rapid identification of cell-specific, internalizing rna aptamers with bioinformatics analyses of a cell-based aptamer selection快速识别的特异性,内化rna寡核苷酸适配子与生物信息学分析细胞的适体的选择.pdfVIP

Rapid Identification of Cell-Specific, Internalizing RNA Aptamers with Bioinformatics Analyses of a Cell-Based Aptamer Selection 1 1 2 1 1 1 William H. Thiel , Thomas Bair , Andrew S. Peek , Xiuying Liu , Justin Dassie , Katie R. Stockdale , 3 1 1,4 Mark A. Behlke , Francis J. Miller, Jr. , Paloma H. Giangrande * 1 Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America, 2 Roche Molecular Systems, San Francisco, California, United States of America, 3 Integrated DNA Technologies, Coralville, Iowa, United States of America, 4 Department of Radiation Oncology, University of Iowa, Iowa City, Iowa, United States of America Abstract Background: The broad applicability of RNA aptamers as cell-specific delivery tools for therapeutic reagents depends on the ability to identify aptamer sequences that selectively access the cytoplasm of distinct cell types. Towards this end, we have developed a novel approach that combines a cell-based selection method (cell-internalization SELEX) with high-throughput sequencing (HTS) and bioinformatics analyses to rapidly identify cell-specific, internalization-competent RNA aptamers. Methodology/Principal Findings: We demonstrate the utility of this approach by enriching for RNA aptamers capable of selective internalization into vascular smooth muscle cells (VSMCs). Several rounds of positive (VSMCs) and negative (endothelial cells; ECs) selection were performed to enrich for aptamer sequences that preferentially internalize into VSMCs. To identify candidate RNA aptamer sequences, HTS data from each round of selection were analyzed using bioinformat