the kinetics of protein binding and dissociation, strengthening the idea that these mechanical factors in vivo may play an important role in the modulation of gene expression regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • DNA / chemistry*
  • DNA / metabolism
  • Kinetics
  • Lac Operon
  • Lac Repressors
  • Microspheres
  • Motion
  • Mutation
  • Nucleic Acid Conformation
  • Operator Regions, Genetic
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*

Substances

  • Bacterial Proteins
  • Lac Repressors
  • Repressor Proteins
  • DNA