title: RAPID-SELEX for RNA aptamers.
abstract: Aptamers are high-affinity ligands selected from DNA or RNA libraries via SELEX, a repetitive in vitro process of sequential selection and amplification steps. 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 enriched pools from both RAPID and SELEX revealed many identical candidate aptamers from the starting pool of 5 × 10(15) sequences. For CHK2, the same sequence was preferentially enriched in both selections as the top candidate and was found to bind to its respective target. These results demonstrate the efficiency and, most importantly, the robustness 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.
authors.affiliation: School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America.
authors.forename: Kylan
authors.initials: K
authors.lastname: Szeto
authors.affiliation: School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America.
authors.forename: David R
authors.initials: DR
authors.lastname: Latulippe
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.
authors.forename: Abdullah
authors.initials: A
authors.lastname: Ozer
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.
authors.forename: John M
authors.initials: JM
authors.lastname: Pagano
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.
authors.forename: Brian S
authors.initials: BS
authors.lastname: White
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.
authors.forename: David
authors.initials: D
authors.lastname: Shalloway
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.
authors.forename: John T
authors.initials: JT
authors.lastname: Lis
authors.affiliation: School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America.
authors.forename: Harold G
authors.initials: HG
authors.lastname: Craighead
mesh_terms: D052157:Aptamers, Nucleotide / Q000302:isolation & purification*; D001483:Base Sequence; D064447:Checkpoint Kinase 2 / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D052156:SELEX Aptamer Technique / Q000379:methods*
chemical_list: D052157:Aptamers, Nucleotide; D064447:Checkpoint Kinase 2