Regulation of one-electron oxidation rate of guanine by base pairing with cytosine derivatives

Effects of base pairing on the one-electron oxidation rate of guanine derivatives, guanine, 8-bromoguanine, and 8-oxo-7,8-dihydroguanine have been studied. The one-electron oxidation rate of guanine derivatives was determined by triplet-quenching experiments, using N,N'-dibutylnaphthaldiimide (NDI) in the triplet excited state (3NDI*) and fullerene (C(60)) in the triplet excited state ((3)C(60*)) as oxidants. In all three guanine derivatives studied here, acceleration of the one-electron oxidation was observed upon hydrogen bonding with cytosine, which demonstrates lowering of the oxidation potential of guanine derivatives by base pairing with cytosine. When a methyl or bromo group was introduced to the C5 position of cytosine, acceleration or suppression of the one-electron oxidation relative to the guanine:cytosine base pair was observed, respectively. The results demonstrate that the one-electron oxidation rate of guanine in DNA can be regulated by introducing a substituent on base pairing cytosine.     

Guanine oxidation: NMR characterization of a dehydro-guanidinohydantoin residue generated by a 2e-oxidation of d(GpT).

The Mn-TMPyP/KHSO(5) system was used to oxidize guanine contained within a dinucleoside monophosphate d(GpT). To identify the guanine oxidation product having a mass with 4 amu above the mass of guanine itself, this relatively unstable compound was reduced to a more stable one. The ESI/MS and NMR data allowed us to propose a dehydro-guanidinohydantoin structure for the (G+4) guanine oxidation product.     

Synthesis of monomers containing guanine or guanine precursors as substituent groups

The synthesis of four new monomers containing guanine or a guanine precursor was achieved. These were two isomeric acid ester derivatives of guanine and two isomeric vinyl ether derivatives of N²-acetylguanine. In the case of the synthesis of the guanine acid esters IV and V, it was necessary to prepare first the guanine alcohol derivatives II and III. These N-7 and N-9 isomeric alcohols of guanine were separated by fractional crystallization. Subsequent esterification of these alcohols with maleic anhydride gave the desired products. In the other case, N²-acetylguanine was alkylated with 2-chloroethyl vinyl ether to yield the N-7 and N-9 isomer VI and VII, respectively. These were separated using flash column chromatography.     

基于BCNTs/GC电极的鸟嘌呤与腺嘌呤电化学行为及其同时检测

利用掺硼碳纳米管（BCNTs）/GC电极研究了鸟嘌呤（G）和腺嘌呤（A）的电化学氧化行为. 与GC和CNTs/GC电极相比,BCNTs/GC电极具有更强的电催化活性,且响应电流明显增加. 两混合样品在BCNTs/GC电极上的氧化峰间隔较大,可实现对A和G的同时检测.     

193 NM LIGHT INDUCES SINGLE STRAND BREAKAGE OF DNA PREDOMINANTLY AT GUANINE

Irradiation of DNA with 193 nm light results in monophotonic photoionization, with the formation of a base radical cation and a hydrated electron (φ_P1 = 0.048–0.065). Although >50% of the photoionization events initially occur at guanine in DNA, migration of the “hole” from the other bases to guanine occurs to yield predominantly its radical cation or its deprotonated form. From sequence analysis, the data reveal that 193 nm light induces single strand breaks (ssb) in double-stranded DNA preferential 3’ to a guanine residue. However, it has previously been reported that 193 nm light yields very low yields of ssb (<2% of the yield of eaq). The distribution of these ssb at guanine is nonrandom, showing a dependence on the neighboring base moiety. The efficiency of ssb formation at nonguanine sites is estimated to be at least one order of magnitude lower. The preferred cleavage at guanine is consistent with migration and localization of the electron loss center at guanine. It is argued that singlet oxygen and the photoionized phosphate group of the sugar moiety are not major precursors to ssb. At present, the mechanisms of strand breakage are not known although a guanine radical or one of its products remain potential precursors.     

Theoretical study of cisplatin binding to purine bases: why does cisplatin prefer guanine over adenine?

