Specific and Nonspecific Metal Ion−Nucleotide Interactions at Aqueous/Solid Interfaces Functionalized with Adenine,Thymine, Guanine, and Cytosine Oligomers

Holland, Joseph G.; Malin, Jessica N.; Jordan, David S.; Morales, Esmeralda; Geiger, Franz M.

doi:10.1021/ja2018306

Cited by 6 publications

(29 citation statements)

References 9 publications

(12 reference statements)

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“…48,53,71,72 The lack of length dependency corroborates our earlier published findings that suggest the difference in free energies are due to variations in electron density of these surface-bound nucleobases. 42 Figure 2b shows that the number of Mg(II) ions bound depends linearly on guanine strand length. This linearity corresponds to approximately 80−120% of the negative charges on the phosphate backbone being screened over the range of strands studied.…”

Section: Resultsmentioning

confidence: 99%

“…The strands were covalently attached to the silica surface via amide bond formation that occurs through the/3AmMO/-3′ modification and the N-hydroxysuccinimide linker. 27,41,42,59,60 Aqueous solutions were prepared using Millipore water and adjusted to pH 7 by the addition of dilute HCl (E.M.D., ACS grade) and dilute NaOH (Sigma-Aldrich, 99.99%). The aqueous solutions of the 0.1 M MgCl 2 stock were prepared by using MgCl 2 (H 2 O)) 6 (Sigma-Aldrich, 99.99%).…”

Section: Methodsmentioning

confidence: 99%

“…Comprehensive experimental details as well as additional background on second harmonic generation can be found in previously published work on Mg(II)/oligonucleotide binding. 41,42 Adsorption isotherms for all experiments presented in this work may be found in the Supporting Information (Figures S1−S10). All E SHG values were normalized by calculating the square root of the I SHG in the presence of Mg(II) divided by the square root of the average I SHG obtained while flowing a 10 mM NaCl solution across the interfaces before and after Mg(II) flow.…”

Section: Methodsmentioning

confidence: 99%

“…27,41,42 While many studies have characterized the binding properties of magnesium to DNA in bulk solution, 43−57 at this time, there is no known way of correctly predicting Mg(II) ion densities and total binding free energies from first principles for interfacial environments. Here, we quantify the free energy of binding and ion density (ions/ strand) of divalent magnesium ions to varied length homooligomers and mixed strands covalently attached to fused silica/ water interfaces maintained at pH 7 and 10 mM NaCl concentration.…”

Section: Introductionmentioning

confidence: 99%

“…Use of the Gouy−Chapman theory for the analysis of divalent metal binding to oligonucleotide-functionalized surfaces, including the treatment of C elec as the sum of the Mg 2+ and NaCl concentration vs just the NaCl concentration, has been discussed in our previous work 41,69,70. Equation 2 was chosen over other electric double layer models because it (a) is applicable to the interfacial potential range covered in these experiments, (b) avoids overparameterization, and (c) aids in the comparison of this data to that of our previously published work.…”

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confidence: 99%

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Importance of Length and Sequence Order on Magnesium Binding to Surface-Bound Oligonucleotides Studied by Second Harmonic Generation and Atomic Force Microscopy

Holland

Geiger

2012

J. Phys. Chem. B

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

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Importance of Length and Sequence Order on Magnesium Binding to Surface-Bound Oligonucleotides Studied by Second Harmonic Generation and Atomic Force Microscopy

Holland

Geiger

2012

J. Phys. Chem. B

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Cooperative and Inhibited Adsorption of d-Ribose onto Brucite [Mg(OH)₂] with Divalent Cations

Estrada

Adcock

Sverjensky

et al. 2017

ACS Earth Space Chem.

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The adsorption and concentration of sugars onto mineral surfaces in geochemical environments, such as hydrothermal systems, may have influenced the evolution of early life on Earth. We conducted batch adsorption experiments between d-Ribose and brucite [Mg(OH)2], a mineral produced from serpentinite-hosted hydrothermal systems, over variable initial ribose concentrations at four ionic strengths resulting from different Mg2+ and Ca2+ ion concentrations in the aqueous phase. Ribose adsorption generally increased with greater initial concentration and up to 0.3 μmol·m–2 ribose attached onto brucite with 0.6 mM Mg2+ present. Ribose adsorption decreased over 6-fold (4.9 × 10–2 μmol·m–2) when the total Mg2+ ion concentration increased to 5.8 mM. Ribose adsorption increased to 0.4 μmol·m–2 when 4.2 mM CaCl2 was added to the system. Substantial amounts (over 21 μmol·m–2) of dissolved Ca also attached to the brucite surface independent of ribose concentration. We characterized the interactions between ribose, Ca, and the brucite surface by fitting a surface complexation model to adsorption data. We propose three types of surface reactions that were consistent with the experimental data and involve (1) a bidentate outer sphere or a “standing” ribose surface species, (2) a monodentate Ca-ribose outer-sphere species, and (3) a monodentate Ca outer-sphere species. Our model predicts brucite particle surface charge is negative at low Mg2+ concentrations and further decreases upon the addition of MgCl2, which may hinder our proposed surface complexation of the ribose species, Rib–. We predict that brucite becomes positively charged with CaCl2 addition, which may be a consequence of the significant extent of Ca adsorption. The increase in ribose adsorption with CaCl2 is likely driven by Ca attachment and the formation of a positively charged, cooperative Ca–ribose species that our model predicts will predominate over the “standing” ribose species on brucite. Our model of the ribose–brucite system, established by a combination of batch adsorption experiments and surface complexation modeling, has enabled predictions of ribose adsorption over a wide range of pH and complex environmental conditions.

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