title: Mass spectrometric studies of alkali metal ion binding on thrombin-binding aptamer DNA.
abstract: The binding sites and consecutive binding constants of alkali metal ions, (M(+) = Na(+), K(+), Rb(+), and Cs(+)), to thrombin-binding aptamer (TBA) DNA were studied by Fourier-transform ion cyclotron resonance spectrometry. TBA-metal complexes were produced by electrospray ionization (ESI) and the ions of interest were mass-selected for further characterization. The structural motif of TBA in an ESI solution was checked by circular dichroism. The metal-binding constants and sites were determined by the titration method and infrared multiphoton dissociation (IRMPD), respectively. The binding constant of potassium is 5-8 times greater than those of other alkali metal ions, and the potassium binding site is different from other metal binding sites. In the 1:1 TBA-metal complex, potassium is coordinated between the bottom G-quartet and two adjacent TT loops of TBA. In the 1:2 TBA-metal complex, the second potassium ion binds at the TGT loop of TBA, which is in line with the antiparallel G-quadruplex structure of TBA. On the other hand, other alkali metal ions bind at the lateral TGT loop in both 1:1 and 1:2 complexes, presumably due to the formation of ion-pair adducts. IRMPD studies of the binding sites in combination with measurements of the consecutive binding constants help elucidate the binding modes of alkali metal ions on DNA aptamer at the molecular level.
authors.affiliation: Bio-Nanotechnology Center, Department of Chemistry, Pohang University of Science and Technology, Pohang, Korea.
authors.forename: Eun Sun
authors.initials: ES
authors.lastname: Hong
authors.forename: Hye-Joo
authors.initials: HJ
authors.lastname: Yoon
authors.forename: Byungjoo
authors.initials: B
authors.lastname: Kim
authors.forename: Yong-Hyeon
authors.initials: YH
authors.lastname: Yim
authors.forename: Hun-Young
authors.initials: HY
authors.lastname: So
authors.forename: Seung Koo
authors.initials: SK
authors.lastname: Shin
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D002942:Circular Dichroism; D005583:Fourier Analysis; D007477:Ions / Q000737:chemistry / Q000378:metabolism; D008672:Metals, Alkali / Q000737:chemistry / Q000378:metabolism*; D008968:Molecular Conformation; D011188:Potassium / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D012964:Sodium / Q000737:chemistry / Q000378:metabolism; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*
chemical_list: D052157:Aptamers, Nucleotide; D007477:Ions; D008672:Metals, Alkali; C081676:thrombin aptamer; D012964:Sodium; D011188:Potassium