RNase T1 mapping of IRES domain III–IV in the presence of aptamer 3-07

Abstract

<p><b>Copyright information:</b></p><p>Taken from "A hepatitis C virus (HCV) internal ribosome entry site (IRES) domain III–IV-targeted aptamer inhibits translation by binding to an apical loop of domain IIId"</p><p>Nucleic Acids Research 2005;33(2):683-692.</p><p>Published online 28 Jan 2005</p><p>PMCID:PMC548359.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> 5′ end-labeled IRES RNA was digested with RNase U2, RNase T1 and an alkaline condition, respectively, were used as markers (lanes 2, 3 and 4). Cleavage reactions for markers were carried out under optimum buffer conditions for respective RNases. RNase T1 digestion with selection buffer was performed on 5′ end-labeled IRES (lane 5), the aptamer indicated (lanes 6 and 9) or mutants of aptamer 3-07 (lanes 7 and 8). Reactions were stopped and run on an 8% denaturing PAGE. Asterisks represent G triplets of domain IIId. Note that cleavage of G triplets was only protected in the presence of aptamer 3-07