The thermodynamics and kinetics for the monofunctional binding of the antitumor drug cisplatin, cis-diamminedichloroplatinum(II), to a purine base site of DNA were studied computationally using guanine and adenine as model reactants. A dominating preference for initial attack at the N7-position of guanine is established experimentally, which is a crucial first step for the formation of a 1,2-intrastrand cross-link of adjacent guanine bases that leads to bending and unwinding of DNA. These structural distortions are proposed ultimately to be responsible for the anticancer activity of cisplatin. Utilizing density functional theory in combination with a continuum solvation model, we developed a concept for the initial Pt-N7 bond formation to atomic detail. In good agreement with experiments that suggested DeltaG++ = approximately 23 kcal/mol for the monofunctional platination of guanine, our model gives DeltaG++ = 24.6 kcal/mol for guanine, whereas 30.2 kcal/mol is computed when adenine is used. This result predicts that guanine is 3-4 orders of magnitude more reactive toward cisplatin than adenine. A detailed energy decomposition and molecular orbital analysis was conducted to explain the different barrier heights. Two effects are equally important to give the preference for guanine over adenine: First, the transition state is characterized by a strong hydrogen bond between the ammine-hydrogen of cisplatin and the O=C6 moiety of guanine in addition to a stronger electrostatic interaction between the two reacting fragments. When adenine binds, only a weak hydrogen bond forms between the chloride ligand of cisplatin and the H(2)N-C6 group of adenine. Second, a significantly stronger molecular orbital interaction is identified for guanine compared to adenine. A detailed MO analysis is presented to provide an intuitive view into the different electronic features governing the character of the Pt-N7 bond in platinated purine bases.     

Theoretical and gas-phase studies of specific cationized purine base quartet

Guanine tetraplexes are biological non-covalent systems stabilized by alkali cations. Thus, self-clustering of guanine, xanthine and hypoxanthine with alkali cations (Na(+), K(+) and Li(+)) is investigated by electrospray ionization mass spectrometry (ESI-MS) in order to provide new insights into G-quartets, hydrogen-bonded complexes. ESI assays displayed magic numbers of tetramer adducts with Na(+), Li(+) and K(+), not only for guanine, but also for xanthine bases. The optimized structures of guanine and xanthine quartets have been determined by B3LYP hybrid density functional theory calculations. Complexes of metal ions with quartets are classified into different structure types. The optimized structures obtained for each quartet explain the gas-phase results. The gas-phase binding sequence between the monovalent cations and the xanthine quartet follows the order Li(+) > Na(+) > K(+), which is consistent with that obtained for the guanine quartet in the literature. The smallest stabilization energy of K(+) and its position versus the other alkali metal ions in guanine and xanthine quartets is consistent with the fact that the potassium cation can be located between two guanine or xanthine quartets, for providing a [gua(or (xan))(8)+K](+) octamer adduct. Even if an abundant octamer adduct with K(+) for xanthine was detected by ESI-MS, it was not the case for guanine.     

Complexes of cadmium ion with guanine bases detected by electrospray ionization mass spectrometry

The complexations of cadmium ion with guanine bases were detected by electrospray ionization mass spectrometry (ESI-MS). In order to explore the toxicity of cadmium, such as oxidative stress to DNA and carcinogenesis, it is very important to determine the interactions between the cadmium ion and nucleotide. The analysis of mixed cadmium ion-guanosine aqueous solution (molar ratio 1 : 9) using ESI-MS (cone voltage 20 V) showed the presence of various cadmium complex ions, such as [n (guanosine) + Cd](2+) (n = 3-8), [2guanine + Cd](2+), [guanosine + guanine + Cd](2+) and [guanosine + 2guanine + Cd](2+). The observed [2guanine + Cd](2+), [guanosine + guanine + Cd](2+) and [guanosine + guanine + Cd](2+) ions are formed through the dissociation of the N-glycoside bond at the interface of ESI-MS. For deoxyguanosine and ethylguanine, similar cadmium complexes were observed. However, the complexes between the cadmium ion and 8-hydroxydeoxyguanosine were not detected. Furthermore, when a higher molar ratio (Cd : guanosine) or cone voltage were used, more of the monovalent ion peaks, such as [Cd(guanine - H)(2) + H](+) and [Cd(guanosine - H)(2) + H](+), were observed and a decrease in the abundance of the divalent ions, such as [n(guanosine)+Cd](2+), occurred.     

