title: In silico analysis of IRES RNAs of foot-and-mouth disease virus and related picornaviruses.
abstract: Foot-and-mouth disease virus (FMDV) uses an internal ribosome entry site (IRES), a highly structured segment of its genomic RNA, to hijack the translational apparatus of an infected host. Computational analysis of 162 type II picornavirus IRES RNA sequences yielded secondary structures that included only base pairs supported by comparative or experimental evidence. The deduced helical sections provided the foundation for a hypothetical three-dimensional model of FMDV IRES RNA. The model was further constrained by incorporation of data derived from chemical modification and enzymatic probing of IRES RNAs as well as high-resolution information about IRES RNA-bound proteins.
authors.affiliation: Department of Animal Sciences, Auburn University, 210 Upchurch Hall, Auburn, AL 36849-5415, USA.
authors.forename: Jody M
authors.initials: JM
authors.lastname: Burks
authors.forename: Christian
authors.initials: C
authors.lastname: Zwieb
authors.forename: Florian
authors.initials: F
authors.lastname: Müller
authors.forename: Iwona K
authors.initials: IK
authors.lastname: Wower
authors.forename: Jacek
authors.initials: J
authors.lastname: Wower
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D029544:Foot-and-Mouth Disease Virus / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010442:Peptide Chain Initiation, Translational; D010849:Picornaviridae / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism*
chemical_list: D012367:RNA, Viral