A Novel, Modification-Dependent ATP-Binding Aptamer Selected from an RNA Library Incorporating a Cationic Functionality

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 comp...

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Bibliographic Details
Published in:Biochemistry (Easton) 2003-07, Vol.42 (29), p.8842-8851
Main Authors: Vaish, Narendra K, Larralde, Rosa, Fraley, Andrew W, Szostak, Jack W, McLaughlin, Larry W
Format: Article
Language:English
Subjects:
Adenosine Triphosphate - chemistry
Adenosine Triphosphate - metabolism
Base Sequence
Binding Sites
Cations
DNA - metabolism
Dose-Response Relationship, Drug
Hydrogen-Ion Concentration
Kinetics
Ligands
Models, Chemical
Molecular Sequence Data
Nucleic Acid Conformation
Oligonucleotides - chemistry
Protein Binding
RNA - chemistry
RNA - metabolism
Sepharose - chemistry
Uridine Triphosphate - chemistry
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Summary: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.
ISSN:0006-2960
1520-4995
DOI:10.1021/bi027354i