Combinatorial selection of a RNA thioaptamer that binds to Venezuelan equine encephalitis virus capsid protein.
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.
Kang
Jonghoon
J
Sealy Center for Structural Biology and Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA.
Lee
Myung Soog
MS
Watowich
Stanley J
SJ
Gorenstein
David G
DG
D052157:Aptamers, Nucleotide / Q000235:genetics*; D001483:Base Sequence; D019921:Biotinylation; D036022:Capsid Proteins / Q000235:genetics*; D020650:Combinatorial Chemistry Techniques; D018983:DNA Footprinting; D004666:Encephalitis Virus, Venezuelan Equine / Q000235:genetics*; D008957:Models, Genetic; D012367:RNA, Viral / Q000235:genetics* / Q000302:isolation & purification
D052157:Aptamers, Nucleotide; D036022:Capsid Proteins; D012367:RNA, Viral