SEQUENCE-DEPENDENT MIGRATION BEHAVIOR OF DOUBLE-STRANDED DNA IN CAPILLARY ELECTROPHORESIS

Capillary electrophoresis (CE) with a replaceable linear polyacrylamid e (LPA) sieving matrix was used to examine sequence-dependent migratio n of double-stranded DNA fragments. It has been found that DNA conform ational effects were significant under high electric field separations , especially using high resolution matrices. Compared to linear DNA-la dder standards, both anomalously slow and rapid DNA fragments were obs erved, with the degree of anomalous migration depending on the electri c field strength, polymer concentration, column temperature, and backg round electrolyte (denaturants, sodium and magnesium ions, DNA-interca lating dyes). By selecting a combination of electrophoretic conditions (e.g. 3% T LPA, elevated capillary temperature, lower electric field strength and addition of DNA intercalating dyes), molecular weight dep endent separations were closely restored.