DNA Bases Guanine Research Articles

Role of structure and dynamics of DNA with cisplatin and oxaliplatin adducts in various sequence contexts on binding of HMGB1a

Anti-cancer drugs, such as cisplatin and oxaliplatin, covalently bind to adjacent guanine bases in DNA to form intra-strand adducts. Differential recognition of drug–DNA adducts by the protein HMGB1a has been related to the differences in efficacy of these drugs in tumours. Additionally, the bases flanking the adduct (the sequence context) also have a marked effect on HMGB1a binding affinity. We perform atomistic molecular dynamics simulations of DNA with cisplatin and oxaliplatin adducts in four sequence contexts (AGGC, CGGA, TGGA and TGGT) in the absence and presence of HMGB1a. The structure of HMGB1a-bound drug–DNA molecules is independent of sequence and drug identity, confirming that differential recognition cannot be explained by the protein-bound structure. The differences in the static and conformational dynamics of the drug–DNA structures in the absence of the protein explain some but not all trends in differential binding affinity of HMGB1a. Since the minor groove width and helical bend of all drug–DNA molecules in the unbound state are lower than the protein-bound state, HMGB1a must actively deform the DNA during binding. The thermodynamic pathway between the unbound and protein-bound states could be an additional factor in the binding affinity of HMGB1a for drug–DNA adducts in various sequence contexts.

Time evolution of the Infrared Laser Induced Breakdown Spectroscopy of DNA bases Guanine and Adenine

Laser-Induced Breakdown Spectroscopy (LIBS) of DNA bases Guanine and Adenine was studied using a high-power CO2 pulsed laser (λ=10.591 μm, τ FWHM=64 ns and fluences ranging from 25 to 70 J/cm2). The strong emission of the adenine and guanine plasma, collected using a high-resolution spectrometer, at medium-vacuum conditions (4 Pa) and at 1 mm from the target, exhibits excited molecular bands of CN (B2 Σ +–X2 Σ +) and excited neutral H and ionized N+ and C+. The medium-weak emission is due to excited species C2+, C3+, N, O, O+, O2+ and molecular band systems of $\mathrm{C}_{2}(\mathrm{d}^{3}\varPi_{\mathrm{g}}\mbox{--}\mathrm{a}^{3}\varPi_{\mathrm{u}};\ \mathrm{D}^{1}\varSigma_{\mathrm{u}}^{+}\mbox{--}\mathrm{X}^{1}\varSigma_{\mathrm{g}}^{+})$ , OH(A2 Σ +–X2 Π), NH(A3 Π–X3 Σ −), CH(A2 Π–X2 Π), $\mathrm{N}_{2}^{+}(\mathrm{B}^{2}\varSigma_{\mathrm{u}}^{+}\mbox{--} \mathrm{X}^{2}\varSigma_{\mathrm{g}}^{+})$ and N2(C3 Π u–B3 Π g). We focus our attention on the temporal evolution of different atomic/ionic and molecular species. The velocity distributions for various (different) species were obtained from time-of-flight (TOF) measurements. Intensities of some lines from C+ were used for determining electron temperature and their Stark-broadened profiles were employed to estimate the temporal evolution of electron density.

Oxidation of DNA Bases Influenced by the Presence of Other Bases

AbstractElectrochemical detection of DNA is a highly important topic. Here we show that the electrochemical responses of one DNA base (guanine, adenine, cytosine or thymine), in terms of oxidation potential, current intensity, peak width and resolution can be highly influenced by the presence of other DNA bases at electrochemically reduced graphene oxide (ER‐GO) as well as standard glassy carbon electrode. We have observed that the effects were more significant for adenine base on ER‐GO and cytosine base on glassy carbon (GC) electrode. Differences in responses were generally low in a mixture of four different DNA bases but interestingly, deviations become significantly larger when only one or two other bases were present. Our findings are of paramount importance for future developments in DNA detection and analysis since individual DNA bases are not present in isolation in nature or in typical biosensing systems.

