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J. Biochem, 1976, Vol. 80, No. 2 253-258
© 1976 Japanese Biochemical Society

research-article

Propidium Diiodide-Cesium Chloride Density Gradient Centrifugation for Buoyant Separations of Duplex DNA Molecules Containing Single-Stranded Regions

Akio FUKUDA

Department of Biophysics and Biochemistry, Faculty of Sciences, the University of Tokyo Hongo, Bunkyo-ku, Tokyo 113

At increasing dye concentrations in propidium diiodide-CsCl density gradients, the relative buoyant density shift was largest for open-circular duplex ØX174 DNA (RFII), next largest for single-stranded viral DNA, and least for closed-circular duplex DNA (RFI). These differential relative buoyant density shifts permitted discrete separations of these ØX DNA forms. Further, in propidium diiodide-CsCl density gradients, the distinctive density of single-stranded DNA permitted separations of rolling-circle intermediates with a single-stranded tail that occur during single-stranded ØX DNA synthesis.

It is suggested that single-strandedness in a duplex DNA structure influences its buoyant density shift due to differential dye binding to the single-stranded region and is an additional physical basis for relative buoyant separations of DNA molecules in propidium diiodide-CsCl density gradients.


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