Recovering Amplified DNA from Silver Stained Gels

Abstract

Individual nucleic acid fragments can be recovered from agarose or Polyacrylamide gels by elution from the electrophoretic matrix (Smith 1980). Table 1 describes some of the methods that have proved effective in eluting nucleic acids into liquid or solid supports. These methods usually require a further purification step by phenol and chloroform extraction, sometimes followed by concentration before subcloning. Fragment isolation is particularly complicated when a complex assortment of nucleic acids has been resolved. This is the case in a number of applications in which Polyacrylamide gel electrophoresis (PAGE) was coupled to silver staining, including DNA sequencing (Doktycz 1993; Storts et al. 1993), single strand conformation polymorphism (SSCP) analysis (Ainsworth et al. 1991; Dock horn-Dworniczak et al. 1991; Mohabeer et al. 1991; Maekawa et al. 1993; Sugano et al. 1993; Ainsworth et al. 1993), DNA profiling (Allen et al. 1989; Budowle et al. 1991), DNA amplification fingerprinting (DAF) with arbitrary oligonucleotide primers (Caetano-Anollés et al. 1991), and differential display (DD) of messenger RNA (see Chap. XXVIII). The majority of these applications are DNA amplification-based and produce a collection of amplification products generally representing one or more discrete portions of a genome.