Affinity labeling of a single guanine bulge

We have developed a conceptually new method for the selective labeling of duplex DNA containing a guanine bulge with a masked form of fluorescent 2-amino-1,8-naphthyridine. A naphthyridine derivative 2 tethering DNA-alkylating epoxide was synthesized from (S)-epichlorohydrin and naphthyridine derivative 1, which selectively binds to the guanine bulge duplex. HPLC analysis of the labeling reaction of bulge duplex d(GTT GTGTTG GA)/d(CAA CA A ACC T) (TGT/A_A) with 2 showed a formation of 2-TGT adduct for the guanine bulge. The reaction proceeded for the guanine bulge and a reduced efficiency for the cytosine bulge, but not at all for adenine and thymine bulges. The site of covalent bond formation in 2-TGT was unambiguously identified at the guanine two bases away from the bulge by the use of MALDI-TOF MS analysis of the oligomer fragments produced by strand scission. The labeling reaction was also observed for the guanine bulge flanking two G-C base pairs (CGC/G_G), producing a 2:1 adduct (2.2-CGC). Upon hydrolysis of 2-TGT and 2.2-CGC with concentrated hydrogen chloride, a release of fluorescent 2-aminonaphthyridine from the adduct was clearly detected, verifying a concept of an affinity labeling of the guanine bulge with a masked fluorescent chromophore. The affinity labeling targeting of the guanine bulge is a conceptually novel method for the postsynthetic labeling of DNA. Hybridization, to the target sequence, of a probe DNA possessing one extra guanine especially between two cytosines provides a unique site for the labeling by masked fluorophore 2. The technique may have broad application in genetic typing without using a conventional synthesis of fluorescent-labeled DNA oligomers.     

Electronic structure of DNA nucleobases and their dinucleotides explored by soft X-ray spectroscopy

The electronic structures of a series of DNA nucleobases and their dinucleotides were investigated by N 1s X-ray absorption, X-ray photoemission, and resonant X-ray emission spectroscopy. Resonant X-ray emission spectra of the guanine base and its dinucleotide indicate that it has a weak structure at the lowest binding energy; at this energy, it isolates from the main valence band and forms the HOMO state. This indicates that the HOMO state is localized in the guanine base, as claimed by valence and core photoemissions and expected from theoretical predictions. In addition, the XAS and XES profiles of the guanine dinucleotide indicate that disruption of the aromatic character of the six-membered ring results in the localization of the pi state at the imine (-N=) site of the guanine base; this may favor charge transfer among stacked guanine bases and further influence the conductivity of DNA.     

Theoretical Study of Hydrated Cd~（2＋） Interactions with Guanine

Theoretical study was performed to investigate how the hydration of cadmium ca-tion influences the structure and properties of guanine.The aqueous environment was simulated by both explicit solvent(1-5 water molecules) model and implicit solvent model.For complexes in which Cd2+ attached to the N(7) and O(6) sites of guanine,energy analysis together with the Natural Bonding Orbital(NBO) analysis were performed to elucidate the bonding characteristics in detail.The most stable structures are penta-coordinate complexes without aqua ligand located at the guanine site.Higher number of water ligands corresponds to higher stabilization energies.Average bonding energies of G-Cd increase with the number of water molecules.Bonding energies of water ligands depend on its position in the complexes.The charge distribution of guanine changed with increasing the number of water ligands,which may also influence the base-pairing pattern of guanine.There is positive charge transfer from guanine to aqua ligand as the number of the hydration waters increases.IEFPCM optimization has results comparable to the [CdG(H2O)5]2+ structure 5a.     

Luminescent double-decker type guanine octets with trivalent lanthanide cations: in situ self-assembling and stability evaluation in homogeneous organic media

Silylated guanine formed luminescent double-decker type octet complexes with trivalent lanthanide cations (lanthanide cation : guanine = 1:8) in organic media, while a deaminated guanine derivative gave only 1:2 complexes. The octet formation was evidenced by characteristic UV/Vis absorption changes, CSI-TOF MS and ¹H NMR spectra. The octet with Tb³⁺ showed intense green luminescence with a long lifetime by photo-excitation of the guanine chromophore. The trivalent lanthanie cations stabilized the octets more effectively than common mono- and divalent metal cations.     

Homopairing possibilities of the DNA bases cytosine and guanine: an ab initio DFT study

All the planar homopairings of cytosine and guanine are reported for the first time in this study. The idea of binding sites suggested for the simple case of adenine homopairs (J. Phys. Chem. B 2005, 109, 11933) is shown to be applicable to more complicated molecules binding to each other via multiple hydrogen bonds and can be considered as a general method for constructing hydrogen bonding structures. As an example we consider homopairs formed by DNA bases cytosine and guanine, suggesting that there may be 13 cytosine and 17 guanine homopairs. However, only 11 cytosine and 15 guanine homopairs remain after atomic relaxation performed using ab initio density functional theory. Most of the homopairs obtained have not been studied before. The homopairs have significant binding energies, varying from -0.19 to -1.12 eV, that are explained by multiple hydrogen bonds formed between monomers in the pairs, up to four hydrogen bonds in most energetically favorable cases. The detailed information on all guanine and cytosine planar homopairs contained in this work can be used to construct various cytosine and guanine superstructures observed on different surfaces.     

