title: Encapsulating an amino acid in a DNA fold.
abstract: Here we present the first solution structure of a ligand-DNA aptamer complex. Our NMR-molecular dynamics structural studies of the interaction between argininamide and a DNA stem-loop complex establishes that the hairpin loop DNA binding site undergoes an adaptive conformational transition on complex formation. The tip of the DNA loop folds down towards the stem and sandwiches the bound argininamide between reversed Hoogsteen A.C and Watson-Crick G.C base pairs. The argininamide is encapsulated within the structured DNA loop and is stabilized by an intricate set of intermolecular hydrogen bonds and stacking interactions. The structure of the complex lays out the molecular principles defining both the architecture of the internal cavity and the recognition elements that could contribute to ligand discrimination.
authors.affiliation: Cellular Biochemistry & Biophysics Program, Memorial Sloan-Kettering Cancer Center New York, New York 10021, USA.
authors.forename: C H
authors.initials: CH
authors.lastname: Lin
authors.forename: D J
authors.initials: DJ
authors.lastname: Patel
mesh_terms: D001120:Arginine / Q000031:analogs & derivatives* / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis
chemical_list: D008024:Ligands; D009838:Oligodeoxyribonucleotides; C069339:argininamide; D004247:DNA; D001120:Arginine