[2] Preparing and using agarose microbeads

This chapter discusses the preparing and using agarose microbeads. High-quality, intact genomic DNA can be rapidly prepared and digested in agarose microbeads with the protocols described in this chapter. The agarose microbeads potentially offer several advantages over agarose blocks, both in ease of handling, and in the speed with which the DNA can be prepared and enzymatically manipulated. Despite this, however, microbeads have not been widely considered to be satisfactory replacements for agarose plugs. This is due for the most part to difficulties many researchers have reported when working with microbead-embedded DNA. Complete lysis and deproteinization are achieved with a combined incubation time of 2 hr or less. Furthermore, digestion with all restriction enzymes tested has been completed within 1 hr, the time typically allowed for the digestion of DNA in solution. Microbeads not only protect large DNA molecules from shear, but also act as giant DNA-carrying “cells,” thus converting DNA into a “solid state” and allowing its easy and rapid transfer to various solutions by sedimenting, washing, and resuspending the microbeads.