DNA binding specificity and function of retinoid X receptor alpha

Retinoid X receptors are members of the erbA superfamily of ligand-inducible transcription factors. Similar to several other members of this gene family, retinoid X receptors are known to bind to the hexameric DNA sequence AGGTCA. After binding to a direct repeat of this hexamer with a one-base pair spacer, retinoid X receptor homodimers are able to activate transcription in the presence of the ligand 9-cis-retinoic acid. However, it is not known if AGGTCA represents the highest affinity binding site for retinoid X receptors. A combination of the electrophoretic mobility shift assay and polymerase chain reaction was used to isolate from a pool of random DNA those sequences that bind retinoid X receptors with highest affinity. This approach, combined with mutational analysis and DNA footprinting, led to the identification of the seven-base pair sequence GGGGTCA as the highest affinity retinoid X receptor binding site. A direct repeat of this sequence is substantially more active than a direct repeat of AGGTCA as a retinoid X response element.