title: A novel, modification-dependent ATP-binding aptamer selected from an RNA library incorporating a cationic functionality.
abstract: An analogue of uridine triphosphate containing a cationic functional group was incorporated into a degenerate RNA library by enzymatic polymerization. In vitro selection experiments using this library yielded a novel receptor that binds ATP under physiological pH and salt conditions in a manner completely dependent on the presence of the cationic functionality. The consensus sequence and a secondary structure model for the ATP binding site were obtained by the analysis of functional sequences selected from a partially randomized pool based on the minimal parental sequence. Mutational studies of this receptor indicated that several of the modified uridines are critical for ATP binding. Analysis of the binding of ATP analogues revealed that the modified RNA receptor makes numerous contacts with ATP, including interactions with the triphosphate group. In contrast, the aptamer repeatedly isolated from natural RNA libraries does not interact with the triphosphate group of ATP. The incorporation of a cationic amine into nucleic acids clearly allows novel interactions to occur during the molecular recognition of ligands, which carries interesting implications for the RNA world hypothesis. In addition, new materials generated from such functionalized nucleic acids could be useful tools in research and diagnostics.
authors.affiliation: Department of Chemistry, Boston College, 140 Commonwealth Avenue, Chestnut Hill, Massachusetts 02467, USA. vaishn@sirna.com
authors.forename: Narendra K
authors.initials: NK
authors.lastname: Vaish
authors.forename: Rosa
authors.initials: R
authors.lastname: Larralde
authors.forename: Andrew W
authors.initials: AW
authors.lastname: Fraley
authors.forename: Jack W
authors.initials: JW
authors.lastname: Szostak
authors.forename: Larry W
authors.initials: LW
authors.lastname: McLaughlin
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry* / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D002412:Cations; D004247:DNA / Q000378:metabolism; D004305:Dose-Response Relationship, Drug; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D008024:Ligands; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D011485:Protein Binding; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012685:Sepharose / Q000737:chemistry; D014544:Uridine Triphosphate / Q000737:chemistry
chemical_list: D002412:Cations; D008024:Ligands; D009841:Oligonucleotides; D012313:RNA; D000255:Adenosine Triphosphate; D004247:DNA; D012685:Sepharose; D014544:Uridine Triphosphate