Divalent metal cation speciation and binding to surface-bound oligonucleotide single strands studied by second
Joseph G Holland1, David S Jordan, Franz M Geiger
1Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States.
The Journal of Physical Chemistry. B
|May 27, 2011
Summary
Divalent metal cations like calcium and cadmium bind to DNA-functionalized silica surfaces. Magnesium ion binding to DNA is influenced by electrolyte concentration, suggesting specific binding pathways for geochemical and biosensing applications.
Area of Science:
- Interfacial Science
- Biophysical Chemistry
- Oligonucleotide Chemistry
Background:
- Understanding metal cation interactions with DNA is crucial for geochemistry and biosensing.
- Silica/water interfaces functionalized with oligonucleotides provide a model system for studying these interactions.
Purpose of the Study:
- To quantify the binding of various divalent metal cations (Sr(II), Ca(II), Mg(II), Ba(II), Mn(II), Zn(II), Cd(II)) to A(15)T(6) oligonucleotide-functionalized silica/water interfaces.
- To investigate the influence of electrolyte concentration on Mg(II) binding.
- To elucidate Mg(II) speciation and binding pathways.
Main Methods:
- Eisenthal χ((3)) technique for quantifying cation binding.
- Adsorption free energy versus interfacial potential analysis.
Main Results:
- Binding free energies ranged from -31.1(6) kJ/mol (Ba(II)) to -33.8(4) kJ/mol (Ca(II)).
- Ion densities varied from 2(1) ions/strand (Zn(II)) to 11(1) ions/strand (Cd(II)).
- Mg(II) binding free energy showed a linear dependence on electrolyte concentration (-39.3(8) to -27(1) kJ/mol over 1-80 mM).
Conclusions:
- Mg(II) likely binds as a fully hydrated cation, displacing Na+ ions from DNA.
- Three potential Mg(II) binding pathways were identified.
- The quantified binding data serve as a benchmark for computational simulations of cation/DNA interactions.
Related Concept Videos
01:19Complexation Equilibria: The Chelate Effect
In complexation reactions, metal atoms or cations interact with ligands to form donor-acceptor adducts called metal complexes. Ligands that bind through one donor site are monodentate, ligands with two donor sites are bidentate, and those with more than two donor sites are polydentate ligands. For example, ethylene diamine is a bidentate ligand that binds through two nitrogen donor atoms, forming a five-membered ring. EDTA is a polydentate ligand that binds through four oxygen and two nitrogen...
00:43Complexometric Titration: Ligands
Different monodentate and polydentate ligands are used as complexing agents in complexometric titration reactions. The formation of complexes by mono- and bidentate ligands involves two or more intermediate steps, limiting their use as complexing agents. In comparison, polydentate ligands can form complexes with metal ions in a single-step process, facilitating sharper end points. This means polydentate ligands, such as amino carboxylic acid derivatives, are most commonly employed in...
02:42Valence Bond Theory
Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
02:51Metal-Ligand Bonds
The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
01:22EDTA: Chemistry and Properties
Polydentate ligands are most widely used in complexometric titrations because they form more stable complexes with the metal ions than mono- or bidentate ligands due to the chelate effect. Examples of polydentate ligands are ethylenediaminetetraacetic acid (EDTA), crown ethers, and cryptands. The most important feature of optimal polydentate ligands is the ability to form 1:1 complexes in a single-step process. Amino carboxylic acid derivatives are frequently used as complexing agents. EDTA is...
03:02Colors and Magnetism
Color in Coordination Complexes
When atoms or molecules absorb light at the proper frequency, their electrons are excited to higher-energy orbitals. For many main group atoms and molecules, the absorbed photons are in the ultraviolet range of the electromagnetic spectrum, which cannot be detected by the human eye. For coordination compounds, the energy difference between the d orbitals often allows photons in the visible range to be absorbed and emitted, which is seen as colors by the human eye.
When atoms or molecules absorb light at the proper frequency, their electrons are excited to higher-energy orbitals. For many main group atoms and molecules, the absorbed photons are in the ultraviolet range of the electromagnetic spectrum, which cannot be detected by the human eye. For coordination compounds, the energy difference between the d orbitals often allows photons in the visible range to be absorbed and emitted, which is seen as colors by the human eye.