Effect of length, topology, and concentration on the microviscosity and microheterogeneity of DNA solutions

The viscoelastic behavior of chromosomal DNA, which is heterogeneously distributed within the nucleus, may influence the diffusion of nuclear organelles and proteins. To identify some of the parameters that affect DNA viscoelasticity, we use the high-throughput method of multiple-particle nanotracking to measure the microviscosity and degree of heterogeneity of solutions of chromosomal DNA, linear DNA, and circular double-stranded DNA over a wide range of concentrations and lengths. The thermally excited displacements of multiple fluorescent microspheres imbedded in DNA solutions are monitored with 5 nm spatial resolution and 30 Hz temporal resolution, from which mean-squared displacement (MSD) and viscosity distributions are generated. For all probed DNA solutions but the most concentrated solution of the longest molecules, the ensemble-averaged MSD increases linearly with time at all probed time scales, a signature of viscous transport. The associated mean viscosity of the DNA solutions increases slowly with concentration for circular DNA and more rapidly for linear DNA, but more slowly than predicted by theory. The heterogeneity of the DNA solutions is assessed by computing the relative contributions of the 10%, 25%, and 50% highest values of MSD and viscosity to the ensemble-averaged MSD and viscosity. For both linear DNA and circular DNA, these contributions are much larger than observed in homogeneous liquids such as glycerol. The microheterogeneity of the linear DNA solutions increases with concentration more significantly for linear DNA than circular DNA. These in vitro results suggest that the topology, local concentration, and length of DNA influence the microrheology and microheterogeneity of the DNA within the nucleus.