Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer

Reagents for proteome research must of necessity be generated by high throughput methods. Apta- mers are potentially useful as reagents to identify and quantitate individual proteins, yet are currently produced for the most part by manual selection pro- cedures. We have developed automated selection methods, but must still individually purify protein targets. Therefore, we have attempted to select apta- mers against protein targets generated by in vitro transcription and translation of individual genes. In order to specifically immobilize the protein targets for selection, they are also biotinylated in vitro .A s a proof of this method, we have selected aptamers against translated human U1A, a component of the nuclear spliceosome. Selected sequences demon- strated exquisite mimicry of natural binding sequences and structures. These results not only reveal a potential path to the high throughput gener- ation of aptamers, but also yield insights into the incredible specificity of the U1A protein for its natural RNA ligands.