The Isolation of Satellite DNA by Density Gradient Centrifugation

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 Cs
2
SO
4
gradients to avoid precipitation of AgCl (
3
). Pharmacia has recently introduced CsCF
3
COO as a gradient material.