Determining the size of DNA or RNA in nucleic acid electrophoresis is accomplished by comparison to size standards, also called markers or ladders. Typical size standards are made up of DNA or RNA fragments in variable length in the range of 10bp to 1000bp (base pair) increments. One universally used DNA ladder measures up to 1 kilobase pair (1Kb) and contains 1-10 Kb fragments. Highly supercoiled DNA or RNA samples that are up to 16Kb require ladders made with restriction enzyme endonuclease digestion. Single stranded markers are noted as length in nucleotides (nt). RNA ladders measuring 10-100 nt are referred to as low molecular weight markers. Traditional gel electrophoresis stains DNA with ethidium bromide which is excited by UV light. Some markers contain other dyes, like ROX, for use in high-throughput genetic analyzers. Whether you are using agarose gel electrophoresis, pulsed-field gel electrophoresis (PFGE), or next generation systems, the optimally sized and tagged nucleic acid standard can assist your band identification efforts.
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