Structure and the energy of base pairing in non-natural bases of nucleic acids: the azaguanine-cytosine and azaadenine-thymine base pairs

Modification of DNA damage mechanisms by nitric oxide during ionizing radiation

Nitric oxide ((•)NO) is a very effective radiosensitizer of hypoxic mammalian cells. In vivo (•)NO may have effects on tumor vasculature and hence on tumor oxygenation and it may also interact with radiation-produced radicals to modify DNA lesions. Few studies have addressed this last aspect, and we report here specific base modifications that result from reaction of (•)NO with radicals in DNA bases and in plasmid DNA after irradiation. 2'-Deoxyxanthosine monophosphate and 2'-deoxy-8-azaguanosine monophosphate (8azadGMP) are formed upon γ-irradiation of 2'-deoxyguanosine monophosphate (dGMP) in the presence of micromolar levels of (•)NO in anoxia. In addition, the presence of (•)NO at physiological pH inhibits the formation of the well-described (•)OH-induced oxidation product of dGMP, 8-oxo-2'-deoxyguanosine monophosphate. Single-strand breaks are induced in plasmid DNA when γ-irradiated in anoxia, whereas in the presence of (•)NO the number of breaks is reduced by approximately threefold, and evidence is shown for the formation of 8azadGMP in these plasmids. The consequence of the base modifications by (•)NO are as yet unknown although additional breaks are revealed in irradiated plasmid DNA after treatment with glycosylases involved in base excision repair. V79-4 cells irradiated in anoxia show an enhancement in the number of γH2AX foci when (•)NO is present, particularly evident a few hours postirradiation, indicative of the formation of replication-induced DNA damage. We propose that the consequence of (•)NO-induced base modifications in anoxia contributes to its radiosensitization of cells.

Theoretical investigation on DNA/RNA base pairs mediated by copper, silver, and gold cations

B3LYP density functional based computations were performed in order to characterize the interactions present in some Cu(+), Ag(+), and Au(+) metal ion-mediated DNA and RNA base pairs from both structural and electronic points of view. Examined systems involve as ligands canonical Watson-Crick, Hoogsteen and Wobble base pairs. Two artificial Hoogsteen base pairs were also taken into account. Binding energy values indicate that complexes involving silver cations are less stable than those in which copper or gold are present, and propose a similar behaviour for these two latter ions. The nature of the bond linking metal ions and bases was described by the NBO analysis that suggests metal coordinative interactions to be covalent. An evaluation of the dispersion contributions for the investigated systems was performed with the B3LYP-D3 functional.

8-Azaguanine reporter of purine ionization states in structured RNAs

The fluorescent nucleotide analogue 8-azaguanosine-5'-triphosphate (8azaGTP) is prepared easily by in vitro enzymatic synthesis methods. 8azaGTP is an efficient substrate for T7 RNA polymerase and is incorporated specifically opposite cytosine in the transcription template, as expected for a nucleobase analogue with the same Watson-Crick hydrogen bonding face as guanine. 8-Azaguanine (8azaG) in oligonucleotides also is recognized as guanine during ribonuclease T1 digestion. Moreover, replacement of guanine by 8azaG does not alter the melting temperature of base-paired RNAs significantly, evidence that 8azaG does not disrupt stacking and hydrogen bonding interactions. 8azaGTP displays a high fluorescent quantum yield when the N1 position is deprotonated at high pH, but fluorescence intensity decreases significantly when N1 is protonated at neutral pH. Fluorescence is quenched 10-fold to 100-fold when 8azaG is incorporated into base-paired RNA and remains pH-dependent, although apparent pKa values determined from the pH dependence of fluorescence intensity shift in the basic direction. Thus, 8azaG is a guanine analogue that does not perturb RNA structure and displays pH-dependent fluorescence that can be used to probe the ionization states of nucleobases in structured RNAs. A key application will be in determining the ionization state of active site nucleobases that have been implicated in the catalytic mechanisms of RNA enzymes.

Accurate interaction energies of hydrogen-bonded nucleic acid base pairs

Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. The study presents reference ab initio structures and interaction energies of selected base pairs with binding energies ranging from -5 to -47 kcal/mol. The molecular structures are obtained using the RI-MP2 (resolution of identity MP2) method with extended cc-pVTZ basis set of atomic orbitals. The RI-MP2 method provides results essentially identical with the standard MP2 method. The interaction energies are calculated using the Complete Basis Set (CBS) extrapolation at the RI-MP2 level. For some base pairs, Coupled-Cluster corrections with inclusion of noniterative triple contributions (CCSD(T)) are given. The calculations are compared with selected medium quality methods. The PW91 DFT functional with the 6-31G basis set matches well the RI-MP2/CBS absolute interaction energies and reproduces the relative values of base pairing energies with a maximum relative error of 2.6 kcal/mol when applied with Becke3LYP-optimized geometries. The Becke3LYP DFT functional underestimates the interaction energies by few kcal/mol with relative error of 2.2 kcal/mol. Very good performance of nonpolarizable Cornell et al. force field is confirmed and this indirectly supports the view that H-bonded base pairs are primarily stabilized by electrostatic interactions.