The electrophoretic behavior of DNA and RNA in gels is effected by their size and shape. Both RNA and DNA can exist as single and double stranded molecules and the single stranded forms have significant secondary and tertiary structure. Therefore single stranded nucleic acids are best separated as denatured structures. This is most often an issue for ssDNA after sequencing reactions, and RNA which can be denatured by urea, methylmercuric hydroxide, formamide, formaldehyde and a number of other agents.

Agarose is a highly purified naturally occurring polysaccharide. Preparation of agarose gels involves simply dissolving the powdered agarose in buffer by heating. The agarose gels upon cooling. Like acrylamide, the pore size of an agarose gel is inversely dependent on the agarose concentration. The pores in agarose gels are generally much larger than those in acrylamide gels and are widely used in separation of nucleic acids. Low molecular weight nucleic acids and oligonucleotides, however, are usually separated by PAGE, due to smaller pore size of the gel matrix.

Many types of different agarose qualities optimized for specific applications are available, e.g.:

• Agarose SERVA Wide Range (cat no. 11406) or Agarose for DNA Electrophoresis (cat. no. 11404) for routine DNA electrophoresis
• Agarose SERVA 3:1 (cat. no. 11385) and Agarose for PCR (cat. no. 11383) for high resolution separation of small (10 bp - 1000 bp) DNA, RNA and PCR fragments
• Agaroses with low melting temperature like Agarose SERVA Low Melting (cat. no. 11408) for the easy recovery of DNA fragments from agarose