Specific and nonspecific bindings of alkaline-earth metal ions to guanine-quadruplex thrombin-binding aptamer DNA

Specific and nonspecific bindings of alkaline-earth metal ions to the thrombin-binding aptamer (TBA) DNA d(GGTTGGTGTGGTTGG) were studied using electrospray ionization (ESI) mass spectrometry (MS). A single-stranded DNA d(AATTAATGTAATTAA) was used as a control for nonspecific binding. Both 1:1 and 2:1 metal-DNA complexes formed in 3:1 water/isopropanol were detected with ESI-MS and their binding constants were determined by the titration method. The 1:1 binding constant (K-1) of Sr2+ or Ba2+ for TBA was three orders of magnitude greater than their K-1 for the control DNA, whereas K-1 of Mg2+ or Ca2+ for TBA was comparable to their K-1 for the control DNA. To the contrary, the second binding constant (K-2) was nearly the same independent of the metal ion and DNA. To see if addition of metal ion led to a structural change in DNA, the circular dichroism (CD) spectra of DNA in ESI solvent were obtained in the presence and absence of metal ion. TBA showed characteristic bands of the chair-type guanine-quadruplex (G4) structure. Significantly, addition of Sr2+ or Ba2+ enhanced the G4 bands of TBA, but neither Mg2+ nor Ca2+ induced a change, indicating that Sr2+ and Ba2+ interact strongly with G4 TBA and stabilize it. Control DNA showed no special motif and none of the four metal ions affected its CD spectra. Binding constants and CD results suggest that only the first binding of Sr2+ and Ba2+ to G4 TBA is specific and the first binding of Mg2+ and Ca2+ as well as the second binding of all four metal ions are nonspecific. The specific and nonspecific bindings of alkaline-earth metal ions to G4 TBA are further rationalized in terms of ionic radius, coordination number, and Gibbs free energy of dehydration of the metal ion. (c) 2012 Elsevier B.V. All rights reserved.