Isoguanine: From Base Pair to Tetrad

Decameric uracil complexes around Li+

Electrospray ionization (ESI) in combination with mass spectrometry (MS) experiments were carried out to study decameric uracil complexes cationized with Li(+) ion. A previous study has shown that, under specific experimental conditions, a particularly intense peak of the decamer U(10)Li(+) is formed, which was referred to as an indication for so-called 'magic number' cluster. In order to gain more insight on the structure of this decameric complex, here, we report experimental studies concerning the kinetics of the fragmentation. In accordance with the new experimental data, structural models were constructed and fully optimized using ab initio and density functional theory quantum chemistry calculations. The theoretical study allowed us to propose a stable gas-phase structure which is compatible with all experimental findings.

Formation of complexes between uracil and calcium ions: an ESI/MS/MS study in combination with theoretical calculations

Cationized uracil clusters around calcium metal ions were generated in the gas phase by electrospray ionization (ESI). A previous study showed that with particular experimental conditions, hexamer, octamer, decamer, dodecamer and tetradecamer uracil clusters are present in high quantities. New experiments were carried out to understand the reasons for the particular stability of these complexes. MS/MS experiments suggested that these uracil clusters belong to the same family. Based on ab initio and DFT quantum chemistry calculations, structures in agreement with experimental results are proposed for these clusters.

The 2'-deoxyadenosine-5'-phosphate anion, the analogous radical, and the different hydrogen-abstracted radical anions: molecular structures and effects on DNA damage

The 2'-deoxyadenosine-5'-phosphate (5'-dAMP) anion and its related radicals have been studied by reliably calibrated theoretical approaches. This study reveals important physical characteristics of 5'-dAMP radical related processes. One-electron oxidation of the 5'-dAMP anion is found on both the phosphoryl group and the adenine base with electron detachment energies close to that of phosphate. Partial removal of electron density from the adenine fragment leads to an extended pi system which includes the amine group of the adenine. Although the radical-centered carbon increases the extent of bonding with its adjacent atoms, it usually weakens the chemical bonds between the atoms at the alpha- and beta-positions. This tendency should be important in predicting the reactivity of the sugar-based radicals. The overall stability sequence of the H-abstracted 5'-dAMP anionic radicals is consistent with the analogous results for the H-abstracted neutral radicals of the adenosine nucleoside: aliphatic radicals > aromatic radicals. The negatively charged phosphoryl group attached to atom C(5)' of the ribose does not change this energetic sequence. All the H-abstraction produced 5'-dAMP radical anions are distonic radical anions. Studies have shown that the charge-radical-separating feature of the distonic radical anions is biologically relevant. This result should be important in understanding the reactive properties of these H-abstraction-produced anion radicals.

Density functional study of isoguanine tetrad and pentad sandwich complexes with alkali metal ions

Isoguanine tetraplexes and pentaplexes contain two or more stacked polyads with intercalating metal ions. We report here the results of a density functional study of sandwiched isoguanine tetrad and pentad complexes consisting of two polyads with Na(+), K(+) and Rb(+) ions at the B3LYP level. In comparison to single polyad metal ion complexes, there is a trend towards increased non-planarity of the polyads in the sandwich complexes. In general, the pentad sandwiches have relatively planar polyad structures, whereas the tetrad complexes contain highly non-planar polyad building blocks. As in other sandwich complexes and in metal ion complexes with single polyads, the metal ion-base interaction energy plays an essential role. In iG sandwich structures, this interaction energy is slightly larger than in the corresponding guanine sandwich complexes. Because the base-base interaction energy is even more increased in passing from guanine to isoguanine, the isoguanine sandwiches are thus far the only examples where the base-base interaction energy is larger than the base-metal ion interaction energy. Stacking interactions have been studied in smaller models consisting of two bases, retaining the geometry from the complete complex structures. From the data obtained at the B3LYP and BH&H levels and with Møller-Plesset perturbation theory, one can conclude that the B3LYP method overestimates the repulsion in stacked base dimers. For the complexes studied in this work, this is only of minor importance because the direct inter-tetrad or inter-pentad interaction is supplemented by a strong metal ion-base interaction. Using a microsolvation model, the metal ion preference K(+) approximately Rb(+) > Na(+) is found for tetrad complexes. On the other hand, for pentads the ordering is Rb(+) > K(+) > Na(+). In the latter case experimental data are available that agree with this prediction.

Characterization of the monovalent ion position and hydrogen-bond network in guanine quartets by DFT calculations of NMR parameters

Conformational stability of G-quartets found in telomeric DNA quadruplex structures requires the coordination of monovalent ions. Here, an extensive Hartree-Fock and density functional theory analysis of the energetically favored position of Li+, Na+, and K+ ions is presented. The calculations show that at quartet-quartet distances observed in DNA quadruplex structures (3.3 A), the Li+ and Na+ ions favor positions of 0.55 and 0.95 A outside the plane of the G-quartet, respectively. The larger K+ ion prefers a central position between successive G-quartets. The energy barrier separating the minima in the quartet-ion-quartet model are much smaller for the Li+ and Na+ ions compared with the K+ ion; this suggests that K+ ions will not move as freely through the central channel of the DNA quadruplex. Spin-spin coupling constants and isotropic chemical shifts in G-quartets extracted from crystal structures of K+- and Na+-coordinated DNA quadruplexes were calculated with B3LYP/6-311G(d). The results show that the sizes of the trans-hydrogen-bond couplings are influenced primarily by the hydrogen bond geometry and only slightly by the presence of the ion. The calculations show that the R(N2N7) distance of the N2-H2...N7 hydrogen bond is characterized by strong correlations to both the chemical shifts of the donor group atoms and the (h2)J(N2N7) couplings. In contrast, weaker correlations between the (h3)J(N1C6') couplings and single geometric factors related to the N1-H1...O6=C6 hydrogen bond are observed. As such, deriving geometric information on the hydrogen bond through the use of trans-hydrogen-bond couplings and chemical shifts is more complex for the N1-H1...O6=C6 hydrogen bond than for the N2-H2...N7 moiety. The computed trans-hydrogen-bond couplings are shown to correlate with the experimentally determined couplings. However, the experimental values do not show such strong geometric dependencies.

Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads

Nucleic acid tetraplexes and lipophilic self-assembling G-quadruplexes contain stacked base tetrads with intercalated metal ions as basic building blocks. Thus far, quantum-chemical studies have been used to explore the geometric and energetic properties of base tetrads with and without metal ions. Recently, for the first time, work on a sandwiched G-tetrad complex has been studied. We report here results of a systematic B3LYP density functional study on sandwiched G-, C-, U-, and T-tetrads with Na+ and K+ at different symmetries that substantially extend the recent work. The results include detailed information on total energies as well as on metal ion tetrad and base-base interaction energies. The geometrical parameters of the sandwiched metal ion complexes are compared to both experimental structures and to calculated geometries of complexes of single tetrads with metal ions. A microsolvation model explains the ion selectivity preference of K+ over Na+ in a qualitative sense.