To minimize the formation of DNA secondary structures or intrastrand hybrid structures that impact DNA separation, electrophoretic separation of short tandem repeat (STR) fragments is performed at a temperature of 60°C (Butler 2004). The ABI Prism^® capillary electrophoresis (CE) instruments have a heated plate to maintain the temperature of the capillary. On ABI Prism^® 310 Genetic Analyzers, the capillary at the inlet and outlet ends are not directly in contact with the heat plate. It is important to maintain room temperature within a few degrees, because fluctuations in room temperature can cause variability in the runs. The newer CE instruments have improved temperature control preventing room temperature fluctuation being a significant issue.

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