Visualizing one-dimensional diffusion of eukaryotic DNA repair factors along a chromatin lattice

Nat Struct Mol Biol. 2010 Aug;17(8):932-8. doi: 10.1038/nsmb.1858. Epub 2010 Jul 25.

Abstract

DNA-binding proteins survey genomes for targets using facilitated diffusion, which typically includes a one-dimensional (1D) scanning component for sampling local regions. Eukaryotic proteins must accomplish this task while navigating through chromatin. Yet it is unknown whether nucleosomes disrupt 1D scanning or eukaryotic DNA-binding factors can circumnavigate nucleosomes without falling off DNA. Here we use single-molecule microscopy in conjunction with nanofabricated curtains of DNA to show that the postreplicative mismatch repair protein complex Mlh1-Pms1 diffuses in 1D along DNA via a hopping/stepping mechanism and readily bypasses nucleosomes. This is the first experimental demonstration that a passively diffusing protein can traverse stationary obstacles. In contrast, Msh2-Msh6, a mismatch repair protein complex that slides while maintaining continuous contact with DNA, experiences a boundary upon encountering nucleosomes. These differences reveal important mechanistic constraints affecting intranuclear trafficking of DNA-binding proteins.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chromatin / metabolism*
  • DNA Repair*
  • DNA, Fungal / metabolism
  • DNA-Binding Proteins / metabolism*
  • Diffusion
  • Eukaryotic Cells / metabolism*
  • Fluorescent Dyes / metabolism
  • Models, Biological*
  • Nucleosomes / metabolism
  • Protein Binding
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / metabolism*

Substances

  • Chromatin
  • DNA, Fungal
  • DNA-Binding Proteins
  • Fluorescent Dyes
  • Nucleosomes
  • Saccharomyces cerevisiae Proteins