Nucleotide Bias Observed with a Short SELEX RNA Aptamer Library
- 1 August 2011
- journal article
- research article
- Published by Mary Ann Liebert Inc in Nucleic Acid Therapeutics
- Vol. 21 (4), 253-263
- https://doi.org/10.1089/nat.2011.0288
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) is a powerful in vitro selection process used for over 2 decades to identify oligonucleotide sequences (aptamers) with desired properties (usually high affinity for a protein target) from randomized nucleic acid libraries. In the case of RNA aptamers, several highly complex RNA libraries have been described with RNA sequences ranging from 71 to 81 nucleotides (nt) in length. In this study, we used high-throughput sequencing combined with bioinformatics analysis to thoroughly examine the nucleotide composition of the sequence pools derived from several selections that employed an RNA library (Sel2N20) with an abbreviated variable region. The Sel2N20 yields RNAs 51 nt in length, which unlike longer RNAs, are more amenable to large-scale chemical synthesis for therapeutic development. Our analysis revealed a consistent and early bias against inclusion of adenine, resulting in aptamers with lower predicted minimum free energies (ΔG) (higher structural stability). This bias was also observed in control, “nontargeted” selections in which the partition step (against the target) was omitted, suggesting that the bias occurred in 1 or more of the amplification and propagation steps of the SELEX process.Keywords
This publication has 39 references indexed in Scilit:
- Monitoring Genomic Sequences during SELEX Using High-Throughput Sequencing: Neutral SELEXPLOS ONE, 2010
- Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumorsNature Biotechnology, 2009
- Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of Dicer substrate siRNAs into HIV infected cellsNucleic Acids Research, 2009
- RNA Aptamer Blockade of Osteopontin Inhibits Growth and Metastasis of MDA-MB231 Breast Cancer CellsMolecular Therapy, 2009
- Assembling OX40 Aptamers on a Molecular Scaffold to Create a Receptor-Activating AptamerCell Chemical Biology, 2008
- Multivalent 4-1BB binding aptamers costimulate CD8+ T cells and inhibit tumor growth in miceJCI Insight, 2008
- Distinct roles of E2F proteins in vascular smooth muscle cell proliferation and intimal hyperplasiaProceedings of the National Academy of Sciences of the United States of America, 2007
- Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structureJournal of Molecular Biology, 1999
- Systematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage T4 DNA PolymeraseScience, 1990
- Stability of ribonucleic acid double-stranded helicesJournal of Molecular Biology, 1974