Journal article
Nucleotide Bias Observed with a Short SELEX RNA Aptamer Library
Nucleic acid therapeutics, Vol.21(4), pp.253-263
08/01/2011
DOI: 10.1089/nat.2011.0288
PMCID: PMC3198618
PMID: 21793789
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 (Δ
G) (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.
Details
- Title: Subtitle
- Nucleotide Bias Observed with a Short SELEX RNA Aptamer Library
- Creators
- William H Thiel - 1Department of Internal Medicine, University of Iowa, Iowa City, IowaThomas Bair - 2DNA Facility, University of Iowa, Iowa City, IowaKristina Wyatt Thiel - 1Department of Internal Medicine, University of Iowa, Iowa City, IowaJustin P Dassie - 3Molecular & Cellular Biology Program, University of Iowa, Iowa City, IowaWilliam M Rockey - 4Department of Radiation Oncology, University of Iowa, Iowa City, IowaCraig A Howell - 1Department of Internal Medicine, University of Iowa, Iowa City, IowaXiuying Y Liu - 1Department of Internal Medicine, University of Iowa, Iowa City, IowaAdam J Dupuy - 5Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IowaLingyan Huang - 6Integrated DNA Technologies, Coralville, IowaRichard Owczarzy - 6Integrated DNA Technologies, Coralville, IowaMark A Behlke - 6Integrated DNA Technologies, Coralville, IowaJames O McNamara - 1Department of Internal Medicine, University of Iowa, Iowa City, IowaPaloma H Giangrande - 4Department of Radiation Oncology, University of Iowa, Iowa City, Iowa
- Resource Type
- Journal article
- Publication Details
- Nucleic acid therapeutics, Vol.21(4), pp.253-263
- Publisher
- Mary Ann Liebert, Inc
- DOI
- 10.1089/nat.2011.0288
- PMID
- 21793789
- PMCID
- PMC3198618
- ISSN
- 2159-3337
- eISSN
- 2159-3345
- Language
- English
- Date published
- 08/01/2011
- Academic Unit
- Anatomy and Cell Biology; Pathology; Cardiovascular Medicine; Radiation Oncology; Obstetrics and Gynecology; Internal Medicine; Ophthalmology and Visual Sciences
- Record Identifier
- 9984025307802771
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