One-dimensional Diffusion of Proteins along DNA

Shimamoto, Nobuo

doi:10.1074/jbc.274.22.15293

Cited by 156 publications

(108 citation statements)

References 44 publications

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“…At present, facilitated diffusion is usually ascribed to 1D diffusion (16,17). However, much of the experimental data that support sliding can be reconciled to other schemes.…”

mentioning

confidence: 89%

Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA

Gowers

Wilson

Halford

2005

Proc. Natl. Acad. Sci. U.S.A.

223

257

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Proteins that act at specific DNA sequences bind DNA randomly and then translocate to the target site. The translocation is often ascribed to the protein sliding along the DNA while maintaining continuous contact with it. Proteins also can move on DNA by multiple cycles of dissociation͞reassociation within the same chain. To distinguish these pathways, a strategy was developed to analyze protein motion between DNA sites. The strategy reveals whether the protein maintains contact with the DNA as it transfers from one site to another by sliding or whether it loses contact by a dissociation͞reassociation step. In reactions at low salt, the test protein stayed on the DNA as it traveled between sites, but only when the sites were <50 bp apart. Transfers of >30 bp at in vivo salt, and over distances of >50 bp at any salt, always included at least one dissociation step. Hence, for this enzyme, 1D sliding operates only over short distances at low salt, and 3D dissociation͞ reassociation is its main mode of translocation.DNA-protein interaction ͉ recognition sequence ͉ restriction enzyme

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“…At present, facilitated diffusion is usually ascribed to 1D diffusion (16,17). However, much of the experimental data that support sliding can be reconciled to other schemes.…”

mentioning

confidence: 89%

Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA

Gowers

Wilson

Halford

2005

Proc. Natl. Acad. Sci. U.S.A.

223

257

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“…Onedimensional diffusion of proteins on DNA is a commonly invoked mechanism of facilitated target location (28,29). However, movement that involves passive diffusion is difficult to measure in bulk assays and often requires theoretical assumptions to interpret the behavior of the proteins under investigation (28,29).…”

Section: Discussionmentioning

confidence: 99%

Long-distance lateral diffusion of human Rad51 on double-stranded DNA

Granéli

Yeykal

Robertson

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

166

161

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Rad51 is the primary eukaryotic recombinase responsible for initiating DNA strand exchange during homologous recombination. Although the subject of intense study for over a decade, many molecular details of the reactions promoted by Rad51 and related recombinases remain unknown. Using total internal reflection fluorescence microscopy, we directly visualized the behavior of individual Rad51 complexes on double-stranded DNA (dsDNA) molecules suspended in an extended configuration above a lipid bilayer. Here we show that complexes of Rad51 can bind to and slide freely along the helical axis of dsDNA. Sliding is bidirectional, does not require ATP hydrolysis, and displays properties consistent with a 1D random walk driven solely by thermal diffusion. The proteins move freely on the DNA for long periods of time; however, sliding terminates and the proteins become immobile upon encountering the free end of a linear dsDNA molecule. This study provides previously uncharacterized insights into the behaviors of human Rad51, which may apply to other members of the RecA-like family of recombinases.DNA repair ͉ homologous recombination ͉ total internal reflection fluorescence microscopy T he repair of double-stranded DNA breaks by homologous recombination is essential for maintaining genome integrity in most organisms (1-3). The importance of homologous recombination is highlighted by the finding that Rad51 null mutations are lethal in mice (4). Furthermore, defects in this repair pathway are associated with a variety of human cancers (5, 6). In eukaryotes, the broken ends of chromosomes are processed by 5Ј to 3Ј exonucleases to yield long single-stranded DNA overhangs (2, 3). Rad51, a DNA-dependent ATPase, assembles onto these overhangs, forming a nucleoprotein filament that is a key intermediate in homologous recombination (1,2,7,8). The primary functions of this filament are to locate homologous sequence that can be used as a template to repair the damaged DNA strand and to initiate strand exchange (1, 7).The structure and function of the complexes formed by Rad51 and the other RecA-like recombinases are conserved throughout evolution (8, 9). In their active states, Rad51 and related recombinases form a helical filament on DNA that induces a 50% extension of the bound DNA molecule (8). The extended nucleoprotein filament is correlated with DNA recombination activity; however, these proteins also form inactive filaments with shortened pitches (Ϸ65-85 Å versus Ϸ90-130 Å) (10). Rad51 and related recombinases also form octameric rings with a central pore large enough to accommodate a double-stranded (dsDNA) molecule (11-16). These ring-like recombinase structures do not appear to be the form of the protein that is active during the strand exchange phase of homologous recombination. Although the biological role of these rings remains unknown, it has been suggested that they may function as DNA ''pumps,'' allowing the proteins to move along DNA (12, 13).Here we have developed a unique total internal reflection fluorescence micr...

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“…As proposed by von Hippel * Electronic address: mich@mit.edu and Berg [9,10], and recently observed in many systems [11], 1D "sliding" of proteins along the DNA molecule is an important component of protein specific site location; at least in prokaryotes. The "sliding" is viewed as an unbiased, thermally activated process.…”

Section: A Protein-dna Interactionmentioning

confidence: 99%

Diffusion in correlated random potentials, with applications to DNA

2004

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Many biological processes involve one dimensional diffusion over a correlated inhomogeneous energy landscape with a correlation length ξc. Typical examples are specific protein target location on DNA, nucleosome repositioning, or DNA translocation through a nanopore, in all cases with ξc ≈ 10 nm. We investigate such transport processes by the mean first passage time (MFPT) formalism, and find diffusion times which exhibit strong sample to sample fluctuations. For a a displacement N , the average MFPT is diffusive, while its standard deviation over the ensemble of energy profiles scales as N 3/2 with a large prefactor. Fluctuations are thus dominant for displacements smaller than a characteristic Nc ≫ ξc: typical values are much less than the mean, and governed by an anomalous diffusion rule. Potential biological consequences of such random walks, composed of rapid scans in the vicinity of favorable energy valleys and occasional jumps to further valleys, is discussed.

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One-dimensional Diffusion of Proteins along DNA

Cited by 156 publications

References 44 publications

Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA

Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA

Long-distance lateral diffusion of human Rad51 on double-stranded DNA

Diffusion in correlated random potentials, with applications to DNA

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