Modeling competitive reaction mechanisms of peroxynitrite oxidation of guanine

5-Guanidino-4-nitroimidazole is a stable product from the peroxynitrite induced one-electron oxidation of guanine. Reaction mechanisms to form the 5-guanidino-4-nitroimidazole as well as 8-nitroguanine, through the combination of the guanine radical cation and nitrogen dioxide radical and through the combination of the deprotonated neutral guanine radical and nitrogen dioxide radical, have been investigated by the use of the B3LYP method of density functional theory. Our calculations suggest that the guanine radical cation mechanism is preferred over the neutral guanine radical mechanism and that a water molecule is involved in the reaction as a catalyst or as a reactant.     

光致电化学鸟嘌呤传感器的制备及其应用

将硫堇电聚合在光透电极的表面,再利用壳聚糖将黄嘌呤氧化酶固定在具有光电活性的聚硫堇光透电极的表面上制备了光致电化学鸟嘌呤传感器.基于同时具有光敏和电子受体功能的聚硫堇光电界面,该传感器能与黄嘌呤氧化酶催化鸟嘌呤氧化而产生的电子供体(过氧化氢)产生光致电化学响应,通过测量光致电化学反应产生的光电流实现了对鸟嘌呤的检测.文中探讨了传感器的光致电化学响应机理,讨论了偏压、酶量、电解质溶液pH对传感器测定鸟嘌呤的影响.在优化的实验条件下,该传感器对鸟嘌呤的测定范围为1.00～200μmol/L,检出限为0.55μmol/L,9次测定的相对标准偏差小于3.92%.应用该传感器对酸解DNA脱出的鸟嘌呤基和药品阿昔洛韦进行的检测实验显示,相对标准偏差小于5.37%,加标回收率为96.8%～106%.该传感器的制备和对鸟嘌呤的检测不需要过氧化物酶,不需要除氧,有经济、简便等优点.     

Synthesis of Bio-Inspired Guanine Microplatelets: Morphological and Crystallographic Control

β-Phase anhydrous guanine (β-AG) crystals are one of the most widespread organic crystals to construct optical structures in organisms. Currently, no synthetic method is available that allows for producing guanine crystals with similar control in size, morphology, and crystallography as in biological ones. Herein, a facile one-step synthesis route to fabricate bio-inspired guanine microplatelets with (100) exposing planes in almost pure β-phase is reported. The synthesis is based on a precipitation process of a guanine sodium hydroxide solution in formamide with poly(1-vinylpyrrolidone-co-vinyl acetate) as a morphological additive. Due to their uniform size (ca. 20 μm) and thickness (ca. 110 nm), the crystals represent the first synthetic guanine microplatelets that exhibit strong structural coloration and pearlescent lusters. Moreover, this synthesis route was utilized as a model system to investigate the effects of guanine analogues, including uric acid, hypoxanthine, xanthine, adenine, and guanosine, during the crystallization process. Our results indicate that the introduction of guanine analogues not only can reduce the required synthesis temperature but also provide a versatile control in crystal morphology and polymorph selection between the α-phase AG (α-AG) and β-AG. Turbidity experiments show that the β-AG microplatelets are formed with a fast precipitation rate in comparison to α-AG, suggesting that the formation of β-AG crystals follows a kinetically driven process.     

PolyGuanine methacrylate cryogels for ribonucleic acid purification

The isolation and purification of ribonucleic acid have attracted attention recently for the understanding of the functions in detail because of the necessity for the treatment of genetic diseases. In this study, guanine‐incorporated polymeric cryogels were developed to obtain highly purified ribonucleic acid. The satisfactory purification performance was achieved with the guanine‐incorporated poly (2‐hydroxyethyl methacrylate‐guanine methacrylate) cryogels. The most crucial advantages to use guanine as a functional monomer are to obtain a real natural interaction between guanine on the polymeric material and cytosine on the ribonucleic acid. Moreover, using cryogel with a highly porous structure and high swelling ratio provide advantages of getting more water within the structure to get more analyte to interact. The characterization of cryogels has proved the success of the synthesis and the perfect natural interaction to be taken place between the ligand (guanine methacrylate) and the cytosine in the ribonucleic acid molecules. Although the pores within the structure of cryogels are small, they provide efficient and fast adsorption. The chromatographic separation performance was investigated for different conditions (pH, temperature etc.). The desorption ratio and reusability were also analyzed at the end of the five adsorption–desorption cycles with no significant changes.     

