title: Thermodynamic stability and statistical significance of potential stem-loop structures situated at the frameshift sites of retroviruses.
abstract: RNA stem-loop structures situated just 3' to the frameshift sites of the retroviral gag-pol or gag-pro and pro-pol regions may make important contributions to frame-shifting in retroviruses. In this study, the thermodynamic stability and statistical significance of such secondary structural features relative to others in the sequence have been assessed using a newly developed method that combines calculations of the lowest free energy of formation of RNA secondary structures and the Monte Carlo simulations. Our results show that stem-loop structures situated just 3' to the frameshift sites are both highly stable and statistically significant relative to others in the gag-pol or gag-pro and pro-pol junction domains (both 300 nucleotides upstream and downstream from the possible frameshift sites are included) of Rous sarcoma virus (RSV), human immunodeficiency virus (HIV-1), bovine leukemia virus (BLV), human T-cell leukemia virus type II (HTLV-II), and mouse mammary tumor virus (MMTV). No other more stable, or significant folding regions are predicted in these domains.
authors.affiliation: Laboratory of Mathematical Biology, National Cancer Institute, Frederick, MD 21701.
authors.forename: S Y
authors.initials: SY
authors.lastname: Le
authors.forename: J H
authors.initials: JH
authors.lastname: Chen
authors.forename: J V
authors.initials: JV
authors.lastname: Maizel
mesh_terms: D001358:Avian Sarcoma Viruses / Q000235:genetics; D001483:Base Sequence; D004355:Drug Stability; D015683:Gene Products, gag; D015497:HIV-1 / Q000235:genetics; D015367:Human T-lymphotropic virus 2 / Q000235:genetics; D001909:Leukemia Virus, Bovine / Q000235:genetics; D008324:Mammary Tumor Virus, Mouse / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D012367:RNA, Viral; D012190:Retroviridae / Q000235:genetics*; D012191:Retroviridae Proteins / Q000235:genetics*; D013816:Thermodynamics
chemical_list: D015683:Gene Products, gag; D012367:RNA, Viral; D012191:Retroviridae Proteins