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DNA surface explora...
DNA surface exploration and operator bypassing during target search
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- Marklund, Emil (author)
- Uppsala universitet,Molekylär systembiologi,Science for Life Laboratory, SciLifeLab
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- van Oosten, Brad (author)
- Uppsala Univ, Dept Cell & Mol Biol, Sci Life Lab, Uppsala, Sweden.
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- Mao, Guanzhong, 1985- (author)
- Uppsala universitet,Molekylärbiologi,Science for Life Laboratory, SciLifeLab
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- Amselem, Elias (author)
- Uppsala universitet,Molekylär systembiologi
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- Kipper, Kalle (author)
- Uppsala Univ, Dept Cell & Mol Biol, Sci Life Lab, Uppsala, Sweden.
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- Sabantsev, Anton (author)
- Uppsala universitet,Molekylär systembiologi,Science for Life Laboratory, SciLifeLab
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- Emmerich, Andrew G (author)
- Uppsala universitet,Molekylärbiologi
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- Globisch, Daniel (author)
- Uppsala universitet,Kemisk biologi för biomarkörer,Science for Life Laboratory, SciLifeLab
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- Zheng, Xuan (author)
- Uppsala Univ, Dept Cell & Mol Biol, Sci Life Lab, Uppsala, Sweden.
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- Lehmann, Laura C. (author)
- Uppsala universitet,Molekylär systembiologi,Science for Life Laboratory, SciLifeLab
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- Berg, Otto (author)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Molekylär systembiologi
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- Johansson, Magnus (author)
- Uppsala universitet,Molekylär systembiologi
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- Elf, Johan (author)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Molekylär systembiologi
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- Deindl, Sebastian (author)
- Uppsala universitet,Molekylär systembiologi,Science for Life Laboratory, SciLifeLab
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(creator_code:org_t)
- 2020-06-24
- 2020
- English.
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In: Nature. - : NATURE RESEARCH. - 0028-0836 .- 1476-4687. ; 583:7818, s. 858-
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Abstract
Subject headings
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- Many proteins that bind specific DNA sequences search the genome by combining three-dimensional diffusion with one-dimensional sliding on nonspecific DNA(1-5). Here we combine resonance energy transfer and fluorescence correlation measurements to characterize how individual lac repressor (LacI) molecules explore the DNA surface during the one-dimensional phase of target search. To track the rotation of sliding LacI molecules on the microsecond timescale, we use real-time single-molecule confocal laser tracking combined with fluorescence correlation spectroscopy (SMCT-FCS). The fluctuations in fluorescence signal are accurately described by rotation-coupled sliding, in which LacI traverses about 40 base pairs (bp) per revolution. This distance substantially exceeds the 10.5-bp helical pitch of DNA; this suggests that the sliding protein frequently hops out of the DNA groove, which would result in the frequent bypassing of target sequences. We directly observe such bypassing using single-molecule fluorescence resonance energy transfer (smFRET). A combined analysis of the smFRET and SMCT-FCS data shows that LacI hops one or two grooves (10-20 bp) every 200-700 mu s. Our data suggest a trade-off between speed and accuracy during sliding: the weak nature of nonspecific protein-DNA interactions underlies operator bypassing, but also speeds up sliding. We anticipate that SMCT-FCS, which monitors rotational diffusion on the microsecond timescale while tracking individual molecules with millisecond resolution, will be applicable to the real-time investigation of many other biological interactions and will effectively extend the accessible time regime for observing these interactions by two orders of magnitude. Single-molecule fluorescence resonance energy transfer and real-time confocal laser tracking with fluorescence correlation spectroscopy together characterize how individual lac repressor molecules bypass operator sites while exploring the DNA surface at microsecond timescales.
Subject headings
- NATURVETENSKAP -- Biologi -- Biofysik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biophysics (hsv//eng)
Keyword
- ENERGY-TRANSFER; SINGLE; PROTEIN; TRANSLOCATION; MICROSCOPY; DIFFUSION; DYNAMICS
Publication and Content Type
- ref (subject category)
- art (subject category)
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Nature
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- By the author/editor
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Marklund, Emil
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van Oosten, Brad
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Mao, Guanzhong, ...
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Amselem, Elias
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Kipper, Kalle
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Sabantsev, Anton
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show more...
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Emmerich, Andrew ...
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Globisch, Daniel
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Zheng, Xuan
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Lehmann, Laura C ...
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Berg, Otto
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Johansson, Magnu ...
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Elf, Johan
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Deindl, Sebastia ...
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Biophysics
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Nature
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Uppsala University