title: Secondary structure conservation of the stem-loop IV sub-domain of internal ribosomal entry sites in human rhinovirus clinical isolates.
abstract: OBJECTIVE
  The aim of this study was to investigate the genetic diversity in the stem-loop (SL) IV sub-domain of the human rhinovirus (HRV) internal ribosomal entry site (IRES), which plays key roles in the initiation of viral translation by host protein interaction.
  
  
  METHODS
  The primary SL-IV sequences of 194 HRVs, consisting of 97 reference strains and 97 clinical isolates, including the IRES sub-domains SL-IVa, SL-IVb, SL-IVc, and SL-IVd, were analyzed using Lasergene, MEGA 4, and WebLogo. Additionally, secondary structures of SL-IV were predicted and classified by RNAfold and CentroidHomfold-LAST.
  
  
  RESULTS
  The predicted secondary structures of SL-IV showed variations in the position of bulbs, size of the loop, and length of stems. SL-IVc had the most highly conserved nucleotide sequence, with structures classified into two groups by the location of the poly(C) loop. Of the SL-IV sequences analyzed, 74 (79.56%) were classified in the major group and 19 (20.44%) in the minor group. Thirteen compensatory substitution pairs of SL-IVc contributed to maintaining the stem structure.
  
  
  CONCLUSIONS
  This study showed that the IRES secondary structures of a large number of reference and clinical HRVs were highly conserved, with several compensatory substitutions. It is expected that these results will facilitate investigations into HRV function based on IRES secondary structures.
authors.affiliation: Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongju-si, Chungbuk, 363-951, Republic of Korea; Department of Biotechnology, Catholic University of Korea, Bucheon-si, Gyeonggi-do, 420-743, Republic of Korea.
authors.forename: Hak
authors.initials: H
authors.lastname: Kim
authors.affiliation: Division of Influenza Virus, Center for Infectious Diseases, Korea National Institute of Health, Cheongju-si, Chungbuk, 363-951, Republic of Korea.
authors.forename: Kisoon
authors.initials: K
authors.lastname: Kim
authors.affiliation: Division of Biosafety Evaluation and Control, Korea National Institute of Health, Cheongju-si, Chungbuk, 363-951, Republic of Korea.
authors.forename: Taesoo
authors.initials: T
authors.lastname: Kwon
authors.affiliation: Division of Biosafety Evaluation and Control, Korea National Institute of Health, Cheongju-si, Chungbuk, 363-951, Republic of Korea.
authors.forename: Dae-Won
authors.initials: DW
authors.lastname: Kim
authors.affiliation: Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongju-si, Chungbuk, 363-951, Republic of Korea.
authors.forename: Sung Soon
authors.initials: SS
authors.lastname: Kim
authors.affiliation: Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongju-si, Chungbuk, 363-951, Republic of Korea. Electronic address: youjin3693@gmail.com.
authors.forename: You-Jin
authors.initials: YJ
authors.lastname: Kim
mesh_terms: D001483:Base Sequence; D004770:Enterovirus / Q000235:genetics; D006801:Humans; D000067556:Internal Ribosome Entry Sites / Q000235:genetics; D055029:Inverted Repeat Sequences / Q000235:genetics*; D009690:Nucleic Acid Conformation; D010850:Picornaviridae Infections / Q000821:virology*; D014176:Protein Biosynthesis; D012367:RNA, Viral / Q000235:genetics; D012229:Rhinovirus / Q000235:genetics*; D012270:Ribosomes
chemical_list: D000067556:Internal Ribosome Entry Sites; D012367:RNA, Viral
keywords: Compensatory substitution; Human rhinovirus; Internal ribosomal entry site; Stem-loop IV