Combinatorial selection of a RNA thioaptamer that binds to Venezuelan equine encephalitis virus capsid protein.
Abstract: A phosphorothioate RNA aptamer (thioaptamer) targeting the capsid protein of Venezuelan equine encephalitis virus (VEEV) was isolated by in vitro combinatorial selection. The selected thioaptamer had a strong binding affinity (approximately 7nM) and high specificity for the target protein. For the binding to the protein, the overall tertiary structure of the thioaptamer is required. We introduce two theoretical methods to examine the effect of phosphorothioate modification on the enhancement of binding affinity and one experimental method to examine the nature of the multiple bands of thioaptamer in a native gel.
Publication Date: 2007-05-04 PubMed ID: 17493617DOI: 10.1016/j.febslet.2007.04.072Google Scholar: Lookup
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- Journal Article
- Research Support
- N.I.H.
- Extramural
- Research Support
- Non-U.S. Gov't
Summary
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The research examines the combinatorial selection of a RNA thioaptamer that successfully binds to the Venezuelan equine encephalitis virus capsid protein, exploring the impact of phosphorothioate modification on its enhanced binding affinity.
RNA Thioaptamer Selection
- The study identifies an RNA thioaptamer exhibiting strong binding affinity and high specificity to Venezuelan equine encephalitis virus (VEEV) capsid protein.
- A selection method known as in vitro combinatorial selection was used to isolate this thioaptamer.
- The binding affinity measured for this RNA thioaptamer with its target protein equated to roughly 7nM, signifying a strong interaction between the two.
Structural Dependence of Thioaptamer
- The research points out an important factor affecting the binding of thioaptamer to the VEEV protein, the overall tertiary structure of the aptamer.
- Maintaining the overall shape and structure appears to be vital for the binding process to take place.
Phosphorothioate Modification
- The article introduces two theoretical approaches to study the impact of phosphorothioate modification on binding affinity enhancement.
- Phosphorothioate modification is a biochemical change that researchers believed could improve the binding affinity of the RNA thioaptamer to the VEEV protein.
- The results from these theoretical investigations can offer insights into the molecular mechanisms pertaining to the pharmacological effects of the phosphorothioate modification.
Analysis of Thioaptamer’s Multiple Bands
- An experimental approach was also carried out to explore the nature of the multiple bands of thioaptamer visualised in a native gel.
- It is implied that these multiple bands may signal diverse conformations of the thioaptamer. This phenomenon could lead to a better understanding of the binding behaviour and structural attributes of the RNA thioaptamer.
Cite This Article
APA
Kang J, Lee MS, Watowich SJ, Gorenstein DG.
(2007).
Combinatorial selection of a RNA thioaptamer that binds to Venezuelan equine encephalitis virus capsid protein.
FEBS Lett, 581(13), 2497-2502.
https://doi.org/10.1016/j.febslet.2007.04.072 Publication
Researcher Affiliations
- Sealy Center for Structural Biology and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA.
MeSH Terms
- Aptamers, Nucleotide / genetics
- Base Sequence
- Biotinylation
- Capsid Proteins / genetics
- Combinatorial Chemistry Techniques
- DNA Footprinting
- Encephalitis Virus, Venezuelan Equine / genetics
- Models, Genetic
- RNA, Viral / genetics
- RNA, Viral / isolation & purification
Grant Funding
- AI 27744 / NIAID NIH HHS
- N01 HV 28184 / NHLBI NIH HHS
- U01 AI 054827 / NIAID NIH HHS
Citations
This article has been cited 11 times.- Navien TN, Yeoh TS, Anna A, Tang TH, Citartan M. Aptamers isolated against mosquito-borne pathogens.. World J Microbiol Biotechnol 2021 Jul 9;37(8):131.
- Hamula CLA, Zhang H, Li F, Wang Z, Chris Le X, Li XF. Selection and analytical applications of aptamers binding microbial pathogens.. Trends Analyt Chem 2011 Nov;30(10):1587-1597.
- Chen C, Zhou S, Cai Y, Tang F. Nucleic acid aptamer application in diagnosis and therapy of colorectal cancer based on cell-SELEX technology.. NPJ Precis Oncol 2017;1(1):37.
- Volk DE, Lokesh GLR. Development of Phosphorothioate DNA and DNA Thioaptamers.. Biomedicines 2017 Jul 13;5(3).
- Leija-Montoya AG, Benítez-Hess ML, Toscano-Garibay JD, Alvarez-Salas LM. Characterization of an RNA aptamer against HPV-16 L1 virus-like particles.. Nucleic Acid Ther 2014 Oct;24(5):344-55.
- Thiviyanathan V, Gorenstein DG. Aptamers and the next generation of diagnostic reagents.. Proteomics Clin Appl 2012 Dec;6(11-12):563-73.
- Yang X, Li N, Gorenstein DG. Strategies for the discovery of therapeutic aptamers.. Expert Opin Drug Discov 2011 Jan;6(1):75-87.
- Ramasamy S, Liu CQ, Tran H, Gubala A, Gauci P, McAllister J, Vo T. Principles of antidote pharmacology: an update on prophylaxis, post-exposure treatment recommendations and research initiatives for biological agents.. Br J Pharmacol 2010 Oct;161(4):721-48.
- Keefe AD, Pai S, Ellington A. Aptamers as therapeutics.. Nat Rev Drug Discov 2010 Jul;9(7):537-50.
- Brudno Y, Liu DR. Recent progress toward the templated synthesis and directed evolution of sequence-defined synthetic polymers.. Chem Biol 2009 Mar 27;16(3):265-76.
- Kang J, Lee MS, Copland JA 3rd, Luxon BA, Gorenstein DG. Combinatorial selection of a single stranded DNA thioaptamer targeting TGF-beta1 protein.. Bioorg Med Chem Lett 2008 Mar 15;18(6):1835-9.
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