Triggered Degradation of Polyacrylamide Gels for DNA Recovery

Abstract

Polyacrylamide gels are commonly used in the analysis and separation of DNA by gel electrophoresis. In some protocols, once a sample of DNA undergoes gel electrophoresis, the DNA sample is recovered from the gel. A common method of doing this is to soak pieces of gel in buffer and wait for the DNA to diffuse out of the gel. This can take many hours or even days for DNA strands longer than 500 base pairs. It would be extremely useful to incorporate a chemically triggerable release mechanism into the polyacrylamide gel that would allow a researcher to decompose the gel network at will and recover the embedded DNA more quickly. We have developed a bis(acrylamide) crosslinker that contains a chemically cleavable group. Polyacrylamide gels made with this crosslinker (“EG2”) decompose quickly when exposed to a DNAcompatible reductants. In principle, due to the shortened time span, less stable nucleic acids such as RNA might be recovered with a reduced amount of decomposition of the actual RNA sample.