Equilibrate the DNA-containing low melting point agarose (SeaPlaque GTG or NuSieve GTG) by washing the solid gel slice twice with 2 volumes of 1X b-Agarase I Buffer on ice for 30 minutes each.*
Remove the remaining buffer and melt the agarose by incubation at 65°C for 10 minutes. Cool to 42°C and incubate the molten agarose with 1 unit of β-Agarase I at 42°C for 1 hour. This procedure will digest up to 200 µl of 1% low melting point agarose. For larger volumes, adjust enzyme accordingly.
*As an alternative method of equilibration, add 1/10 volume of 10X β-Agarase I Reaction Buffer and melt together with the agarose. This faster equilibration method requires the amount of enzyme used to be doubled. This method is recommended when working with DNA fragments shorter than 500 base pairs because it avoids diffusion of DNA during washing.
β-Agarase I Reaction Buffer