The Isolation of Satellite DNA by Density Gradient Centrifugation

  • Craig A. Cooney
  • Harry R. Matthews
Part of the Methods in Molecular Biology book series (MIMB, volume 2)


The term satellite DNA is used for a DNA component that gives a sharp band in a density gradient and can be resolved from the broader main band of DNA in the gradient. The usual gradient material is CsCl in aqueous buffer and the Cs+ ions form a density gradient in a centrifugal field. DNA in the solution sediments to its isopycnic point. The density of DNA is a function of base composition and sequence and so a homogeneous or highly repeated DNA sequence will form a sharp band in CsCl density gradients at a characteristic density. The resolution of this procedure may be enhanced or modified by binding ligands to the DNA. For example, netropsin binds specifically to A + T-rich regions of DNA and reduces their density (1,2). Another useful ligand is Ag+, which must then be centrifuged in Cs2SO4 gradients to avoid precipitation of AgCl (3). Pharmacia has recently introduced CsCF3COO as a gradient material.


Flow Path Sharp Band Vertical Rotor CsCl Gradient Centrifugal Field 
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Copyright information

© The Humana Press Inc. 1984

Authors and Affiliations

  • Craig A. Cooney
    • 1
  • Harry R. Matthews
    • 1
  1. 1.Department of Biological Chemistry, School of MedicineUniversity of CaliforniaDavisUSA

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