Guanine Molecules Research Articles

Interaction and damage of nucleobases of DNA and RNA caused by silicon nanoparticle and crystalline silica: First principles study

We use density functional theory (DFT) to report the interaction of silicon nanoparticle and crystalline silica with the nucleobases of DNA/RNA-adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U). We obtain and analyse the binding energies, structural parameters and charge transfer to determine the strength between silicon cluster/quartz and nucleobases. The results show that the strength of the silicon cluster interaction with the nucleobases molecules follows the order G > C > U > A > T and the quartz-nucleobases interaction follows the order G > U > T > C > A. The amount of charge transferred from nucleobases to silicon cluster and quartz, is the highest in case of silicon-guanine and quartz-guanine complex and is the lowest in case of the silicon-thymine and quartz-thymine complex. Charge transfer trend is reversed in case of silicon-uracil and quartz-uracil complex. The computed results show that the silicon cluster made maximum damage to guanine molecule while its interaction with the uracil is the lowest.

Ionization of guanine, adenine and thymine molecules by electron impact

The method and results of the study of positive ions yield in the mass-spectrometric investigations by electron impact ionization of molecules of guanine, adenine and thymine are described. Mass spectrum obtained by electron impact has been measured in a crossed electron–molecule beam experiment ionization at the electron energy 70 eV. The ionization energy of the molecule and the appearance potential of some fragment ions were obtained. The mass spectra and fragmentation schemes of adenine and thymine molecules by electron impact were analyzed. The analysis of measured mass spectra is carried out, schemes of fragmentation of guanine, adenine and thymine molecules are proposed, which illustrate the most probable channels for the formation of ionic fragments in an electron impact, when the energy of the incident electrons is much higher than the ionization potential of the molecule. An explanation of the behaviours of the obtained temperature dependences of ions can be due to the difference in the character of the formation and fragmentation of the guanine, thymine and adenine molecules by electron impact.

Nanosized iron telluride for simultaneous nanomolar voltammetric determination of dopamine, uric acid, guanine and adenine

Herein, an efficient electrochemical sensor based on nano-sized iron telluride material (FeTe2) have been developed for the first time for simultaneous nanomolar determination of dopamine, uric acid, guanine and adenine molecules.

Molecular SIMS Ionization Probability Studied with Laser Postionization: Influence of the Projectile Cluster

The formation probability of (quasi-)molecular secondary ions released from an organic film under bombardment with a 20 keV cluster ion beam is investigated using combined time-of-flight secondary ion and neutral mass spectrometry (ToF-SIMS/SNMS) experiments. The emitted neutral molecules are postionized after their ejection using strong-field photoionization in an intense short infrared laser pulse. Comparing the (quasi)-molecular secondary ion signal with that of the corresponding neutral molecules, the ionization probability of sputtered intact coronene and guanine molecules is determined. The results are compared between two different projectile cluster ions, namely (i) C60+ and (ii) Arn+ with n ∼ 1000. It is shown that both projectiles deliver different SNMS spectra, indicating pronounced differences in the collision-induced fragmentation of the emitted molecules. For guanine, the ionization probability obtained with both projectiles is of the same order of magnitude (∼10–3), with the fullerene cluster producing a slightly larger ionization efficiency than the rare gas cluster. For coronene, on the other hand, a substantially lower ionization efficiency is found for the gas cluster projectile.

Potential of metal–fullerene hybrids as strong nanocarriers for cytosine and guanine nucleobases: A detailed DFT study

In this article, the adsorption of cytosine and guanine molecules on the surface of Cr-doped C20 fullerene (C19Cr) and Ni-doped C20 fullerene (C19Ni) are studied using first-principles density functional theory (DFT) calculations. In order to thoroughly comprehend the influences of the molecules on the metal-fullerene complexes, the geometric parameters, the binding energies, transferred charges, the magnitude of dipole moments, thermochemical parameters, frontier molecular orbitals, and the global indices of activities are calculated. The results highlighted that the interactions of both cytosine and guanine molecules with metal-fullerene complexes are highly exothermic, suggesting that these molecules might be chemisorbed on their adsorbents. The C19Cr exhibits a better adsorption behavior toward the molecules compared to C19Ni, and cytosine has the higher binding energies with metal-fullerene complexes in comparison with guanine. Further analyses showed that the C19Cr experiences significant changes in its electronic properties upon adsorption of the cytosine molecule. However, the small variations in the electronic properties of C19Ni after complexation with guanine indicate that this complex is not sensitive to the guanine. Furthermore, the results of frontier molecular orbital reveal the strong (moderate) interactions between the C19Cr with the cytosine (guanine) molecule and moderate (weak) interactions between the C19Ni with the cytosine (guanine) molecule. Therefore, the C19Cr and C19Ni have moderate sensitivities to cytosine and guanine molecules. More excitingly, our findings divulge promising potential of the Cr-fullerene complex as a biochemical adsorbent for cytosine.

