Videomicroscopy of DNA electrophoresis

Modern photomicrographic techniques allow one to observe the extended structure of a fluorescently labeled DNA strand as it travels through solution. Analyses of these shape changes give direct tests of models for electrophoresis and polymer dynamics. Early work on videomicroscopy of DNA electrophoresis in polymer solutions is due to Carlsson, et a/.(15) and Shi, et a/.(16). de Carmejane, et al. show three-dimensional imaging techniques that reduce ambiguities in simpler measurements( 17). 

examined electrophoretic motion of yeast artificial chromosome fragments in 439 kDahydroxyethylcellulose solutions(16). Solution viscosities implied 

Hammond, etal. studied monodisperse 167 kbpT2 DNA undergoing pulsed-field electrophoresis in 0.01-0.1 % wlw hydroxyethylcellulose(19). Oscillating fields have less effect on electrophoretic motion when the matrix concentration is small. The conformation fluctuations reported by Shi, et al, continued to be seen(16). The observed mechanics of DNA migration did not differ qualitatively between nominally dilute and and nominally semidilute matrix solutions. Hammond, et al concluded that there exists a unified treatment of DNA electrophoresis that covers dilute and nondilute solutions, and steady and pulsed applied electric fields. 

In an extremely important paper, Heuer, et al. used photomicrography to examine electrophoresis of synthetic DNA stars in linear polyacrylamide having an estimated molecular weight of 5-6 MDa(13). Polymer concentrations covered 0.5-10 g/1, the nominal overlap concentration (estimated in several ways) being near 1.6 g/1. Stars were created via the approach of Seeman(22) four short (44 bp) synthetic oligonucleotides, whose complementary sequences cause them to self-assemble into a four-arm star, and whose arms bind X-phage DNA ends, were synthesized, leading to monodisperse star polymers. 

The challenge created by the fluctuation-dissipation theorem and linear response theory is that the modes of motion and mechanisms of dissipation that are driven by the weakest linear perturbations are required to be the same as the modes of motion and mechanisms of dissipation that appear in the corresponding diffusive process(24). If teuthidic motion represents the linear translational response to a weak applied field, then the fluctuation-dissipation theorem and linear response theory guarantee that teuthidic motion must also characterize diffusion of star polymers through a polymer solution matrix. 

---