Y(III) Interactions with Guanine Oligonucleotides Covalently Attached to Aqueous/Solid Interfaces

Abstract

The binding of Y(III) ions to surface-immobilized single-stranded 20-mers of guanine was studied using the Eisenthal χ((3)) technique and AFM. The free energy of binding for Y(III) to the G(20) sequence was found to be -39.5(8) kJ/mol. Furthermore, yttrium binds much more strongly to surface-immobilized oligonucleotides than the divalent metals previously reported. At maximum surface coverage, Y(III) ion densities range between one to three ions bound per strand. Comparatively, Mg(II) binds to the G(20)-functionalized interface in much higher ion densities. This result may be explained, in part, by the larger hydration sphere radius of Y(III) compared to that of Mg(II). The ion loading and binding free energy results, in conjunction with other surface and bulk aqueous phase studies, suggest that a fully hydrated +2 or +3 yttrium ion binds to the oligonucleotides through an outer-sphere mechanism. Tapping mode AFM results indicate that oligonucleotide height does not appreciably decrease following Y(III) binding. These results, together with the low ion densities for Y(III) ions, indicate that Y(III) strand loading may not significantly decrease the intrastrand Coulombic repulsions in order to cause a significant decrease in oligomer height.

Biomolecular Structure at Solid–Liquid Interfaces As Revealed by Nonlinear Optical Spectroscopy

“…This process, known as electric field induced second harmonic (EFISH) generation, has been demonstrated to be well suited to the determination of p K a values of protonation sites at oxide–water interfaces, the measurement of the isoelectric point, , and, as shown later in this review, the measurement of cation–DNA binding energies. − All of these studies rely on measurment of increased signal that occurs with charge buildup at the interface.…”

“…Most research on the interaction of ions with DNA at interfaces has been done by the SHG χ (3) method − since its signal is related to the charge of the interface. In 2011 the Geiger group demonstrated that the Eisenthal method was well-suited to study metal ion interaction with ssDNA at the silica–water interface .…”

“…A recent study looked at the binding of a trivalent metal cation, Y 3+ , on ssDNA tethered to silica. The strands, made of 20 guanine nucleotides, were analyzed by the SHG χ (3) method . Guanine was used because of it has the strongest binding with cations .…”

“…The strands, made of 20 guanine nucleotides, were analyzed by the SHG χ (3) method. 72 Guanine was used because of it has the strongest binding with cations. 70 The binding energy of Y 3+ on G 20 was found to be −39.5 kJ/mol, showing a much stronger binding than any of the cations studied previously.…”

Interaction of Magnesium Ions with Pristine Single-Layer and Defected Graphene/Water Interfaces Studied by Second Harmonic Generation

“…Tracking the change of I SHG with increasing electrolyte concentration can produce valuable interface specific parameters, such as surface charge density, interfacial potential, and subsequently thermodynamic binding parameters. By applying an appropriate surface complexation model, the χ (3) method has been successfully utilized to determine these important interface specific parameters for a variety of systems including oxides, ,,,− DNA, − and lipid bilayers …”