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When is a Distribution Not a Distribution, and Why Would You Care: Single-Molecule Measurements of Repressor Protein 1-D Diffusion on DNA

  • Y.M. Wang
  • H. Flyvbjerg
  • E.C. Cox
  • R.H. Austin
Part of the Lecture Notes in Physics book series (LNP, volume 711)

Abstract

We address the long-standing puzzle of why some proteins find their targets faster than allowed by 3D diffusion. To this end, we measured the onedimensional diffusion of LacI repressor proteins along elongated Lambda DNA using single molecule imaging techniques. We find that (1) LacI diffuses along nonspecific sequences of DNA in the form of 1D Brownian motion; (2) the observed 1D diffusion coefficients DDNA vary over an unexpectedly large range, from 2.3×10-12 cm2/s to 1.3 × 10-9 cm2/s; (3) the lengths of DNA covered by these 1D diffusions vary from 120nm to 2920 nm; and (4) the mean values of DDNA and the diffusional lengths indeed predict a LacI target binding rate 90 times faster than the 3D diffusion limit. The first half of this chapter is a tutorial on the models we use to think about the physics, the limited and noisy data, and how to squeeze the maximum amount of physics from these data. The second half is about our experiments and results.

Keywords

Random Motion Stochastic Error Random Trajectory Conformational Substate Conformational Distribution 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer 2007

Authors and Affiliations

  • Y.M. Wang
    • 1
  • H. Flyvbjerg
    • 2
  • E.C. Cox
    • 3
  • R.H. Austin
    • 1
  1. 1.Department of PhysicsPrinceton UniversityPrinceton
  2. 2.Biosystems Department and Danish Polymer CentreRisø National LaboratoryRoskildeDenmark
  3. 3.Department of Molecular BiologyPrinceton UniversityPrincetonUSA

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