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Issue 39, 2015
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Universal scaling of crowding-induced DNA mobility is coupled with topology-dependent molecular compaction and elongation

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Abstract

Using single-molecule fluorescence microscopy and particle-tracking techniques, we elucidate the role DNA topology plays in the diffusion and conformational dynamics of crowded DNA molecules. We focus on large (115 kbp), double-stranded ring and linear DNA crowded by varying concentrations (0–40%) of dextran (10, 500 kDa) that mimic cellular conditions. By tracking the center-of-mass and measuring the lengths of the major and minor axes of single DNA molecules, we characterize both DNA mobility reduction as well as crowding-induced conformational changes (from random spherical coils). We reveal novel topology-dependent conformations, with single ring molecules undergoing compaction to ordered spherical configurations ∼20% smaller than dilute random coils, while linear DNA elongates by ∼2-fold. Surprisingly, these highly different conformations result in nearly identical exponential mobility reduction dependent solely on crowder volume fraction Φ, revealing a universal critical crowding concentration of Φc ≅ 2.3. Beyond Φc DNA exhibits topology-independent conformational relaxation dynamics despite highly distinct topology-driven conformations. Our collective results reveal that topology-dependent conformational changes, unique to crowded environments, enable DNA to overcome the classically expected mobility reduction that high-viscosity crowded environments impose. Such coupled universal dynamics suggest a mechanism for DNA to maintain sufficient mobility required for wide-ranging biological processes despite severe cellular crowding.

Graphical abstract: Universal scaling of crowding-induced DNA mobility is coupled with topology-dependent molecular compaction and elongation

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Publication details

The article was received on 28 Jul 2015, accepted on 18 Aug 2015 and first published on 19 Aug 2015


Article type: Paper
DOI: 10.1039/C5SM01882J
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Soft Matter, 2015,11, 7762-7768

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    Universal scaling of crowding-induced DNA mobility is coupled with topology-dependent molecular compaction and elongation

    S. M. Gorczyca, C. D. Chapman and R. M. Robertson-Anderson, Soft Matter, 2015, 11, 7762
    DOI: 10.1039/C5SM01882J

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