Ag+ and cysteine detection by Ag+–guanine interaction based on graphene oxide and G-quadruplex DNA

Sensitive and selective techniques for both Ag+ and Cys detection have been designed based on graphene oxide (GO) and G-quadruplex DNA. The G-quadruplex structure can capture the fluorescent molecule acridine orange (AO) from the surface of graphene oxide (GO), which will recover the fluorescence of AO that was initially quenched by GO. Then the addition of Ag+ will release AO back to GO, because Ag+ can destroy the G-quadruplex structure, giving a fluorescence quenching process again. Based on this “turn off” principle, a highly sensitive and selective Ag+ detection method was developed. In addition, cysteine (Cys) can capture Ag+ from the guanine base of DNA which will result in the regeneration of the G-quadruplex DNA structure and thus the regeneration of the fluorescence signal. This “turn on” principle can be used for the development of a highly selective and sensitive detection method for Cys.

8-Hydroxydeoxyguanosine: Not mere biomarker for oxidative stress, but remedy for oxidative stress-implicated gastrointestinal diseases

Reactive oxygen species (ROS) attack guanine bases in DNA easily and form 8-hydroxydeoxyguanosine (8-OHdG), which can bind to thymidine rather than cytosine, based on which, the level of 8-OHdG is generally regarded as a biomarker of mutagenesis consequent to oxidative stress. For example, higher levels of 8-OHdG are noted in Helicobacter pylori-associated chronic atrophic gastritis as well as gastric cancer. However, we have found that exogenous 8-OHdG can paradoxically reduce ROS production, attenuate the nuclear factor-κB signaling pathway, and ameliorate the expression of proinflammatory mediators such as interleukin (IL)-1, IL-6, cyclo-oxygenase-2, and inducible nitric oxide synthase in addition to expression of nicotinamide adenine dinucleotide phosphate oxidase (NOX)-1, NOX organizer-1 and NOX activator-1 in various conditions of inflammation-based gastrointestinal (GI) diseases including gastritis, inflammatory bowel disease, pancreatitis, and even colitis-associated carcinogenesis. Our recent finding that exogenous 8-OHdG was very effective in either inflammation-based or oxidative-stress-associated diseases of stress-related mucosal damage has inspired the hope that synthetic 8-OHdG can be a potential candidate for the treatment of inflammation-based GI diseases, as well as the prevention of inflammation-associated GI cancer. In this editorial review, the novel fact that exogenous 8-OHdG can be a functional molecule regulating oxidative-stress-induced gastritis through either antagonizing Rac-guanosine triphosphate binding or blocking the signals responsible for gastric inflammatory cascade is introduced.

Photocrosslinking between Peptide–Peptide or Peptide–Oligonucleotide by RuII–TAP Complexes

Ru(II)-TAP complexes have been shown to be very attractive compounds in the frame of developments of new anticancer drugs targeting the genetic material. This increasing interest originates from observations of covalent bond formations, triggered by photo-induced electron transfer (PET) between Ru(II)-TAP complexes and guanine bases of DNA. This photoreaction has recently been extended to the tryptophan (Trp) amino acid for future applications involving peptides. Thus, a double photo-addition of Trp residues of peptides on Ru(II) complexes is demonstrated by mass spectrometry with some structural issues. Such bi-adduct formations offer the possibility of photocrosslinking two Trp-containing biomolecules, which is investigated in this study. Thus, photocrosslinking between two complementary oligonucleotides (ODNs) derivatized by Trp-containing tripeptides is demonstrated by polyacrylamide gel electrophoresis (PAGE) in the presence of Ru(II)-TAP complexes. Both PAGE and MS indicate that such photocrosslinkings arise from two reaction pathways: either via the double addition of Trp residues on the Ru complex or from dimerization of Trp radicals. The competition between these two pathways depends on the experimental conditions. Heterobridgings between guanine bases and tryptophan residues mediated by Ru(II)-TAP complexes is also examined, opening the way to ODN-peptide photocrosslinkings.

