Nucleic Acid Electrophoresis
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.