A DFT investigation on interactions between asymmetric derivatives of cisplatin and nucleobase guanine

The interactions of hydrolysis products of cisplatin and its asymmetric derivatives cis- and trans-[PtCl2(iPram)(Mepz)] with guanine were studied using DFT methods. These interactions are dominated by electrostatic effects, namely hydrogen bond contributions and there exists a charge flow from H-atoms of ligands to the O-atoms of guanine. The replacement of NH3 moieties by larger functional groups accompanies with a moderate reaction between PtII and guanine molecule, diminishing the cytotoxicity of the drug. The asymmetric and symmetric NH2 stretching modes of complexes having strong hydrogen bond interactions are red shifted importantly as compared to complexes without presence of hydrogen bond interactions.

Ionization Probability in Molecular Secondary Ion Mass Spectrometry: Protonation Efficiency of Sputtered Guanine Molecules Studied by Laser Postionization

The prospect of improved secondary ion yields for secondary ion mass spectrometry (SIMS) experiments drives innovation of new primary ion sources, instrumentation, and postionization techniques. An important factor affecting the detection sensitivity in molecular SIMS and other desorption techniques as well is believed to be the poor ionization probability of a sputtered molecule, a value which is often assumed to be as low as 10–5 but at present is basically unknown. In order to estimate how much headroom there is for future developments toward strategies aimed at enhancing the ionization probability, we study the protonation efficiency of sputtered guanine molecules for formation of [M + H]+ secondary ions using strong field laser postionization (LPI) to detect the corresponding neutral molecules. In order to allow a quantitative comparison of secondary ion and neutral yields, the postionization signal is corrected for undersampling of the principally detectable plume of sputtered neutral particles by t...

On‐Surface Dual‐Response Structural Transformations of Guanine Molecules and Fe Atoms

Structural transformation of metal-organic nanostructures holds great promise for structural diversity and flexibility and opens the way towards an adaptive and evolutive chemistry owing to the dynamic characteristic of coordination bonds. It is thus generally interesting and also challenging to develop systems showing reversible structural transformations which involve multiple metal-organic motifs on surfaces. Here, we have successfully constructed a system that presents structural transformations on a solid surface, in which controllable formation of multiple metal-organic nanostructures (with different coordination binding modes by use of distinct binding sites) in response to both metal atoms and molecules is achieved at room temperature (RT) under ultrahigh vacuum (UHV) conditions. The key to making these interconversions successful is the intrinsic dynamic characteristic of coordination bonds together with the coordination priority and diversity.

Mobility enhancement of organic field-effect transistor based on guanine trap-neutralizing layer

We introduced a nucleic acid component guanine as a trap-neutralizing layer between silicon dioxide gate dielectric and a pentacene semiconducting layer to obtain increased field-effect mobility in organic field-effect transistors (OFETs). A tripling of the field-effect mobility, from 0.13 to 0.42 cm2/V s, was achieved by introducing a 2 nm guanine layer. By characterizing the surface morphology of pentacene films grown on guanine, we found that the effect of guanine layer on the topography of pentacene film was not responsible for the mobility enhancement of the OFETs. The increased field-effect mobility was mainly attributed to the hydrogen bonding capacity of otherwise unassociated guanine molecules, which enabled them to neutralize trapping sites on the silicon dioxide surface.

Adsorption of guanine at the interface electrode-acetic buffer solution and its influence on zinc cation electroreduction

Guanine plays an important role in many biological processes since it constitutes the buildings blocks of DNA and RNA. Solutions of guanine were prepared to cover the range from 5 × 10−5 to 8 × 10−4 M. Adsorption of guanine on a mercury electrode in acetic buffers at pH 4 and pH 6 is described by means of the adsorption isotherms constants calculated from the surface pressure as a function of electrode potential and adsorbate bulk concentration. The adsorption parameters from the double layer were calculated based on the data from the differential capacity–potential curves. The entirely different change in the differential capacity in two applied acetate buffers in the absence of guanine results from different buffer composition, as in a solution with a pH 4 adsorption primarily involves acetic acid molecules, whereas in a buffer with a pH 6-acetate ions. The possibility to accurately determine E max and σ max parameters points to a physical character of guanine adsorption, which must be associated with the fact that adsorbed guanine molecules are vertically or diagonal oriented. Obtained R A (charge transfer resistance at formal potential) changes are minor and comply with changes in ΔE. Therefore, it may be concluded that in the tested range of guanine concentrations, it has no effect on kinetics of zinc cation depolarisation at a mercury electrode both in the buffer with pH 4 and pH 6.

