Dynamics of DNA molecules in gel studied by fluorescence microscopy

Abstract

The dynamics of individual DNA molecules in a thin gel were studied with fluorescence microscopy. Driven by an electric field, molecules hooked around isolated obstacles and became extended. By analyzing molecular images, we identified the reptation tube and primitive chain. When the field was turned off, the molecules relaxed. The relaxation time τ1 and primitive chain length (L) at equilibrium depend on N, the size of the molecule in base pairs, consistently with reptation theory. Using five yeast chromosomal DNAs ranging in size from 245 kb to 980 kb, we found that: (L)(μm) = 0.0749[N/1000] - 6.94 τ1(sec) = 0.017[N/1000]1.45 [1]. These results constitute a way of sizing individual DNA molecules by imaging rather than by gel electrophoresis.