In vivo pair correlation analysis of EGFP intranuclear diffusion reveals DNA-dependent molecular flow.
No methods proposed thus far have the capability to measure overall molecular flow in the nucleus of living cells. Here, we apply the pair correlation function analysis (pCF) to measure molecular anisotropic diffusion in the interphase nucleus of live cells. In the pCF method, we cross-correlate fluctuations at several distances and locations within the nucleus, enabling us to define migration paths and barriers to diffusion. We use monomeric EGFP as a prototypical inert molecule and measure flow in and between different nuclear environments. Our results suggest that there are two disconnect molecular flows throughout the nucleus associated with high and low DNA density regions. We show that different density regions of DNA form a networked channel that allows EGFP to diffuse freely throughout, however with restricted ability to traverse the channel. We also observe rare and sudden bursts of molecules traveling across DNA density regions with characteristic time of ≈300 ms, suggesting intrinsic localized change in chromatin structure. This is a unique in vivo demonstration of the intricate chromatin network showing channel directed diffusion of an inert molecule with high spatial and temporal resolution.
Hinde
Elizabeth
E
Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA.
Cardarelli
Francesco
F
Digman
Michelle A
MA
Gratton
Enrico
E
D021581:Active Transport, Cell Nucleus; D000818:Animals; D001562:Benzimidazoles; D016466:CHO Cells; D002467:Cell Nucleus / Q000378:metabolism*; D002843:Chromatin / Q000378:metabolism; D006224:Cricetinae; D003412:Cricetulus; D004247:DNA / Q000378:metabolism*; D055459:Facilitated Diffusion; D005456:Fluorescent Dyes; D049452:Green Fluorescent Proteins / Q000378:metabolism*; D018613:Microscopy, Confocal; D008954:Models, Biological; D011994:Recombinant Proteins / Q000378:metabolism; D014162:Transfection
D001562:Benzimidazoles; D002843:Chromatin; D005456:Fluorescent Dyes; D011994:Recombinant Proteins; C485184:enhanced green fluorescent protein; D049452:Green Fluorescent Proteins; D004247:DNA; C017807:bisbenzimide ethoxide trihydrochloride
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