The luminescence of guanine molecules in the gas phase under the electron beam

The luminescence of guanine molecules in the gas phase under the electron beam

Vibrational investigations of guanine, thioguanine and their singly charged cations and anions

The complete vibrational studies have been done with help of quantum mechanics for the neutral Guanine (Gua) and Thioguanine (TGua) molecules and their singly charged cations and anions employing the B3LYP/6-311++G** method. Neutral Thioguanine and cations of Guanine and Thioguanine show planar structures and belong to Cs point group symmetry while the neutral Guanine and anions of Guanine and Thioguanine possess non-planar structure with C1 point group symmetry. Vibrational studies of ionic radicals of Gua and its thio- derivative are not available in literatures. Such extensive studies have been attempted for the first time. The normal modes of all the species have been assigned on the basis using potential energy distributions (PEDs) using GAR2PED software. The PEDs have also been calculated to make a conspicuous assignment as animation available in GaussView is not a guarantee for correct normal mode assignment. Charge transfer occurs in the molecule have been shown by the calculated highest occupied molecular orbital—lowest unoccupied molecular orbital (HOMO–LUMO) energies. The mapping of electron density iso-surface with electrostatic potential, has been carried out to get the information about the size, shape, charge density distribution and site of chemical reactivity of the molecule. The electronic properties HOMO and LUMO energies have been measured. The energy gap from HOMO to LUMO of the Gua is 5.0547 eV and TGua 4.0743 eV.

Study on the structure and electronic property of adsorbed guanine on aluminum doped graphene: First principles calculations

The adsorption of guanine on aluminum doped graphene was theoretically studied using density functional theory to explore its potential application as an adsorbent for guanine. We found that the structural and electronic properties of the graphene–guanine complex strongly depend on the Al atom. Guanine molecule is adsorbed imperceptibly on pristine graphene, while strong chemisorption is observed on Al-doped graphene. The adsorption configurations are discussed using the charge transfers, dipole moment, Frontier molecular orbital, and density of states (DOSs). This work proves that the adsorbent capability of graphene for guanine can be considerably improved by incorporation of Al dopant.

Absolute effective cross sections of ionization of adenine and guanine molecules by electron impact

Effective cross sections of the formation of positive ions of nitrous nucleic acids of adenine and guanine are determined by the crossed electron and molecular beam method in the energy interval from the threshold to 200 eV. It is found that the maximal value of the total cross section of adenine ionization is attained at an energy of 90 eV and is equal to (2.8 +/- 0.6) x 10(-15) cm(2). The maximal value of the total cross section of guanine ionization is equal to (3.2 +/- 0.7) x 10(-15) cm(2) and is observed at an energy of 88 eV. The energy ionization thresholds are determined, which amount to (8.8 +/- 0.2) eV for adenine and to (8.3 +/- 0.2) eV for guanine. The adenine and guanine mass spectra are measured. The absolute values of partial ionization cross sections of adenine and guanine molecules are determined.

Atomic-Scale Insight into Tautomeric Recognition, Separation, and Interconversion of Guanine Molecular Networks on Au(111)

Although tautomerization may directly affect the chemical or biological properties of molecules, real-space investigation on the tautomeric behaviors of organic molecules in a larger area of molecular networks has been scarcely reported. In this paper, we choose guanine (G) molecule as a model system. From the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we have successfully achieved the tautomeric recognition, separation, and interconversion of G molecular networks (formed by two tautomeric forms G/9H and G/7H) with the aid of NaCl on the Au(111) surface in ultrahigh vacuum (UHV) conditions. Our results may serve as a prototypical system to provide important insights into tautomerization related issues, which should be intriguing to biochemistry, pharmaceutics, and other related fields.

Crystal structure of disodium 2-amino-6-oxo-6,7-di-hydro-1H-purine-1,7-diide hepta-hydrate.

In the title compound, disodium 2-amino-6-oxo-6,7-di-hydro-1H-purine-1,7-diide hepta-hydrate, 2Na(+)·C5H3N5O(2-)·7H2O, the structure is composed of alternating (100) layers of guanine mol-ecules and hydrated Na(+) ions. Within the guanine layer, the mol-ecules are arranged in centrosymmetric pairs, with a partial overlap between the guanine rings. In this compound, guanine exists as the amino-keto tautomer from which deprotonation from N1 and N7 has occurred (purine numbering). There are no direct inter-actions between the Na(+) cations and the guanine anions. Guanine mol-ecules are linked to neighboring water mol-ecules by O-H⋯N and O-H⋯O hydrogen bonds into a network structure.

