This article reports nonlinear optical measurements that quantify, for the first time directly and without labels, how many Mg(2+) cations are bound to DNA 21-mers covalently linked to fused silica/water interfaces maintained at pH 7 and 10 mM NaCl, and what the thermodynamics are of these interactions. The overall interaction of Mg(2+) with adenine, thymine, guanine, and cytosine is found to involve -10.0 ± 0.3, -11.2 ± 0.3, -14.0 ± 0.4, and -14.9 ± 0.4 kJ/mol, and nonspecific interactions with the phosphate and sugar backbone are found to contribute -21.0 ± 0.6 kJ/mol for each Mg(2+) ion bound. The specific and nonspecific contributions to the interaction energy of Mg(2+) with oligonucleotide single strands is found to be additive, which suggests that within the uncertainty of these surface-specific experiments, the Mg(2+) ions are evenly distributed over the oligomers and not isolated to the most strongly binding nucleobase. The nucleobases adenine and thymine are found to bind only three Mg(2+) ions per 21-mer oligonucleotide, while the bases cytosine and guanine are found to bind eleven Mg(2+) ions per 21-mer oligonucleotide.

The binding of Sr(II), Ca(II), Mg(II), Ba(II), Mn(II), Zn(II), and Cd(II) to silica/water interfaces functionalized with A(15)T(6) oligonucleotides was quantified at pH 7 and 10 mM NaCl using the Eisenthal χ((3)) technique. The binding free energies range from -31.1(6) kJ/mol for Ba(II) to -33.8(4) kJ/mol for Ca(II). The ion densities were found to range from 2(1) ions/strand for Zn(II) to 11(1) ions/strand for Cd(II). Additionally, we quantified Mg(II) binding in the presence of varying background electrolyte concentrations which showed that the binding free energies changed in a linear fashion from -39.3(8) to -27(1) kJ/mol over the electrolyte concentration range of 1-80 mM, respectively. An adsorption free energy versus interfacial potential analysis allowed us to elucidate the speciation of the bound Mg(II) ions and to identify three possible binding pathways. Our findings suggest that Mg(II) binds as a fully hydrated divalent cation, most likely displacing DNA-bound Na ions. These measurements will serve as a benchmark for computer simulations of divalent metal cation/DNA interactions for geochemical and biosensing applications.

The adsorption of divalent Sr ions at the fused silica/water interface was studied using the Eisenthal χ(3) technique to quantify Sr2+ adsorption at neutral pH as a function of screening electrolyte concentration. We determine binding constants, adsorption free energies, absolute adsorbate number densities, and interfacial charge densities and examine the relationships between the measured adsorption free energies and the electric double layer interfacial potential present at each electrolyte concentration. Our results provide the first direct experimental investigation into the widely used additive adsorption free energy expression in which the observed free energy is modeled as the sum of an electrostatic free energy and an intrinsic chemical free energy. At screening electrolyte concentrations of 10 mM and lower, the free energy for Sr2+ adsorption to the fused silica/water interface depends directly on the interfacial potential, while the observed adsorption free energy becomes independent of the interfacial potential at higher electrolyte concentrations. This change in the free energy/interfacial potential relationship indicates that the charge of adsorbing strontium species changes from +2 to +1 at screening electrolyte conditions exceeding 10 mM. This finding is consistent with the formation of ion pairs which are thermodynamically favored at the interface but not in the aqueous bulk. Additional experiments using bromide and iodide show anion polarizability effects contribute about 10% to the chemical free energy.

Fused silica hemispheres were used as the substrates for functionalization with ssDNA (ISP Optics). Prior to DNA functionalization, each hemisphere was cleaned in the following manner. First, the lens was treated with NoChromix (Godax Laboratories) for 1 hr. The hemispheres were then rinsed with Millipore water (18.2 M_), and

The binding of magnesium ions to surface-bound single-stranded oligonucleotides was studied under aqueous conditions using second harmonic generation (SHG) and atomic force microscopy (AFM). The effect of strand length on the number of Mg(II) ions bound and their free binding energy was examined for 5-, 10-, 15-, and 20-mers of adenine and guanine at pH 7, 298 K, and 10 mM NaCl. The binding free energies for adenine and guanine sequences were calculated to be -32.1(4) and -35.6(2) kJ/mol, respectively, and invariant with strand length. Furthermore, the ion density for adenine oligonucleotides did not change as strand length increased, with an average value of 2(1) ions/strand. In sharp contrast, guanine oligonucleotides displayed a linear relationship between strand length and ion density, suggesting that cooperativity is important. This data gives predictive capabilities for mixed strands of various lengths, which we exploit for 20-mers of adenines and guanines. In addition, the role sequence order plays in strands of hetero-oligonucleotides was examined for 5'-A(10)G(10)-3', 5'-(AG)(10)-3', and 5'-G(10)A(10)-3' (here the -3' end is chemically modified to bind to the surface). Although the free energy of binding is the same for these three strands (averaged to be -33.3(4) kJ/mol), the total ion density increases when several guanine residues are close to the 3' end (and thus close to the solid support substrate). To further understand these results, we analyzed the height profiles of the functionalized surfaces with tapping-mode atomic force microscopy (AFM). When comparing the average surface height profiles of the oligonucleotide surfaces pre- and post- Mg(II) binding, a positive correlation was found between ion density and the subsequent height decrease following Mg(II) binding, which we attribute to reductions in Coulomb repulsion and strand collapse once a critical number of Mg(II) ions are bound to the strand.