[38] Fractionation of low molecular weight DNA or RNA in polyacrylamide gels containing 98% formamide or 7 M urea

This chapter describes the techniques for fractionation of low molecular weight DNA or RNA in polyacrylarnide gels containing 98% formamide or 7 M urea. The chain length of small, single-stranded DNA or RNA molecules can be determined by electrophoresis in polyacrylamide gels containing 7 M urea or 98% formamide. Under the appropriate conditions, the electrophoretic mobility of these molecules is independent of base composition and secondary structure. Denaturing polyacrylamide gels containing 7 M urea or 98% formamide are used to purify nucleic acids because of the high resolution afforded by the technique and the ease and efficiency by which nucleic acids can be recovered from the gels. The chapter describes the procedures for preparing polyacrylamide gels containing 7 M urea or 98% formamide and a procedure for extracting nucleic acids from these gels.