Spectroscopic Study of Orientation Dynamics of DNA during Electrophoresis in Entangled and Dilute Polyacrylamide Solutions

Neutron-scattering probe of complexes of sodium dodecyl sulfate and serum albumin during polyacrylamide gel electrophoresis

Small-angle neutron scattering (SANS) is used to probe the conformation of SDS-BSA protein surfactant complexes during electrophoresis in cross-linked polyacrylamide gels. Contrast variation permits independent probing of the structure of protein-surfactant complexes with negligible scattering contributions from the polyacrylamide matrix. The conformation of the protein complexes in the gel is found to be independent of the electric fields that are applied in this work (10 V/cm). Furthermore, there are no signs of large-scale macromolecular orientation (anisotropy) in the scattering patterns. However, the scattering shows that there are significant interparticle correlations between the protein-surfactant complexes that are electrophoretically inserted into the gel. These interactions develop when the total concentration of protein in the gels reaches values that are larger than approximately 1 mg/mL. The correlations are due to molecular crowding in the small fraction of pores that are available for protein migration.

Stepwise capillary electrophoretic separation of DNA fragments using poly(ethylene oxide) solutions in the presence of electroosmotic flow

Single-base resolution in the separation of DNA markers V and VI was achieved in the presence of electroosmotic flow (EOF), using poly(ethylene oxide) (PEO) solutions containing ethidium bromide (EtB) under isocratic conditions. Furthermore, a new approach called stepwise capillary electrophoresis (SCE) has been developed for DNA analysis, including stepwise changes in PEO concentration, EtB concentration as well as both PEO and EtB concentrations, wherein the EOF was used to introduce different PEO solutions into the capillary during the separation. DNA fragments smaller than 80 bp were both detected under isocratic conditions using 20 micrograms/ml EtB, and SCE using 1 and 20 micrograms/ml EtB, but not under isocratic conditions using 1 microgram/ml EtB. Resolution and speed of the DNA separation in SCE were different from those obtained from isocratic means, indicating that DNA underwent different concentrations of PEO and EtB in SCE. For example, DNA fragments with 458 and 504 base pairs (bp) were partially resolved in SCE, but not under isocratic conditions. The results further suggest that it is worth developing gradient techniques for widening the separation range and enhancing resolution in DNA analysis.

Recent developments in DNA electrophoretic separations

DNA electrophoresis is now a fairly mature technology. Nevertheless, as we approach the 21st century, new ideas are frequently suggested that could lead to a revolution for DNA sequencing and mapping. Here, we review some of the novel concepts that have been studied since ca. 1990. Our review focuses on new separation mechanisms, new sieving matrices and recent conceptual advances.