ArticleScientific reports2016
High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
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Who cites it
50 citing papers in PubMed, 104 citations in OpenAlex.
- Retention-Based, Dissociation-Sensitive Pre-Screening of Aptamers Using a Centrifugal Microspin Filter.Biosensors · 2026Article
- SELEX-Based Aptamer Technologies for Toxin Analysis: Screening, Optimization, and Computational Assisted Design.Toxins · 2026Review
- Assessing Molecular Dynamics in Predicting Aptamer-Ligand Binding Thermodynamics: Insights from the OTA Binding Aptamers.Journal of chemical information and modeling · 2026Article
- Review
- Universal Baseline forbioRxiv : the preprint server for biology · 2026Article
- The Diagnostic and Therapeutic Potential of Oligonucleotide Aptamers in Alzheimer's Disease.Cells · 2025Review
- 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
- Direct Modeling of DNA and RNA Aptamers with AlphaFold 3: A Promising Tool for Predicting Aptamer Structures and Aptamer-Target Interactions.ACS synthetic biology · 2025Article
- Engineering functionally-optimized aptamers against SARS-Cov-2 for blocking spike-ACE2 interaction and aptasensor detection.Materials today. Bio · 2025Article
- Single-step discovery of high-affinity RNA ligands by UltraSelex.Nature chemical biology · 2025Article
- Selection and characterization of DNA aptamers targeting the surface Borrelia protein CspZ with high-throughput cross-over SELEX.Communications biology · 2025Article
- Evolution Driven Microscale Combinatorial Chemistry in Intracellular Mimicking Droplets to Engineer Thermostable RNA for Cellular Imaging.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Article
- Precision Nanomedicine for Cancer: Innovations, Strategies, and Translational Challenges.OncoTargets and therapy · 2025Review
- Article
- Optimized Construction of a Yeast SICLOPPS Library for UnbiasedBiochemistry · 2024Article
- Current developments of SELEX technologies and prospects in the aptamer selection with clinical applications.Journal, genetic engineering & biotechnology · 2024Review
- High-affinity one-step aptamer selection using a non-fouling porous hydrogel.Nature biotechnology · 2024Article
- New Insights into Aptamers: An Alternative to Antibodies in the Detection of Molecular Biomarkers.International journal of molecular sciences · 2024Review
- Single-Round Circular Aptamer Discovery Using Bioinspired Magnetosome-Like Magnetic Chain Cross-Linked Graphene Oxide.Research (Washington, D.C.) · 2024Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct "biased sequences" and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the "biased sequences" was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.