CAPILLARY ELECTROPHORESIS AS A TECHNIQUE TO ANALYZE SEQUENCE-INDUCED ANOMALOUSLY MIGRATING DNA FRAGMENTS

Sequence-induced anomalous migration of double-stranded (ds) DNA in na tive gel electrophoresis is a well known phenomenon, The retardation o f migration is more obvious in polyacrylamide compared with agarose ge ls, and is greatly affected by the concentration of the gel and the te mperature. This anomalous migration results in a difference between ca lculated and actual sizes of the affected DNA fragments. A low viscosi ty polymer solution (DNA Fragment Analysis Reagent) under investigatio n for use in dsDNA analysis by capillary electrophoresis is shown to b e useful for the visualization of anomalies in migration of dsDNA frag ments. Comparable with traditional slab gel systems, the retardation e ffect, indicative of bent or curved DNA, is strongly dependent on poly mer concentration and separation temperature. These dependencies have implications on the accurate sizing of dsDNA fragments with unknown se quences and secondary structures.