DNA Electrophoresis in Polyacrylamide Gels Protocols

Acrylamide Gels for Resolving Small (25bp-700bp) DNA Fragments Protocol Protocol for acrylamide gels for resolving small (25bp-700bp) DNA fragments.

Detection of DNA in Polyacrylamide Gels by Autoradiography Protocol Detection of radioactive DNA in polyacrylamide gels by autoradiography.

Detection of DNA in Polyacrylamide Gels by Staining Protocol Staining bands of DNA in polyacrylamide gels with ethidium bromide, SYBR-Gold, and methylene blue.

Gel Retardation Assays for DNA-binding Proteins Protocol Protocol exploits differences in electrophoretic mobility through a nondenaturing polyacrylamide gel between a rapidly migrating target DNA and a more slowly migrating DNA-protein complex.

Isolation of DNA Fragments from Polyacrylamide Gels by the Crush and Soak Method Protocol The "crush and soak" method, which works best for DNAs <1 kb in size, can be used to recover both singleand double-stranded DNAs from polyacrylamide gels.  The yield of eluted DNA varies from <30% to >90% depending on the size of the DNA fragment.

Preparation of Denaturing Polyacrylamide Gels Protocol Protocol for preparation of denaturing polyacrylamide gels.

Purification of Synthetic Oligonucleotides by Polyacrylamide Gel Electrophoresis Protocol Protocol for purification of synthetic oligonucleotides by polyacrylamide gel electrophoresis. As a rule of thumb, oligonucleotides >25 nucleotides should be purified by polyacrylamide gel electrophoresis, as should oligonucleotides of any length that yield anomalous results.  After electrophoresis, the oligonucleotide is eluted from the gel and concentrated by reversed-phase chromatography on Sep-Pak C18 columns.

Recovery of DNA from Agarose and Polyacrylamide Gels: Electroelution into Dialysis Bags Protocol A messy but reliable technique that works well for DNAs ranging in size from 200 bp to >50 kb.