title: Denaturing gel electrophoresis for sequencing.
abstract: The accuracy of DNA sequence determination depends largely upon resolution of the sequencing products in denaturing polyacrylamide gels. This unit provides a detailed description of the setup, electrophoresis, and processing of such gels. In general, the gels required for DNA sequencing are 40-cm long, of uniform thickness, and contain 4% to 8% acrylamide and 7 M urea. Modifications of this protocol increase the length of readable sequence information which can be obtained from a single gel (i.e., forming the gel with wedge-shaped spacers to create a field gradient, or incorporating a buffer gradient, an electrolyte gradient, or an acrylamide step gradient into the gel). A modification to the Basic Protocol--inclusion of formamide in the sequencing gel--is designed to overcome gel compressions arising from secondary structure in the sequencing products during gel electrophoresis. A discussion of acrylamide concentrations and electrophoresis conditions is included in the Commentary.
authors.affiliation: New England Biolabs, Beverly, Massachusetts, USA.
authors.forename: B E
authors.initials: BE
authors.lastname: Slatko
authors.forename: L M
authors.initials: LM
authors.lastname: Albright
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods*; D005782:Gels; D007202:Indicators and Reagents; D009691:Nucleic Acid Denaturation; D012680:Sensitivity and Specificity
chemical_list: D005782:Gels; D007202:Indicators and Reagents; D004247:DNA