Genomic SELEX: a discovery tool for genomic aptamers
| Autor: | Bob Zimmermann, Ivana Bilusic, Renée Schroeder, Christina Lorenz |
|---|---|
| Rok vydání: | 2010 |
| Předmět: |
Genetics
Genomic Library Biochemistry Genetics and Molecular Biology(all) Aptamer In silico SELEX Aptamer Technique Chromosome Mapping Review Article Biology Aptamers Nucleotide General Biochemistry Genetics and Molecular Biology Deep sequencing Nucleic acid RNA Genomic library Molecular Biology Selection (genetic algorithm) Systematic evolution of ligands by exponential enrichment |
| Zdroj: | Methods (San Diego, Calif.) |
| ISSN: | 1095-9130 |
| Popis: | Genomic SELEX is a discovery tool for genomic aptamers, which are genomically encoded functional domains in nucleic acid molecules that recognize and bind specific ligands. When combined with genomic libraries and using RNA-binding proteins as baits, Genomic SELEX used with high-throughput sequencing enables the discovery of genomic RNA aptamers and the identification of RNA–protein interaction networks. Here we describe how to construct and analyze genomic libraries, how to choose baits for selections, how to perform the selection procedure and finally how to analyze the enriched sequences derived from deep sequencing. As a control procedure, we recommend performing a “Neutral” SELEX experiment in parallel to the selection, omitting the selection step. This control experiment provides a background signal for comparison with the positively selected pool. We also recommend deep sequencing the initial library in order to facilitate the final in silico analysis of enrichment with respect to the initial levels. Counter selection procedures, using modified or inactive baits, allow strengthening the binding specificity of the winning selected sequences. |
| Databáze: | OpenAIRE |
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