The Isolation of Satellite DNA by Density Gradient Centrifugation

Abstract

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.