ArticlePloS one2010
Monitoring genomic sequences during SELEX using high-throughput sequencing: neutral SELEX.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Selection, characterization, and biosensing applications of DNA aptamers targeting cyanotoxin BMAA.RSC advances · 2024Article
- FASTAptameR 2.0: A web tool for combinatorial sequence selections.Molecular therapy. Nucleic acids · 2022Article
- Generating aptamers towards human sperm cells using massively parallel sequencing.Analytical and bioanalytical chemistry · 2021Article
- High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers.International journal of molecular sciences · 2021Review
- A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers.PLoS computational biology · 2021Article
- Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology.International journal of molecular sciences · 2020Review
- SELEX tool: a novel and convenient gel-based diffusion method for monitoring of aptamer-target binding.Journal of biological engineering · 2020Article
- Side chain determinants of biopolymer function during selection and replication.Nature chemical biology · 2019Article
- Designed and Evolved Nucleic Acid Nanotechnology: Contrast and Complementarity.Bioconjugate chemistry · 2019Review
- SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data.International journal of biological sciences · 2019Article
- Systematic evaluation of error rates and causes in short samples in next-generation sequencing.Scientific reports · 2018Article
- A comparative Study of Aptasensor Vs Immunosensor for Label-Free PSA Cancer Detection on GQDs-AuNRs Modified Screen-Printed Electrodes.Scientific reports · 2018Article
- Compositional Bias in Naïve and Chemically-modified Phage-Displayed Libraries uncovered by Paired-end Deep Sequencing.Scientific reports · 2018Article
- Simple Methods and Rational Design for Enhancing Aptamer Sensitivity and Specificity.Frontiers in molecular biosciences · 2018Article
- Novel RNA aptamers targeting gastrointestinal cancer biomarkers CEA, CA50 and CA72-4 with superior affinity and specificity.PloS one · 2018Article
- Aptamer Bioinformatics.International journal of molecular sciences · 2017Review
- Aptamer Cell-Based Selection: Overview and Advances.Biomedicines · 2017Review
- Natural RNA Polymerase Aptamers Regulate Transcription in E. coli.Molecular cell · 2017Article
- NMR monitoring of the SELEX process to confirm enrichment of structured RNA.Scientific reports · 2017Article
- Applications of High-Throughput Sequencing for In Vitro Selection and Characterization of Aptamers.Pharmaceuticals (Basel, Switzerland) · 2016Review
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSELEX is a well established in vitro selection tool to analyze the structure of ligand-binding nucleic acid sequences called aptamers. Genomic SELEX transforms SELEX into a tool to discover novel, genomically encoded RNA or DNA sequences binding a ligand of interest, called genomic aptamers. Concerns have been raised regarding requirements imposed on RNA sequences undergoing SELEX selection. METHODOLOGY/PRINCIPAL
findingsTo evaluate SELEX and assess the extent of these effects, we designed and performed a Neutral SELEX experiment omitting the selection step, such that the sequences are under the sole selective pressure of SELEX's amplification steps. Using high-throughput sequencing, we obtained thousands of full-length sequences from the initial genomic library and the pools after each of the 10 rounds of Neutral SELEX. We compared these to sequences obtained from a Genomic SELEX experiment deriving from the same initial library, but screening for RNAs binding with high affinity to the E. coli regulator protein Hfq. With each round of Neutral SELEX, sequences became less stable and changed in nucleotide content, but no sequences were enriched. In contrast, we detected substantial enrichment in the Hfq-selected set with enriched sequences having structural stability similar to the neutral sequences but with significantly different nucleotide selection. CONCLUSIONS/SIGNIFICANCE: Our data indicate that positive selection in SELEX acts independently of the neutral selective requirements imposed on the sequences. We conclude that Genomic SELEX, when combined with high-throughput sequencing of positively and neutrally selected pools, as well as the gnomic library, is a powerful method to identify genomic aptamers.
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