Identification of RNA aptamers against recombinant proteins with a hexa-histidine tag

Artificial riboswitches that respond to the concentrations of intracellular proteins are a promising tool with a variety of applications. They can be designed and engineered using existing RNA aptamers that target proteins. Aptamers are generated via an iterative selection-amplification process, known as systematic evolution of ligands by exponential enrichment (SELEX). This chapter describes a SELEX procedure for the identification of RNA aptamers against hexa-histidine-tagged proteins. For the efficient enrichment of higher affinity aptamers, the selection stringency should be gradually increased. Undesired RNA species that bind to affinity resins can be eliminated from the pool by using a negative selection step and alternating different types of resins.