Application of alkaline sucrose gradient centrifugation in the analysis of DNA replication after DNA damage

Sucrose density gradient ultracentrifugation is a powerful technique for fractionating macromolecules like DNA, RNA, and proteins. For this purpose, a sample containing a mixture of different size macromolecules is layered on the surface of a gradient whose density increases linearly from top to bottom. During centrifugation, different size macromolecules sediment through the gradient at different rates. The rate of sedimentation depends, in addition to centrifugal force, on the size, shape, and density of the macromolecules, as well as on the density and viscosity of the gradient. In this way, macromolecules are separated by size with larger ones sedimenting towards the bottom and lighter ones remaining close to the top of the gradient. The method has been particularly successful in the size fractionation of large DNA molecules and has been extensively used to measure induction and repair of DNA breaks after exposure to clastogenic factors. Here, we describe an adaptation of this method that can be used in the analysis of newly synthesized DNA formed during DNA replication. Through size analysis of nascent DNA in alkaline sucrose gradients, variations in replication activity can be measured after exposure of cells to DNA-damaging agents. The method is particularly useful as it allows distinction between DNA damage-mediated effects on chain elongation vs. replicon initiation, which is essential for an in-depth analysis of the intra-S-phase checkpoint. This ability makes the technique unique and justifies its somewhat labour-intensive nature.