Role of backbones on the interaction of metal ions with deoxyribonucleic acid and peptide nucleic acid: A DFT study

Metal ion interaction with deoxyribonucleic acid and peptide nucleic acid were studied using B3LYP-D3/6-311++g(d,p)//B3LYP/6-31 + G(d) level of theory in aqueous phase employing polarized continuum (PCM) model. This study reports the role of backbones on deoxyribonucleic acid and peptide nucleic acid for complexation with different metal ions. The systematic study performed with DFT calculations reveals that central binding (Type-4) shows the strongest binding compared to the other binding modes because of the involvement of the backbone as well as the nitrogenous bases. The charged backbone of DNA nucleotides contributes significantly towards binding with the metal ions. The deoxyguanosine monophosphate (dGMP) clearly indicates the strongest binding upon complexation with Mg²⁺ (-49.6 kcal/mol), Zn²⁺ (-45.3 kcal/mol) and Cu²⁺ (-148.4 kcal/mol), respectively. The neutral backbone of PNA also assists to complex the metal ions with PNA nucleotides. The Mg²⁺ and Cu²⁺ prefer to bind with the PNA-Cytosine (-32.9 kcal/mol & -132.9 kcal/mol) in central binding mode (type-4). PNA-Adenine-Zn²⁺ (-29.1 kcal/mol) is the preferred binding mode (type-4) compared to other modes of interaction for this metal ion with PNA-Adenine nucleotide. The Cu²⁺ ion showed the superior complexation ability with deoxyribonucleic acid and peptide nucleic acid compared to Mg²⁺ and Zn²⁺ ions. The cation-π complexation with the bases of nucleotides was also obtained with Cu²⁺ ion. The AIM (atoms in molecule) theory has been applied to examine the nature of the interaction of Mg²⁺, Zn²⁺, and Cu²⁺ ion to the deoxyribonucleic acid and peptide nucleic acid. The alkaline earth metal, Mg²⁺ ion shows electrostatic nature while interaction with deoxyribonucleic acid and peptide nucleic acid, however, the transition metal ions (Zn²⁺, Cu²⁺) showed partly covalent nature as well with deoxyribonucleic acid and peptide nucleic acid. The optical properties calculated for the binding of metal ions with deoxyribonucleic acid and peptide nucleic acid showed a diagnostic signature to ascertain the interaction of metal ions with such nucleotides. Cu²⁺ ion showed larger red shifts in the absorption spectrum values upon complexation with the DNAs and PNAs. The calculated results suggest that such metal ions would prefer to bind with the DNA compared to PNA in DNA-PNA duplexes. The preference for the binding of metal ions with DNA nucleotides is largely attributed to the contribution of charged backbones compared to the neutral PNA backbones.

Development of Vibrational Frequency Maps for Nucleobases

Vibrational spectroscopy provides a powerful tool to probe the structure and dynamics of nucleic acids because specific normal modes, particularly the base carbonyl stretch modes, are highly sensitive to the hydrogen bonding patterns and stacking configurations in these biomolecules. In this work, we develop vibrational frequency maps for the C═O and C═C stretches in nucleobases that allow the calculations of their site frequencies directly from molecular dynamics simulations. We assess the frequency maps by applying them to nucleobase derivatives in aqueous solutions and nucleosides in organic solvents and demonstrate that the predicted infrared spectra are in good agreement with experimental measurements. The frequency maps can be readily used to model the linear and nonlinear vibrational spectroscopy of nucleic acids and elucidate the molecular origin of the experimentally observed spectral features.

Application of spectral methods for studying DNA damage induced by gamma-radiation

Spectral methods can provide a variety of possibilities to determine several types of radiation-induced DNA damage, such as nucleobase destruction and local denaturation. DNA UV absorption and CD spectra measured at room temperature undergo noticeable alteration under the action of γ-radiation. We have applied the Spirin method of total nucleobases determination, and have measured the molar extinction coefficient of DNA and DNA CD spectra for solutions with different NaCl concentrations (3mM-3.2M) and containing MgCl₂, exposed to γ-radiation with the doses of 0-10³Gy. The melting temperatures of DNA in irradiated solutions at the doses of 0-50Gy were obtained with the help of spectrophotometric melting. It was found that the amount of destructed nucleobases and radiation-induced loss of DNA helicity significantly decreases with the rise of the ionic strength of the irradiated solution. Substitution of a portion of Na⁺ ions on Mg²⁺ while keeping the total ionic strength constant (μ=5mM) does not affect the considered radiation effects. The role of the structure and composition of the DNA secondary hydration layer in the radiation-induced damages is discussed.