Guanine Molecules Research Articles

Binding of singlet oxygen with a stacked guanine dimer

AbstractGeometry optimization calculations were performed using the B3LYP/6‐31+G* method on the complexes of 1O2 and 3O2 molecules with a stacked dimer of planar guanine, varying the distance (D) between the planes of the guanine molecules. In this process, geometries of the guanine molecules were held fixed, D was fixed at different values, while the bond lengths of 1O2 and 3O2 as well as their orientations with respect to the guanine molecules were optimized for each value of D. The complexes in their most stable geometries were solvated in water using the integral equation formalism of the polarized continuum model of the self‐consistent reaction field theory. In gas phase, the most stable complex between 1O2 and the guanine dimer (2G.1O2) is formed when D is about 6 Å, while the most stable complex between 3O2 and the guanine dimer (2G.3O2) is formed when D is about 3.75 Å. In the minimum total energy geometry of 2G.1O2, 1O2 is located between the guanine molecules, above the imidazole ring of one of them. However, in the minimum total energy geometry of 2G.3O2, 3O2 is located outside the stack of guanine molecules, near the amino group of one of them. The solvation calculations showed that in aqueous media, 1O2 would bind with the stacked guanine dimer more strongly than in gas phase, while 3O2 would not bind with the same. The mode of binding of 1O2 with the stacked guanine dimer is such that it seems that 1O2 would replace one basepair in DNA, as happens in the intercalative mode of binding of drugs and other molecules, and it can lead to the formation of 8‐oxoguanine that has a mutagenic nature. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Solvation of Al−Guanine Complexes with NH3: A Theoretical Study

Geometry optimizations on complexes composed of an Al atom, a guanine molecule, and an ammonia molecule have been performed with density functional methods. In the most stable structures, the ammonia molecule forms hydrogen bonds with previously studied Al-guanine complexes. The two lowest structures correspond to an unusual tautomer of guanine in which both N atoms of the five-membered ring, N7 and N9, are protonated. Within 3 kcal/mol in energy lie two additional structures in which a proton is shifted from N9 to N3. Ionization energies calculated with ab initio, electron-propagator methods for the two latter structures are in close agreement with the experimentally observed ionization threshold. Higher ionization energies are obtained for the two lowest structures. Dyson orbitals for the lowest ionization energies are guanine π* functions. The order of isomers in the cationic species is different from that of the neutrals. Energies of ammonia dissociation are approximately equal for all forms of the Al-guanine-NH 3 complex, except for a structure with an Al-NH 3 dative bond.

Electronic properties of guanine-based nanowires

We present a first-principles study of the electronic and conduction properties of a few classes of nanowires composed of guanine (G) molecules, self-assembled in different geometries. We first analyze the effect of the vertical π–π interaction in model G-stack columns. Then, we exploit the results obtained from those models to interpret the features of realistically stacked and hydrogen-bonded aggregates, namely the guanine quadruple helices and the planar ribbons. With respect to natural DNA, the different structures drastically affect the bonding pattern among the bases, introducing novel features in the electronic properties of the systems. These supramolecular G-aggregates, alternative to DNA, are expected to show interesting properties for molecular electronics applications.

Electrochemical characterization of a mixed self-assembled monolayer of 6-thioguanine and guanine on a mercury electrode

A monolayer constituted by chemisorbed 6-thioguanine and physisorbed guanine molecules was formed on a hanging mercury drop electrode from deoxygenated solutions of 6-thioguanine (6TG) and guanine (G). The mixed monolayer was characterized by chronoamperometry, cyclic voltammetry, and phase-sensitive ac voltammetry under in situ conditions, and the experimental data revealed a compact packing of molecules in the film. Ex situ measurements in the presence of dissolved oxygen proved that the mixed monolayer is stable in solutions lacking 6TG and G.

Electrochemical characterization of a mixed self-assembled monolayer of 6-thioguanine and guanine on a mercury electrode

A monolayer constituted by chemisorbed 6-thioguanine and physisorbed guanine molecules was formed on a hanging mercury drop electrode from deoxygenated solutions of 6-thioguanine (6TG) and guanine (G). The mixed monolayer was characterized by chronoamperometry, cyclic voltammetry, and phase-sensitive ac voltammetry under in situ conditions, and the experimental data revealed a compact packing of molecules in the film. Ex situ measurements in the presence of dissolved oxygen proved that the mixed monolayer is stable in solutions lacking 6TG and G.

