Sagan Selena M, Nasheri Neda, Luebbert Christian, Pezacki John Paul
Steacie Institute for Molecular Sciences, The National Research Council of Canada, Ottawa, ON K1A 0R6, Canada.
Chem Biol. 2010 May 28;17(5):515-27. doi: 10.1016/j.chembiol.2010.04.011.
Hepatitis C virus (HCV) is a global health problem. Designing therapeutic agents that target HCV's RNA genome remains challenging. HCV genomic RNA is large and highly structured with long-range genome-scale ordered RNA structures. Predicting the secondary- and tertiary-structure elements that reveal the accessibility of target sites within HCV RNA is difficult because of the abundance of long-range interactions. Target site accessibility remains a significant barrier to the design of effective therapeutics such as small interfering RNAs (siRNAs) against different strains of HCV. Here we developed two methods that interrogate the folding of HCV RNA, an approach involving viral RNA microarrays (VRMs) and an HCV viral RNA-coated magnetic bead-based (VRB) assay. VRMs and VRBs were used to determine target site accessibility for siRNAs designed against the HCV genome. Both methods predicted potency of siRNAs in cell-culture models for HCV replication that are not easily predicted by informatic means.
丙型肝炎病毒（HCV）是一个全球性的健康问题。设计针对HCV RNA基因组的治疗药物仍然具有挑战性。HCV基因组RNA很大且高度结构化，具有长程基因组规模的有序RNA结构。由于存在大量的长程相互作用，预测揭示HCV RNA内靶位点可及性的二级和三级结构元件很困难。靶位点可及性仍然是设计针对不同HCV毒株的有效治疗药物（如小干扰RNA（siRNA））的重大障碍。在此，我们开发了两种探究HCV RNA折叠的方法，一种是涉及病毒RNA微阵列（VRM）的方法，另一种是基于HCV病毒RNA包被磁珠（VRB）的检测方法。VRM和VRB被用于确定针对HCV基因组设计的siRNA的靶位点可及性。这两种方法都预测了siRNA在HCV复制细胞培养模型中的效力，而这些效力通过信息学方法不容易预测。