Experimental and first-principles investigation of the adsorption and entrapping of guanine with SiO2 clusters of sol-gel silicate material for understanding DNA photodamage.

We report a first principles density functional theoretical (DFT) investigation of guanine (G) adsorption onto SiO2 clusters, viz., Si2O4, Si3O6, Si4O8 and Si5O10 in terms of geometry, binding energy (EB), binding site, energy gap (Eg), and electronic and spectral properties. Guanine entrapped within a Si9O18 cluster was also studied in terms of geometry, energy gap (Eg), electronic and spectral properties. We observed that the most stable forms of the cluster were Si5O10 and Si9O18. Guanine adsorbed onto SiO2 (G-SiO2) and guanine entrapped within SiO2 (GE-SiO2) were analyzed by the B3LYP/LanL2DZ method. The HOMO-LUMO energies illustrate that charge transfer from ligand to metal (L → M) occurs in G-SiO2 clusters as guanine to SiO2. The composite of guanine with nanostructured silica material was prepared by simple precipitation and chemical sol-gel processes. The prepared G-SiO2 and GE-SiO2 composites were characterized by FT-IR and FE-SEM with EDX analysis. The resulting experimental evidence is included for better understanding the guanine adsorption and entrapment. The adsorption and entrapping of G-SiO2 and GE-SiO2 was also confirmed by UV-vis spectroscopy. Experimental results are compared with the DFT results. Furthermore, the sol-gel silicate material used to protect the DNA base (guanine) from UVA-irradiation has been highlighted.

Microfluidic devices for rapid and sensitive identification of organisms.

Microfluidic devices for rapid and highly sensitive detection of living organisms were developed for two applications. First, a zebrafish embryo genotyping system was developed and shown to be able to genotype embryos in the first 48 hours of the embryos life without damaging the embryos in any apparent way. Second, a highly sensitive bacteria detection platform has been developed for the rapid detection of pathogens. The system relies on a magnetic bead extraction followed by secondary bead attachment. The secondary beads are barcoded with DNA sequences highly enriched for Gs. The guanine molecules generate an electrochemical response after they are released from the secondary beads and detected at a sensing location downstream from the beads. The amplification with the efficient washing procedures leads to a limit of detection of 3 CFU in 100 mL of water.

Fragmentation of the adenine and guanine molecules induced by electron collisions.

Secondary electron emission is the most important stage in the mechanism of radiation damage to DNA biopolymers induced by primary ionizing radiation. These secondary electrons ejected by the primary electron impacts can produce further ionizations, initiating an avalanche effect, leading to genome damage through the energy transfer from the primary objects to sensitive biomolecular targets, such as nitrogenous bases, saccharides, and other DNA and peptide components. In this work, the formation of positive and negative ions of purine bases of nucleic acids (adenine and guanine molecules) under the impact of slow electrons (from 0.1 till 200 eV) is studied by the crossed electron and molecular beams technique. The method used makes it possible to measure the molecular beam intensity and determine the total cross-sections for the formation of positive and negative ions of the studied molecules, their energy dependences, and absolute values. It is found that the maximum cross section for formation of the adenine and guanine positive ions is reached at about 90 eV energy of the electron beam and their absolute values are equal to 2.8 × 10(-15) and 3.2 × 10(-15) cm(2), respectively. The total cross section for formation of the negative ions is 6.1 × 10(-18) and 7.6 × 10(-18) cm(2) at the energy of 1.1 eV for adenine and guanine, respectively. The absolute cross-section values for the molecular ions are measured and the cross-sections of dissociative ionization are determined. Quantum chemical calculations are performed for the studied molecules, ions and fragments for interpretation of the crossed beams experiments.

Thymine dimer splitting in the TT-G trinucleotide model system: A semiclassical dynamics and TD-DFT study

The mechanism leading to bond cleavage of a thymine–thymine cyclobutane dimer (T<>T) in a model system consisting of the dimer flanked by guanine trinucleotide was studied using semiclassical dynamics simulation. Pulsed laser excitation of the guanine molecule is found to cause electron transfer from the guanine molecule to the dimer, which then dissociates via sequential cleavage of the C5C5′ and C6C6′ bonds. Subsequently, electrons transfer back to the guanine molecule as the dimer splits into two monomers. The splitting of the cyclobutane dimer was found to be in the femtosecond time scale.