Capturing Transient Endoperoxide in the Singlet Oxygen Oxidation of Guanine

The chemistry of singlet O₂ toward the guanine base of DNA is highly relevant to DNA lesion, mutation, cell death, and pathological conditions. This oxidative damage is initiated by the formation of a transient endoperoxide through the Diels–Alder cycloaddition of singlet O₂ to the guanine imidazole ring. However, no endoperoxide formation was directly detected in native guanine or guanosine, even at ?100 °C. Herein, gas‐phase ion–molecule scattering mass spectrometry was utilized to capture unstable endoperoxides in the collisions of hydrated guanine ions (protonated or deprotonated) with singlet O₂ at ambient temperature. Corroborated by results from potential energy surface exploration, kinetic modeling, and dynamics simulations, various aspects of endoperoxide formation and transformation (including its dependence on guanine ionization and hydration states, as well as on collision energy) were determined. This work has pieced together reaction mechanisms, kinetics, and dynamics data concerning the early stage of singlet O₂ induced guanine oxidation, which is missing from conventional condensed‐phase studies.     

生物小分子的电分析化学研究 Ⅱ.鸟嘌呤、腺嘌呤和次黄嘌呤在粗热解石墨电极上的分子定向和表面相互作用

本文讨论了鸟嘌呤、腺嘌呤和次黄嘌呤等嘌呤类生物小分子在几种电极上的反应活性,并选用粗热解石墨电极研究了它们的电化学性质.实验结果表明它们的电极过程是受吸附作用控制的.在粗热解石墨电极上鸟嘌呤以C(2)-NH~2、腺嘌呤以C(6)-NH~2、次黄嘌呤以N(1)-H基团按垂直方向吸附于电极表面,电极表面分子间存在着相斥的相互作用.鸟嘌呤、腺嘌呤和次黄嘌呤的吸附平衡常数分别为:(3.34±1.00)×10^5,和(4.38±1.20)×10^5和(4.13±1.21)×10^5;吸附能分别为:(31.5±0.77),(32.1±0.70)和(32.0±0.75)kJ/mol.这些数值表明它们在粗热解石墨电极上具有中等偏强的物理吸附作用.     

Molecular recognition of cytosine- and guanine-functionalized nucleolipids in the mixed monolayers at the air-water interface and Langmuir-Blodgett films

Molecular recognition of mixed nucleolipids of 1-(2-octadecyloxycarbonylethyl)cytosine and 7-(2-octadecyloxycarbonylethyl)guanine in the monolayers at the air-water interface and Langmuir-Blodgett (LB) films has been investigated in detail using surface pressure/potential-area isotherms, infrared reflection-absorption spectroscopy (IRRAS), and Fourier transform infrared (FTIR) transmission spectroscopy, respectively. Prior to molecular recognition, the cytosine moieties in the monolayer were hydrogen bonded with an almost flat-on orientation, the alkyl chains were uniaxially oriented with respect to the film normal, the guanine moieties in the monolayer were stacked probably through pi-pi interaction with an end-on orientation, and the C-C-C planes of the alkyl chains were preferentially oriented parallel to the water surface. In the monolayer of equimolar mixture, molecular recognition between the cytosine and guanine moieties occurred together with the ring planes of base pairing and the C-C-C planes of the alkyl chains favorably oriented parallel to the water surface. The guanine moieties underwent an orientation change from an end-on mode before molecular recognition to a flat-on one after molecular recognition. The base pairing between the cytosine and guanine moieties in the monolayers was achieved since the N7-substituted guanine derivatives suppressed the formation of guanine tetramers. Both the IRRAS spectra of the monolayers and the FTIR spectra of the LB films presented the exact sites in the cytosine and guanine moieties for the formation of triple hydrogen bonds. The base pairing resulted in a change in molecular orientation and interaction, and the corresponding LB film exhibited a different phase transition behavior from a typical crystal transition for the cytosine-functionalized nucleolipids and an analogous glass transition for the guanine-functionalized nucleolipids. The thermal stability of the mixed LB film was improved in comparison to the LB films of pure components.