An anomalous dissociation of protonated cluster ions of DNA guanine-cytosine base-pair

In the collisionally-activated dissociation of the proton-bound cluster ions of DNA base guanine (G) and cytosine(C), G••H+••C, the abundance of [CH+] ions was found to be higher than that of [GH+] despite the fact that G has a higher protonaffinity than C. This unexpected observation seems to demonstrate another example that the simple kinetic method scheme doesnot work. We suggest that a kinetic factor or detailed dynamics governing the proton transfer and dissociation should be carefullyconsidered in the applications of the kinetic method to the proton affinity measurements.

A novel approach for stress-induced gastritis based on paradoxical anti-oxidative and anti-inflammatory action of exogenous 8-hydroxydeoxyguanosine

Reactive oxygen species (ROS) attack guanine bases in DNA and form 8-hydroxydeoxyguanosine (8-OHdG), which has been regarded simply as an oxidative mutagenic by-product. On the other hand, our previous report showed paradoxically ROS attenuating action of generated 8-OHdG. In the current study, both in vitro and in vivo experiments were executed in order to document anti-oxidative and anti-inflammatory actions of 8-OHdG in cell model and to elucidate the therapeutic efficacy against water immersion restraint stress (WIRS)-induced gastritis animal model. Electron spin resonance measurements showed that 8-OHdG at >5 μg/ml completely scavenged OH − radicals, which was further confirmed by checking 2′-7′-dichlorodihydrofluorescein diacetate (DCFDA) spectroscopy. On molecular assay, 8-OHdG antagonized the action of GTP on Rac, a small GTP binding protein, without affecting Rac-guanosine exchange factor (GEF) or phosphoinositide 3-kinases (PI3K) activity. In Raw264.7 cells, 8-OHdG was found to be associated with marked attenuations of NOX1, NOXO1, and NOXA1 accompanied with the decreased expressions of LPS-induced inflammatory mediators including COX-2, iNOS, IL-1β, and IL-6. Similarly, 8-OHdG attenuated hypoxia-induced angiogenesis and platelet endothelial cell adhesion molecule-1 (PECAM-1), COX-2, iNOS, IL-8, and VEGF expressions in HUVEC cells. At transcriptional level, 8-OHdG inhibited the nuclear translocation of NF-κB, inhibitory κB kinase (IKK) β kinase activation, and decreased phospho-IκBα levels. 8-OHdG efficiently ameliorated WIRS-induced gastric mucosal injury as evidenced with improvement of gross lesion index and attenuation of engaging mediators. Taken together, exogenous 8-OHdG can be a functional molecule regulating oxidative stress-induced gastritis through either antagonizing Rac-GTP binding or blocking the signals responsible for gastric inflammatory cascade.

Stacks of Nucleic Acids as Molecular Wires: Direct Measurement of the Intermolecular Band Dispersion in Multilayer Guanine Assemblies

The intermolecular band dispersion related to the highest occupied molecular orbital in highly ordered, hydrated multilayer films of the DNA base guanine has been measured using photon-energy-dependent ultraviolet photoelectron spectroscopy. A bandwidth of 331 ± 8 meV at room temperature and a small effective mass of about 1.11 times that of a free charge suggest a high intrinsic hole mobility along quasi-one-dimensional stacks formed perpendicular to layered, hydrogen-bound networks.

Reactions of the OOH radical with guanine: Mechanisms of formation of 8-oxoguanine and other products

The mutagenic product 8-oxoguanine (8-oxoGua) is formed due to intermediacy of peroxyl (OOR) radicals in lipid peroxidation and protein oxidation-induced DNA damage. The mechanisms of these reactions are not yet understood properly. Therefore, in the present study, the mechanisms of formation of 8-oxoGua and other related products due to the reaction of the guanine base of DNA with the hydroperoxyl radical (OOH) were investigated theoretically employing the B3LYP and BHandHLYP hybrid functionals of density functional theory and the polarizable continuum model for solvation. It is found that the reaction of the OOH radical with guanine can occur following seven different mechanisms leading to the formation of various products including 8-oxoGua, its radicals, 5-hydroxy-8-oxoguanine and CO 2. The mechanism that yields 8-oxoGua as an intermediate and 5-hydroxy-8-oxoGua as the final product was found to be energetically most favorable.