Vacuum ultraviolet spectroscopic ellipsometry investigations of guanine layers on H-passivated Si(1 1 1) surfaces

Guanine layers deposited by organic molecular beam deposition onto H-passivated Si(1 1 1) substrates under ultra-high vacuum conditions were investigated by means of vacuum ultraviolet spectroscopic ellipsometry. The experimental absorption bands are compared to the transition energies calculated for a single guanine molecule using time-dependent density functional theory in the 6-31G(d) variational basis set at the B3LYP level of theory. Taking into account that the imaginary part of the effective dielectric function measured in ellipsometry is affected by thickness interferences and the impact of the substrate, the calculated oscillator strengths of the higher transition energies are in reasonable agreement with the experimental features.

Self-assembled oligonucleotide semiconductor conjugated to GaN nanostructures for biophotonic applications

ABSTRACTWe investigate the optical properties of a new class of wide-bandgap semiconductor based biomaterial system. We have synthesized a guanosine derivative with a strong dipole moment, which self-assemble in ∼ 50 –100 nm confined pits to form a ribbon like semiconductor structure (SAGC). SAGC were successfully self-assembled on GaN/AlN QD matrix and the luminescence from GaN QDs can be resonantly transferred to the SAGC molecules resulting in a significant enhancement in emission from the guanine molecules. We also propose the design of ultraviolet-visible photonic bandgap structures based on hybrid SAGC-GaN photonic crystal.

Solution, solid state and biological characterization of ruthenium(III)-DMSO complexes with purine base derivatives

Two new complexes of Ru(III) with purine base derivatives, [ mer-RuCl 3(acv)(DMSO-S)(C 2H 5OH)] · C 2H 5OH ( 1) (acv=acyclovir, DMSO=dimethyl sulfoxide) and [ trans-RuCl 4(guaH)(DMSO-S)] · 2H 2O ( 2) (guaH=protonated molecule of guanine), were prepared from the same Ru(III) precursor, [ trans-RuCl 4(DMSO-S) 2] −, by substitution of one DMSO-S. Coordination of acv induced also replacement of one chloride by an ethanol molecule. This reactivity difference was explained by striking contrasts in the hydrogen bonding schemes of the two complexes, evidenced in their X-ray crystal structures. In 1 the guanine derivative acyclovir is coordinated to ruthenium through the N(7) atom, while in 2 the protonated guanine molecule is bound through the N(9) atom. Both complexes were also characterized by various physico-chemical methods in the solid state and in the solution. In vitro, the biological activity of 2 and of the previously described complexes [ mer-RuCl 3(acv)(DMSO-S)(CH 3OH)] · 0.5CH 3OH ( 3) and [ mer-RuCl 3(acv)(DMSO-S)(H 2O)] · H 2O ( 4) on tumour cells appear to be very similar to that of NAMI-A (NAMI-A=[ImH][ trans-RuCl 4(DMSO-S)Im]). All compounds are only weakly active on tumour cell proliferation but show an interesting proadhesive effect that suggest possible activity on tumour malignancy.

Effect of static electric field on the HF band structure of a guanine stack

AbstractPutting dipoles in different arrangements in the planes of the guanine molecules in a stack in DNA B conformation, in a model calculation the effect of the electric field on the ab initio Hartree–Fock band structure was studied. The calculations were performed at the stacking distances 3.12, 3.36, and 3.60 Å, respectively. The electric fields of the dipoles decreased the very broad conduction band of a guanine stack, caused some shifts in the band structure, but hardly influenced the fundamental gap. The computed effective masses at the physically interesting band edges correspond to the bandwidth changes due to the electric field. The electric field significantly influences the deformation potentials at the band edges and with it the transport properties of the guanine stack. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004

Thermoelectric effect in molecular electronics

We provide a theoretical estimate of the thermoelectric current and voltage over a Phenyldithiol molecule. We also show that the thermoelectric voltage is (1) easy to analyze, (2) insensitive to the detailed coupling to the contacts, (3) large enough to be measured and (4) give valuable information, which is not readily accessible through other experiments, on the location of the Fermi energy relative to the molecular levels. The location of the Fermi-energy is poorly understood and controversial even though it is a central factor in determining the nature of conduction (n- or p-type). We also note that the thermoelectric voltage measured over Guanine molecules with an STM by Poler et al., indicate conduction through the HOMO level, i.e., p-type conduction.

