title: Structural analysis of ribonucleopeptide aptamer against ATP.
abstract: A ribonucleopeptide aptamer against ATP was obtained by the in vitro selection method. This ribonucleopeptide aptamer comprises a randomized and selected RNA linked to the Rev-responsive element (RRE) in complex with a peptide derived from an HIV Rev protein. The ribonucleopeptide aptamer selectively binds ATP in the presence of the Rev-derived peptide, exclusively. Here, we present the structural analysis of the ribonucleopeptide aptamer with NMR. The secondary structure of the RNA part of the aptamer, the selected RNA region linked to RRE, in the presence of the Rev-derived peptide was determined in an Ado-bound form. G:A and G:G base pairs, together with canonical base pairs, are formed in a duplex of RRE. The selected RNA region plays a crucial role in target binding. It has been found that the two U residues located in the selected RNA region trap Ado through the formation of the U:A:U base triple. This was directly confirmed by the HNN-COSY experiment through the detection of spin-spin couplings across the hydrogen bonds for Watson-Crick and Hoogsteen A:U base pairs in the U:A:U base triple.
authors.affiliation: Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan.
authors.forename: Tsukasa
authors.initials: T
authors.lastname: Mashima
authors.forename: Akimasa
authors.initials: A
authors.lastname: Matsugami
authors.forename: Shun
authors.initials: S
authors.lastname: Nakano
authors.forename: Masafumi
authors.initials: M
authors.lastname: Inoue
authors.forename: Masatora
authors.initials: M
authors.lastname: Fukuda
authors.forename: Takashi
authors.initials: T
authors.lastname: Morii
authors.forename: Masato
authors.initials: M
authors.lastname: Katahira
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism*; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D010455:Peptides / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D020218:Response Elements; D054321:rev Gene Products, Human Immunodeficiency Virus / Q000737:chemistry
chemical_list: D052157:Aptamers, Nucleotide; D010455:Peptides; D054321:rev Gene Products, Human Immunodeficiency Virus; D012313:RNA; D000255:Adenosine Triphosphate