Formation of 8-Nitroguanine Due to Reaction between Guanyl Radical and Nitrogen Dioxide: Catalytic Role of Hydration

8-Nitroguanine (8-NitroG) is known to be a potent mutagenic product obtained from the guanine base of DNA that induces GC to AT transversion mutation. Its formation by the reaction of guanyl radical with nitrogen dioxide radical (NO(2)(*)) has been observed experimentally. The reaction was studied here theoretically considering different reactant complexes, transition states, intermediate complexes, and product complexes. The solvent effect due to one, two, three, and six specific water molecules and the bulk solvent effect of aqueous media on the reaction were considered. With one, two, and three complexed water molecules, geometry optimization calculations were performed using the B3LYP and BHandHLYP functionals of density functional theory along with the 6-31G (d,p) and the AUG-cc-pVDZ basis sets in gas phase which was followed by single point energy calculations at the MP2/AUG-cc-pVDZ level. With six complexed water molecules, geometry optimization was performed at the BHandHLYP/6-31G(d,p) level of theory followed by single point energy calculations at all the other levels of theory mentioned above. Solvation in bulk aqueous media was treated at all the above-mentioned levels of theory using the polarizable continuum model (PCM). Specific water molecules were found to play catalytic roles in proton transfer processes that usually lowered the barrier appreciably.

Electrochemical Investigation of Interactions between Potential DNA Targeted Compounds, 2,4-Di- and 2,3,4-Trisubstituted Benzimidazo[1,2-a]pyrimidines and Nucleic Acid

The electrochemical aspects of interactions between DNA and two organic compounds are discussed herein. Potential DNA targeted compounds, 2-methyl-4-phenyl-benzo[4,5]imidazo[1,2-a]pyrimidine (C1) and 2,3,4-trimethyl-benzo[4,5]imidazo[1,2-a]pyrimidine (C2), were synthesized and their cytotoxic and/or growth inhibitory effects were studied previously. Disposable sensor technology was used to explore the interaction between the compounds and nucleic acid, such as fish sperm DNA at the electrode surface and in the solution phase. The changes upon encountering oxidation signals of electroactive DNA base-guanine and these compounds were monitored electrochemically.

2009 ACS NATIONAL AWARD WINNERS

FOLLOWING is the eighth set of vignettes of recipients of awards administered by the American Chemical Society for 2009. C&EN will publish the vignettes of the remaining recipients in March. JAMES FLACK NORRIS AWARD IN PHYSICAL ORGANIC CHEMISTRY Sponsored by the ACS Northeastern Section Chemical radicals, with their unpaired electrons, are crucial—and detrimental— to many biological processes, from their involvement in DNA damage and repair to their roles in aging and numerous diseases. Yet their fleeting, reactive nature makes them difficult to study. Bernd Giese, professor at the University of Basel, in Switzerland, has made a career of investigating and harnessing these reactions. He is receiving the award for his contributions to the field of bioorganic radical chemistry. Giese is perhaps best known for his work on electron transfer reactions in DNA and peptides. He examined the oxidation of the DNA base guanine and proposed a now widely accepted mechanism in which electrons “hop” from ...

Single‐Walled Carbon Nanotubes Modified Graphite Electrodes for Electrochemical Monitoring of Nucleic Acids and Biomolecular Interactions

AbstractSingle‐walled carbon nanotubes (SWCNT) modified disposable graphite electrodes (SWCNT‐PGEs) were investigated in our study for the improved electrochemical monitoring of nucleic acids and biomolecular interactions based on the higher signal enhancement comparison to bare PGEs. The surface morphologies of bare PGE and SWCNT‐PGE were firstly explored using scanning electron microscopy (SEM) analysis. The easy surface modification of disposable graphite electrodes with carbon nanotubes was performed by passive adsorption, and DNA was then immobilized onto the SWCNT‐PGEs by the formation of covalent coupling between the carboxylated ends of nanotubes and the amine group in the guanine bases of DNA. The overall performance of SWCNT‐PGEs has also been studied, and discussed in terms of optimum analytical conditions; such as, the effect of pretreatment step, CNT concentration, DNA concentration, etc. The reproducible detection of DNA represent a very attractive approach for the further detection of interaction between the anticancer drug, daunorubicin (DNR) and double stranded DNA (dsDNA). Voltammetric results were complemented with electrochemical impedance spectroscopy (EIS), that was used to characterize the successful construction of carbon nanotubes modification onto the surface of PGEs.

Characterization of oxidized guanosine 5′-triphosphate as a viable inhibitor of soluble guanylyl cyclase

The guanine base is prone to oxidation by free radicals regardless of the cellular moiety it is bound to. However, under conditions of oxidative stress, 8-oxoguanosine triphosphate (oxo 8GTP) formation has been shown to occur without oxidation of the guanine base in DNA. In vitro studies have suggested that oxo 8GTP could impact G-protein signaling and RNA synthesis. Whether increased levels of oxo 8GTP translate into cellular malfunction is unknown. Data presented herein show that oxo 8GTP is formed in cell-free preparations as well as in PC12 cells after exposure to physiologically relevant oxidative conditions generated with 10 μM copper sulfate and 1 mM l-ascorbic acid (Cu/Asc). We also determined that oxo 8GTP has biological activity as a potent inhibitor of nitric oxide-stimulated soluble guanylyl cyclase (sGC). The increase in oxo 8GTP formation in purified GTP and PC12 cells exposed to Cu/Asc caused a significant reduction in the product of sGC activity, cGMP. This oxidation of GTP was attenuated by the addition of reduced glutathione under these same Cu/Asc conditions, thus preventing the decrease in sGC activity. This suggests that oxo 8GTP is produced by free radicals in vivo and could have significant impact on cell functions regulated by sGC activity such as synaptic plasticity in the central nervous system.

Vacuum ultraviolet ellipsometry investigation of ultrathin organic films and their heterostructures

Thin layers and multilayer structures of the DNA bases guanine and cytosine on ZnO substrates were prepared by organic molecular beam deposition under ultra-high vacuum conditions and measured in situ by means of vacuum ultraviolet spectroscopic ellipsometry at the synchrotron source BESSY. Using the dielectric function of the individual layers the optical response of the G/C and C/G heterostructures was modeled. Deviations between simulated and experimental data were mainly attributed to the ordering of cytosine over guanine in the G/C and C/G structures and to the influence of the substrate.

Reactions of NO2Cl with Imidazole: A Model Study for the Corresponding Reactions of Guanine

Reactions of nitryl chloride NO(2)Cl with imidazole, taken as a model for the guanine base of DNA, leading to the formation of 2-oxoimidazole (2-oxoIm), 2-chloroimidazole (2-chloroIm), and 2-nitroimidazole (2-nitroIm) corresponding to the 8-oxo, 8-chloro, and 8-nitro derivatives of guanine were studied at the B3LYP and MP2 levels of theory employing the 6-31+G* and AUG-cc-pVDZ basis sets in gas phase. In order to incorporate solvent effect, all the B3LYP/AUG-cc-pVDZ optimized structures were solvated in aqueous media at the B3LYP/AUG-cc-pVDZ and MP2/AUG-cc-pVDZ levels of theory using the polarizable continuum model (PCM). A single mechanism was found for the formation of 2-oxoIm, while two and three mechanisms were found for the formation of 2-nitroIm and 2-chloroIm respectively. Each of these reaction mechanisms involves two steps. The calculated barrier energies show that the formation of 2-nitroIm would occur more efficiently than those of 2-oxoIm and 2-chloroIm. It suggests that formation of 8-nitroguanine would be the main DNA lesion caused by NO(2)Cl, which is consistent with experimental observations.