Ab Initio Study of the Prototropic Tautomerism of Cytosine and Guanine and Their Contribution to Spontaneous Point Mutations

High-level quantum-chemical and quantum-dynamics calculations are reported on the tautomerization equilibria and rate constants of isolated and monohydrated cytosine and guanine molecules. The results are used to estimate the fraction of the bases present in the cell during DNA synthesis as the unwanted tautomers that forms irregular base pairs, thus giving rise to a spontaneous GC → AT point mutation. A comparison of the estimated mutation frequencies with the observed frequency in E. coli is used to analyze two proposed mechanisms, differing in the degree of equilibration reached in the tautomerization reaction. It was found that the fraction of the rare tautomer in monohydrated complex of cytosine as well as guanine significantly exceed the amount responsible for the observed values of the GC → AT mutations. In the absence of water the equilibrium concentration of tautomeric forms is relatively large, but the barrier to their formation is high. It is possible that the mechanism in which a high tautomerization barrier keeps the tautomeric transformation far from a state of equilibrium is more likely than a mechanism in which water and/or polymerases produce a low equilibrium concentration of the tautomeric forms.

Self-assembled guanine ribbons as wide-bandgap semiconductors

We present a first principle study about the stability and the electronic properties of a new biomolecular solid-state material, obtained by the self-assembling of guanine (G) molecules. We consider hydrogen-bonded planar ribbons in isolated and stacked configurations. These aggregates present electronic properties similar to inorganic wide-band gap semiconductors. The formation of Bloch-type orbitals is observed along the stacking direction, while it is negligible in the ribbon plane. Global band-like conduction may be affected by a dipole-field which spontaneously arises along the ribbon axis. Our results indicate that G-ribbon assemblies are promising materials for biomolecular nanodevices, consistently with recent experimental results.

Ab initiostudy of model guanine assemblies: The role ofπ−πcoupling and band transport

Several assemblies of guanine molecules are investigated by means of first-principles calculations. Such structures include stacked and hydrogen-bonded dimers, as well as vertical columns and planar ribbons, respectively, obtained by periodically replicating the dimers. Our results are in good agreement with experimental data for isolated molecules, isolated dimers, and periodic ribbons. For stacked dimers and columns, the stability is affected by the relative charge distribution of the $\ensuremath{\pi}$ orbitals in adjacent guanine molecules. $\ensuremath{\pi}\ensuremath{-}\ensuremath{\pi}$ coupling in some stacked columns induces dispersive energy bands, while no dispersion is identified in the planar ribbons along the connections of hydrogen bonds. The implications for different materials comprised of guanine aggregates are discussed. The band structure of dispersive configurations may justify a contribution of band transport (Bloch type) in the conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations band transport should be negligible.

The role of dimer formation in the self-assemblies of DNA base molecules on Cu(111) surfaces: A scanning tunneling microscope study

For the purpose of understanding the self-assembly formation mechanism of DNA base molecules, guanine, adenine, cytosine, and thymine molecules were deposited on Cu(111) surfaces, and were observed using a low-temperature (≈80 K) scanning tunneling microscope (STM). Single-molecular-scale STM images revealed that guanine, adenine, and cytosine molecules can form ordered one- and/or two-dimensional unique structures, but thymine molecules, however, randomly aggregate into small clusters. Semiempirical molecular orbital (MO) calculation indicates that there exists predominantly stable dimer structures for the former three molecules, while such phenomena cannot be observed among the possible thymine dimer and even trimer structures. Based on experimental and theoretical results, we have concluded that specific hydrogen-bonded nucleus formation is a decisive process in the two-dimensional self-assembly formation of DNA base molecules on Cu(111) surfaces.

Conformational flexibility of di- and tetrahydropyrimidine rings in nucleic acid bases. An ab initio [formula omitted] study

Using ab initio HF 6–31 G∗∗ method of calculation it is shown that dihydropyrimidinone and tetrahydropyrimidin-2,4-dione rings in the uracil, thymine, cytosine, isocytosine and guanine molecules are not conformationally rigid. A change in the relevant torsion angles of ± 20° causes an energy increase of about 1.5 kcal/mol. The main reason for conformational flexibility is the non-aromatic and anti-aromatic character of the cyclic π-systems in these molecules. A decrease in the exocyclic double bond polarity and the presence of electron-donating substituents increase the non-rigidity of the pyrimidine rings.

Infrared and Raman spectra of alkylated guanine derivatives

The infrared and Raman spectra of 9-methylguanine, 9-ethylguanine and 1,9-dimethylguanine in the solid state are reported and discussed. Hydrogen bonds in the solid guanine derivatives bring about strong perturbations in the spectra from those of the isolated molecules. The results are discussed in terms of structural data from X-ray diffraction studies. The infrared spectra of guanine derivatives are compared with the spectra of these molecules isolated in low temperature argon matrices. This comparison allows the determination of the frequency changes due to hydrogen bonding and the interpretation of their vibrational spectra in terms of the normal modes calculated for the isolated guanine molecule.

Fast atom bombardment mass spectrometric (FAB MS) study of the molecular structure of DI-Μ-guanino-Μ-guanine BIS(CIS-Chlorodiammineplatinum(II))

A new compound of cis-chlorodiammineplatinum(II) with normal and deprotonated guanine has been synthesized and studied by FAB MS. The compound has a molecular structure of a binuclear complex. The mass spectrometric behavior of the complex is dictated by the variable valence of platinum and chemical ionization of fragments by protons, as well as by the fact that the guanine molecule bridges the two cis-PtCl(NH3)2 groups by its N7 and OC6 atoms and the two gpanine anions bridge the groups by their N1 and OC6 atoms. The differences in the mutual arrangement of the anions and the guanine molecule are responsible for the formation of the head-to-head and head-to-tail structural isomers.

STM images of guanine on graphite surface and the role of tip–sample interaction

A combined experimental and theoretical study is conducted on guanine molecules adsorbed on graphite substrate. The main effort is to understand the scanning tunneling microscopic images and the effect of scanning tip force on guanine molecules and their images. The force on guanine molecule is determined from the tip-induced deformation in the substrate and is found to be a few nano-Newtons per guanine molecule. A jellium substrate is used to model the graphite substrate in ab initio calculations of electronic density of states. Both the equilibrium height of guanine and tip force on guanine are determined using pseudopotential density functional calculations of system’s total energy. The calculated height of guanine molecule above the substrate is in good agreement with measurements. Electronic states are calculated and it is shown that features in surface density of states are mostly due to admixture with the guanine LUMO and the admixture increases with increasing scanning tip force.

Structural characteristics of the coordination nodes of the anticarcinogenic dimeric complex di-μ-guanine-bis[cis-dichloroaquoplatinum(II)] in the crystalline tetrahydrate

Structural characteristics of coordination nodes in the anticarcinogenic crystalline hydrate of the di-μ-guanine-bis-[cis-dichloroaquoplatinum(II)] dimeric complex were investigated by IR, NMR (1H,13C, and195Pt), and EXAFS methods. The guanine molecules in the keto form of the complex bridge the platinum atoms by the head-to-tail principle, and the coordination nodes are polyhedra of pentaccordinated platinum(II), PtCl2NO2, with the distances R(Pt−Cl)=2.44 A and R(Pt−N(O))=2.06 A. The distances from the platinum atom to the nearest atoms not chemically bonded to the metal are R(Pt−C)=2.86 A and R(Pt−Pt)=5A.

Fast atom bombardment mass-spectrometric study of a paramagnetic platinum oligomer with guanine

The mass-spectrometric behavior of a paramagnetic platinum oligomer with guanine was determined by the fast atom bombardment method. The complex is built of PtCl2 groups linked by guanine molecules into a chain via the imidazole N7 atom and the exocyclic OC6, atom. In a dimethylsulfoxide solution, the degree of oligomerization of the complex is n=4.