Visualizing one-dimensional diffusion of eukaryotic DNA repair factors along a chromatin lattice.
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.
Gorman
Jason
J
Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, USA.
Plys
Aaron J
AJ
Visnapuu
Mari-Liis
ML
Alani
Eric
E
Greene
Eric C
EC
D002843:Chromatin / Q000378:metabolism*; D004260:DNA Repair; D004271:DNA, Fungal / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004058:Diffusion; D005057:Eukaryotic Cells / Q000378:metabolism*; D005456:Fluorescent Dyes / Q000378:metabolism; D008954:Models, Biological; D009707:Nucleosomes / Q000378:metabolism; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*
D002843:Chromatin; D004271:DNA, Fungal; D004268:DNA-Binding Proteins; D005456:Fluorescent Dyes; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins