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Partitioning of protein–DNA complexes from protein-unbound DNA is a key step in selection of DNA aptamers. Conceptually, the partitioning step is characterized by two parameters: transmittance for protein-bound DNA (binders) and transmittance for unbound DNA (nonbinders). IFCE is preferable for large-size protein targets while NECEEM should be the method of choice for small-size protein targets.
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