title: RNA recognition by Tat-derived peptides: interaction in the major groove?
abstract: Replication of human immunodeficiency virus requires binding of the viral Tat protein to its RNA target sequence TAR; peptides derived from Tat bind to a TAR "contact site" spanning 5 bp and a trinucleotide pyrimidine bulge. We find that high affinity binding requires a U residue in the bulge loop and 2 specific adjacent base pairs. Other bulged RNAs bind in a lower affinity nonspecific manner; sequence-specific binding requires a bulge loop of more than 1 nucleotide. Reaction with diethyl pyrocarbonate indicates that one effect of the bulge is to make the otherwise deep and narrow RNA major groove accessible. A model consistent with these data involves local distortion of A-form geometry at the bulge, which bends the helix and permits protein binding and interactive access in the RNA major groove.
authors.affiliation: Department of Chemistry, Yale University, New Haven, Connecticut 06511.
authors.forename: K M
authors.initials: KM
authors.lastname: Weeks
authors.forename: D M
authors.initials: DM
authors.lastname: Crothers
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D002352:Carrier Proteins / Q000378:metabolism*; D004047:Diethyl Pyrocarbonate / Q000737:chemistry; D015696:Gene Products, tat / Q000378:metabolism*; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D002352:Carrier Proteins; D015696:Gene Products, tat; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D004047:Diethyl Pyrocarbonate