Here is a short description of markers and reagents that are more commonly used for DNA analysis.
DNA molecular weight markers
Ambion offers basic DNA molecular weight markers for routine analysis of end point PCR, restriction digests, or other analyses on native agarose gels. These markers span a wide range of DNA sizes and can be visualized by ethidium bromide staining or radioactive end-labeling. After end-labeling with Klenow polymerase or T4 PNK, the pUC19 DNA markers can also be successfully used in 5-8% polyacrylamide/6-8 M urea gels.
Lambda DNA--Hind III digested: 8 fragments, size range: 125-23, 130 bp
pUC19--Sau3A I digested: 14 fragments, size range: 8-955 bp
pUC19--Hpa II digested: 11 fragments, size range: 34-501 bp
Agarose-Le™ General Use
Easy-to-handle, low percentage gels can be prepared, because of high gel strength. For example, 0.4% Agarose-LE gels can be used to separate larger DNA fragments (10-20 kb). DNA can be rapidly recovered from this agarose (e.g. with Ambion Spin Columns, Cat #10065) and will be compatible with restriction endonuclease digestion and ligation.
Agarose-LM™ Low Melt
After fractionating DNA in Agarose-LM by electrophoresis, individual DNA fragments can be easily cut out from the gel. Nucleic acids can be purified from melted agarose for use in a variety of applications (e.g. restriction enzyme digestion, PCR). DNA also may be used directly in ligation reactions after melting the agarose at 68°C.
Gel Loading Solution--All-purpose, native agarose
This 10X solution of 40% sucrose, 0.17% xylene cyanol, and 0.17% bromophenol blue is suitable for use in nucleic acid native agarose gel electrophoresis.
25X TAE running buffer is supplied as packages (1 L of 25X TAE per package) of ultra pure, molecular biology grade powder. The buffer will contain 40 mM Tris-Acetate and 1 mM Na2EDTA when diluted to the 1X working solution.
- Gorokhova E (2005) Effects of preservation and storage of microcrustaceans in RNAlater on RNA and DNA degradation, Limnol. Oceanogr Methods 3:143–148.