title: Footprinting, circular dichroism and UV melting studies on neomycin B binding to the packaging region of human immunodeficiency virus type-1 RNA.
abstract: We have studied the binding of neomycin to a 171mer RNA (psi-RNA) from the packaging region of the LAI strain of human immunodeficiency virus type-1, HIV-1 (LAI). The RNase I footprinting studies reveal that the primary binding site for the drug is in stem-loop 1, which contains the dimer initiation site of HIV-1. Loading this site with neomycin causes a structural change in the RNA, allowing nucleotides in the neighboring stem-loop 2 to participate in the drug site. Drug binding to secondary sites induces structural changes in other stem-loops of the RNA. Footprinting plots, showing cutting at a site as a function of drug concentration, were analyzed using a two-state model to obtain relative site-specific binding constants. Circular dichroism measurements show that neomycin binding to psi-RNA changes the intensity of the strong negative CD band at 208 nm, confirming that neomycin induces structural changes. Melting studies of the RNA showed melting transitions in the absence of drug at 28.2, 37.2, 47.4, 55.5 and 60.8 degrees C. Only the first two were affected by drug binding, the reason for this being explained by our analysis.
authors.affiliation: Department of Chemistry, Center for Science and Technology, Room 1-014, Syracuse University, Syracuse, NY 13244-4100, USA.
authors.forename: Mark P
authors.initials: MP
authors.lastname: McPike
authors.forename: Julie M
authors.initials: JM
authors.lastname: Sullivan
authors.forename: Jerry
authors.initials: J
authors.lastname: Goodisman
authors.forename: James C
authors.initials: JC
authors.lastname: Dabrowiak
mesh_terms: D001483:Base Sequence; D002942:Circular Dichroism; D018983:DNA Footprinting; D005601:Framycetin / Q000378:metabolism* / Q000494:pharmacology; D015497:HIV-1 / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009691:Nucleic Acid Denaturation / Q000187:drug effects; D011485:Protein Binding; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013056:Spectrophotometry, Ultraviolet; D013696:Temperature; D019065:Virus Assembly / Q000235:genetics*
chemical_list: D012367:RNA, Viral; D005601:Framycetin