RAPID-SELEX for RNA Aptamers

Aptamers are high-affinity ligands selected from DNA or RNA libraries via SELEX, a repetitive in vitro process of sequential selection and amplification step. RNA SELEX is more complicated than DNA SELEX because of the additional transcription and reverse transcription steps. Here, we report a new selection scheme, RAPID-SELEX (RNA Aptamer isolation via Dual-cycles SELEX), that simplifies this process by systematically skipping unnecessary amplification steps. Using affinity microcolumns, we were able to complete a multiplex selection for protein targets, CHK2 and UBLCP1, in a third of the time required for analogous selections using a conventional SELEX Approach. High-throughput sequencing of the encriched pools from both RAPID and SELEX revealed many identical candiate aptamers from the starting pool of 5x10(15) sequences. For CHK2, the same sequence was preferentially enriched in both selections as the top candiate and was found to bind to ists respectiv3e target. These results demonstrate the efficiency and, most importantly, the roubustness of our selection scheme. RAPID provides a generalized approach that can be used with any selection technology to accelerate the rate of aptamer discovery, without compromising selection performance.