title: Multiple stepwise pattern for potential of mean force in unfolding the thrombin binding aptamer in complex with Sr2+.
abstract: Using all-atom molecular dynamics simulation in conjunction with umbrella sampling, we obtained the unfolding free energy and the force extension profiles of the thrombin binding DNA aptamer (15-TBA) in complex with Sr(2+) (Protein Data Bank code: 1RDE). The resulting potential of mean force (PMF) displays a multiple stepwise pattern with distinct plateau regions. The detailed analysis of the simulation result indicated that each plateau was created by the interplay of the metal ion interacting with self-arranging guanine bases and the successive uptakes of water molecules. The current PMF simulation provides a quantitative description of the unfolding process of 15-TBA DNA driven by stretching and gives molecular insight on its detailed changes of base pair interactions in the presence of the metal cation.
authors.affiliation: Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 609-735, South Korea.
authors.forename: Changwon
authors.initials: C
authors.lastname: Yang
authors.forename: Soonmin
authors.initials: S
authors.lastname: Jang
authors.forename: Youngshang
authors.initials: Y
authors.lastname: Pak
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D013324:Strontium / Q000378:metabolism*; D013816:Thermodynamics; D013917:Thrombin / Q000378:metabolism*
chemical_list: D052157:Aptamers, Nucleotide; D004247:DNA; D013917:Thrombin; D013324:Strontium