Synthesis, spectroscopic studies of new water-soluble Co(II) and Cu(II) macrocyclic complexes of 4,15-bis(2-hydroxyethyl)-2,4,6,13,15,17-hexaazatricyclodocosane: their interaction studies with calf thymus DNA and guanosine 5′ monophosphate

New water soluble Co(II) 1, Ni(II) 2 and Cu(II) 3 complexes of 4,15-bis(2-hydroxyethyl)-2,4,6,13,15,17-hexaazatricyclodocosane Co(II) were synthesized and characterized by various techniques, viz. elemental analysis, conductivity measurements, infrared, electronic, ESI-MS, 1H and 13C NMR spectroscopy. Molar conductance measurements in aqueous solution showed that complexes 1, 2 and 3 are ionic in nature. On the basis of spectroscopic data, a square planar geometry was assigned to the complexes involving four N-atoms of the two cyclohexane moieties. Interaction studies of 1 and 3 with CT-DNA were carried using UV/Visible absorption spectroscopy, fluorescence spectrophotometry, cyclic voltammetry and viscosity measurements. Absorption spectral traces reveal 27.7 and 23.3% hyperchromism for complexes 1 and 3, respectively indicative of strong binding to CT-DNA. These results were authenticated by fluorescence quenching experiments and viscosity measurements. The intrinsic binding constants K b of 1 and 3 are 2.94 × 104 and 2.71 × 104 M−1, respectively. Early transition metals show preference for O6 position while later ones copper and cobalt prefer N7 position of DNA base guanine. To validate this hypothesis, interaction studies of copper (II) and cobalt (II) complexes were carried out with 5′GMP, which revealed electrostatic interactions are more favored along with hydrogen bonding than coordinate covalent interaction to N7 position of guanine.

Structure of Low-Lying Excited States of Guanine in DNA and Solution: Combined Molecular Mechanics and High-Level Coupled Cluster Studies

High-level ab-initio equation-of-motion coupled-cluster methods with singles, doubles, and noniterative triples are used, in conjunction with the combined quantum mechanical molecular mechanics approach, to investigate the structure of low-lying excited states of the guanine base in DNA and solvated environments. Our results indicate that while the excitation energy of the first excited state is barely changed compared to its gas-phase counterpart, the excitation energy of the second excited state is blue-shifted by 0.24 eV.

Photo-Cross-Linking between Polymers Derivatized with Photoreactive Ruthenium−1,4,5,8-Tetraazaphenanthrene Complexes and Guanine-Containing Oligonucleotides

We have shown previously that complexes containing 1,4,5,8-tetraazaphenanthrene (TAP) ligands are able to form photoadducts with the guanine bases of DNA and oligonucleotides. In this work, we have exploited this specific photoreaction for carrying out photo-cross-linkings between guanine-containing oligonucleotides (G-ODNs) and biodegradable polymers derivatized with the photoreactive Ru(II) compounds. The aim in the future is to use these polymer conjugates as vectorizing agents of the metallic compounds inside the cells. Thus, photooxidizing Ru(II) complexes such as [Ru(TAP)3]2+ and [Ru(TAP)2phen]2+ (phen = 1,10-phenanthroline) have been derivatized by an oxyamine function to attach them, via an oxime ether linkage, to a soluble 6 or 80 kDa poly-[N-(2-hydroxyethyl)-l-glutamine] polymer that contains pendent aldehyde groups. It is demonstrated that the resulting Ru-labeled polymers exhibit photophysical properties and a photochemistry that are comparable with those of the free, nonattached complexes. The photo-cross-linkings with the G-ODNs are clearly detected by gel electrophoresis with the 6 kDa Ru conjugates upon illumination.