title: Universal scaling of crowding-induced DNA mobility is coupled with topology-dependent molecular compaction and elongation.
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.
authors: Department of Physics, University of San Diego, 5998 Alcala Park, San Diego, CA 92110, USA. randerson@sandiego.edu.
authors: Stephanie M
authors: SM
authors: Gorczyca
authors: Cole D
authors: CD
authors: Chapman
authors: Rae M
authors: RM
authors: Robertson-Anderson
mesh_terms: D001583:Benzoxazoles / Q000737:chemistry; D004269:DNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D003911:Dextrans / Q000737:chemistry; D004058:Diffusion; D004926:Escherichia coli / Q000235:genetics; D008856:Microscopy, Fluorescence; D009690:Nucleic Acid Conformation; D011806:Quinolinium Compounds / Q000737:chemistry
chemical_list: D001583:Benzoxazoles; D004269:DNA, Bacterial; D003911:Dextrans; D011806:Quinolinium Compounds; C075296:1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium