title: Direct structural evidence for formation of a stem-loop structure involved in ribosomal frameshifting in human immunodeficiency virus type 1.
abstract: Programmed ribosomal frameshifting in viral messenger RNA occurs in response to neighboring sequence elements consisting of: a frameshift site, a spacer, and a downstream enhancer sequence. In human immunodeficiency virus type 1 (HIV-1) mRNA, this sequence element has a potential to form either a stem-loop or a pseudoknot structure. Based on many mutational studies, the stem-loop structure has been proposed for the downstream enhancer region of the HIV-1 mRNA. This stimulatory stem-loop structure is separated from the shift site by a spacer of seven nucleotides. In contrast, a recent report has proposed an alternative model in which the bases in the spacer sequence form a pseudoknot structure as the downstream enhancer sequence [Du et al., Biochemistry 35 (1996) 4187-4198.]. Using UV melting and enzymatic mapping analyses, we have investigated the conformation of the sequence region involved in ribosomal frameshifting in HIV-1. Our S1, V1, and T1 endonuclease mappings, together with UV melting analysis, clearly indicate that this sequence element of the HIV-1 mRNA frameshift site forms a stem-loop structure, not a pseudoknot structure. This finding further supports the stem-loop structure proposed by many mutational studies for the downstream enhancer sequence of the HIV-1 mRNA.
authors.affiliation: Kumho Life and Environmental Science Laboratory, Korea Kumho Petrochemical Co. Ltd., Kwangju, South Korea. hskang@ksc.kumho.co.kr
authors.forename: H
authors.initials: H
authors.lastname: Kang
mesh_terms: D004722:Endoribonucleases / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D018965:Frameshifting, Ribosomal; D015497:HIV-1 / Q000235:genetics*; D009154:Mutation; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D006163:Ribonuclease T1 / Q000378:metabolism; D015719:Single-Strand Specific DNA and RNA Endonucleases / Q000378:metabolism; D014466:Ultraviolet Rays
chemical_list: D012367:RNA, Viral; D004722:Endoribonucleases; C032825:ribonuclease V(1); D006163:Ribonuclease T1; D015719:Single-Strand Specific DNA and RNA Endonucleases