Infrared Absorption Detection of Metal Ion-Deoxyguanosine Monophosphate Binding: Experimental and Theoretical Study

Abstract

Metal ion interactions with nucleic acids attract attention because of the environmental and biological consequences. The formation of the complex is often monitored by the vibrational spectroscopy. To identify characteristic binding patterns and marker bands on a model DNA component, infrared absorption spectra of the deoxyguanosine monophosphate complexes with Na + , Mg 2+ , Ca 2+ , Ni 2+ , Cu 2+ , Zn 2+ , and Cd 2+ cations were recorded and interpreted on the basis of density-functional computations. The aqueous environment was simulated by continuum and combined continuum-explicit solvent models. For the binding to the N7 position of the guanine base, the computation predicted a characteristic frequency upshift and splitting of the 1578 cm -1 band, which is in accord with available experimental data. Contrary to the expectation, the modeling suggests that the binding to the carbonyl group might not be detectable, as the metal causes smaller spectral changes if compared to the hydrogen-bound water molecules. The binding to the phosphate group causes significant spectral changes in the sugar-phosphate vibrating region (∼800-1200 cm -1 ), but also notable frequency shifts of the carbonyl vibrations. The Cu 2+ and Zn 2+ ions induced the largest alterations in observed vibrational absorption, which corresponds to the calculated strong interaction energies in the N7-complexes and to previous experimental experience. Additional changes in the vibrational spectra of the copper complexes were observed under high metal concentration, corresponding to the simultaneous binding to the phosphate residue. The two-step Cu 2+ binding process was also confirmed by the microcalorimetry titration curve. The computations and combination of more techniques thus help us to assign and localize spectral changes caused by the metal ion binding to nucleic acids. IntroductionComplexes of metal ions with nucleic acids participate in various biological processes, such as DNA replication and transcription, enzymatic cleavages, mutagenesis, carcinogenesis, and DNA packing in a living cell and also stabilize particular nucleic acid secondary structures. 1-6 A vast number of experimental and theoretical studies have been dedicated to metal interactions with nucleic acids and their components. [5][6][7][8][9][10] In the present work we systematically investigate interactions of some common metal ions with deoxyguanosine monophosphate (dGMP) as a model system, in order to better explain previously observed changes in infrared absorption (IR) spectra of nucleic acids upon the interaction with the metals.Being relatively simple and widely available, infrared spectroscopy provided precious information about the interaction of metal ions with nucleic acids (e.g., see refs 11-23). Detailed structural information could be obtained from the IR spectra when observed bands were assigned to particular bonds or DNA functional groups. [24][25][26][27] In practice, however, the assignment is complicated by solvent interference, overlapped and naturally bro...

Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides

“…We have recently found that the popular for biomolecular calculations hybrid B3LYP 99 functional when used with COSMO, results in a very similar bandshape as BPW91, but produces slightly up-shifted frequencies compared to the latter, thus providing closer match with the experimental values. 86,128 At the same time, BPW91 functional produces frequencies closer to the experiment when used for vacuum or explicit solvent model calculations. 86,104,115,128 Refinement of a Molecular Secondary Structure Based on the CCT Method…”

“…86,128 At the same time, BPW91 functional produces frequencies closer to the experiment when used for vacuum or explicit solvent model calculations. 86,104,115,128 Refinement of a Molecular Secondary Structure Based on the CCT Method…”

“…Similar trend was noticed in other calculations where the BPW91 functional was used in combination with the COSMO solvent model. 128 This shift might be contributed to slight overestimation of the implicit solvent effect on the polar groups by BPW91. We have recently found that the popular for biomolecular calculations hybrid B3LYP 99 functional when used with COSMO, results in a very similar bandshape as BPW91, but produces slightly up-shifted frequencies compared to the latter, thus providing closer match with the experimental values.…”

Bioinspired interactions studied by vibrational circular dichroism

“…A number of previously published VCD experimental materials is treated mostly empirically, without an attempt to model a structural consequence of interactions more exactly. Recently, 19 the DFT calculation of IR absorption was performed on the guanosine monophosphate interaction with biogenetic metals by taking into account the implicit and explicit solvent effect of water. Such calculation can be taken as a first step, which can also expand VCD in the future.…”

Structural Analysis of the Cu-binding Site in the [Cu·dCMP·dCMP-H]1-Complex

“…[6][7][8][9][10][11] Metal cations prefer the phosphate anions; however, several experimental results showed that the base moieties had also been regarded as the preferred binding sites in the formation of [M·(nucleoside monophosphate)] complexes. As a member of [M·(nucleoside monophosphate)] complexes, [M·dCMP] (dCMP = deoxycytidine monophosphate) complexes have been extensively studied.…”