ArticlePloS one2012
Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed.
- Aptamer-Based Heterobifunctional Targeted Degraders in Disease Treatment.Molecules (Basel, Switzerland) · 2026Review
- ASSET: A Framework for Decoding Aptamer Specificity of an Enriched Library by Next-Generation Sequencing of Experimental Samples.bioRxiv : the preprint server for biology · 2025Article
- Review
- RNA aptamer-mediated RNA nanotechnology for potential treatment of cardiopulmonary diseases.Pharmacological research · 2025Review
- AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers.Molecular therapy. Nucleic acids · 2024Article
- Diagnostic and Therapeutic Aptamers: A Promising Pathway to Improved Cardiovascular Disease Management.JACC. Basic to translational science · 2024Review
- AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers.bioRxiv : the preprint server for biology · 2023Article
- Selection of a novel cell-internalizing RNA aptamer specific for CD22 antigen in B cell acute lymphoblastic leukemia.Molecular therapy. Nucleic acids · 2023Article
- Selective Delivery to Cardiac Muscle Cells Using Cell-Specific Aptamers.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Combination of protein and cell internalization SELEX identifies a potential RNA therapeutic and delivery platform to treat EphA2-expressing tumors.Molecular therapy. Nucleic acids · 2023Article
- Targeted systematic evolution of an RNA platform neutralizing DNMT1 function and controlling DNA methylation.Nature communications · 2023Article
- Evolution of Cell-Type-Specific RNA Aptamers via Live Cell-Based SELEX.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Advances in Aptamer-Based Biosensors and Cell-Internalizing SELEX Technology for Diagnostic and Therapeutic Application.Biosensors · 2022Review
- Local intraluminal delivery of a smooth muscle-targeted RNA ligand inhibits neointima growth in a porcine model of peripheral vascular disease.Molecular therapy. Nucleic acids · 2022Article
- FASTAptameR 2.0: A web tool for combinatorial sequence selections.Molecular therapy. Nucleic acids · 2022Article
- Selection of DNA Aptamers for Differentiation of Human Adipose-Derived Mesenchymal Stem Cells from Fibroblasts.Applied biochemistry and biotechnology · 2021Article
- Machine learning guided aptamer refinement and discovery.Nature communications · 2021Article
- Base-modified aptamers obtained by cell-internalization SELEX facilitate cellular uptake of an antisense oligonucleotide.Molecular therapy. Nucleic acids · 2021Article
- Therapeutic Interventions into Innate Immune Diseases by Means of Aptamers.Pharmaceutics · 2020Review
- Aptamers Against Live Targets: Is In Vivo SELEX Finally Coming to the Edge?Molecular therapy. Nucleic acids · 2020Review
17 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
backgroundThe 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
findingsWe 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 bioinformatics methods: (1) metrics of selection enrichment; and (2) pairwise comparisons of sequence and structural similarity, termed edit and tree distance, respectively. Correlation analyses of experimentally validated aptamers or rounds revealed that the best cell-specific, internalizing aptamers are enriched as a result of the negative selection step performed against ECs. CONCLUSIONS AND SIGNIFICANCE: We describe a novel approach that combines cell-internalization SELEX with HTS and bioinformatics analysis to identify cell-specific, cell-internalizing RNA aptamers. Our data highlight the importance of performing a pre-clear step against a non-target cell in order to select for cell-specific aptamers. We expect the extended use of this approach to enable the identification of aptamers to a multitude of different cell types, thereby facilitating the broad development of targeted cell therapies.
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