A supramolecular optic receptor for selective recognition CDP in neutral aqueous solution

We designed and synthesized a Cu-coordination complex based on a seven-membered amide cycle and studied its binding ability with nucleotides (cytidine 5′-monophosphate (CMP), cytidine 5′-diphosphate (CDP), cytidine 5′-triphosphate (CTP), cytidine d-5′-monophosphate (dCMP), and thymidine d-5′-monophosphate (dTMP)) by UV-Vis spectroscopy. Results indicate that the compound shows the highest binding ability with CDP among the studied nucleotides and can selectively and strongly bind nucleotides in neutral aqueous solution. The compound can be used as optical receptor for the detection of CDP.     

2’-脱氧胞苷-5’-磷酸羟基加合物的分子结构与电子结构

使用密度泛函理论(DFT)的B3LYP/DZP++研究了羟基自由基与2’-脱氧胞苷-5’-磷酸(dCMP)的胞嘧啶环加成产物的分子结构与电子结构. 结果表明, dCMP胞嘧啶环中各C原子上的单羟基加合物的相对稳定性顺序为C5>C6>>C4≥C2. 加合物的稳定性、自旋密度、静电势以及dCMP的电子密度、静电势、电荷分布分析表明, dCMP遭遇多个羟基自由基攻击时, 第一个羟基自由基加在dCMP的C5上, 而C6则成为第二个羟基自由基的进攻目标. 反应中一旦形成了C2-位单羟基加合物, 则极有可能在DNA复制过程中引起致命的基因突变, 也可能诱发DNA-DNA以及DNA-蛋白质的链间交联, 引起更复杂的损伤. 相反, C5、C6-位上单羟基加合物的形成对DNA的稳定性不构成直接威胁.     

Ab initio crystal orbital calculations on three-dimensional crystals of large bioorganic molecules and polymers

Ab initio crystal orbital calculations on three-dimensional crystals of tetrathiafulvalene-tetracyanoquinodimethane (TTF-TCNQ), diprotonated deoxycytidine-5′-monophosphate monohydrate (5′-dCMP*2H*1Water), disodium deoxyguanosine-5′-monophosphate tetrahydrate (5′-dGMP*2Na*4Water), disodium uridine-3′-monophosphate tetrahydrate (3′-UMP*2Na*4Water), monosodium monoprotonated deoxyadenosine-5′-monophosphate hexahydrate (5′-dAMP*1H*1Na*6Water), disodium deoxycytidine-5′-monophosphate heptahydrate (5′-dCMP*2Na*7Water), cis-polyacetylene (cis-PA), and polythiophene (PTP) were carried out using the CRYSTAL92 routine package. A suitable basis set has been found that enables one to carry out the above calculations at the STO -3G level of accuracy using SILICON GRAPHICS workstations. However, to obtain reasonable results for three-dimensional crystals of polymers, one has to use much more extended basis sets. © 1996 John Wiley & Sons, Inc.     

Cover Feature: OH Radical-Induced Oxidation in Nucleosides and Nucleotides Unraveled by Tandem Mass Spectrometry and Infrared Multiple Photon Dissociation Spectroscopy (ChemPhysChem 23/2023)

OH⋅-induced oxidation products of DNA nucleosides and nucleotides have been structurally characterized by collision-induced dissociation tandem mass spectrometry (CID-MS²) and Infrared Multiple Photon Dissociation (IRMPD) spectroscopy. CID-MS² results have shown that the addition of one oxygen atom occurs on the nucleobase moiety. The gas-phase geometries of +16 mass increment products of 2’-deoxyadenosine (dA(O)H⁺), 2’-deoxyadenosine 5’-monophosphate (dAMP(O)H⁺), 2’-deoxycytidine (dC(O)H⁺), and 2’-deoxycytidine 5’-monophosphate (dCMP(O)H⁺) are extensively investigated by IRMPD spectroscopy and quantum-chemical calculations. We show that a carbonyl group is formed at the C8 position after oxidation of 2’-deoxyadenosine and its monophosphate derivative. For 2’-deoxycytidine and its monophosphate derivative, the oxygen atom is added to the C5 position to form a C−OH group. IRMPD spectroscopy has been employed for the first time to provide direct structural information on oxidative lesions in DNA model systems.     

Interaction of dipropyltin(IV) with amino acids,peptides, dicarboxylic acids and DNA constituents

Interaction of dipropyltin(IV) with selected amino acids, peptides, dicarboxylic acids or DNA constituents was investigated using potentiometric techniques. Amino acids form 1?:?1 and 1?:?2 complexes and, in some cases, protonated complexes. The amino acid is bound to dipropyltin(IV) by the amino and carboxylate groups. Serine is complexed to dipropyltin(IV) with ionization of the alcoholic group. A relationship exists between the acid dissociation constant of the amino acids and the formation constants of the corresponding complexes. Dicarboxylic acids form both 1?:?1 and 1?:?2 complexes. Diacids forming five- and six-membered chelate rings are the most stable. Peptides form complexes with stoichiometric coefficients 111(MLH), 110(ML) and 11-1(MLH_?1)(tin: peptide: H⁺). The mode of coordination is discussed based on existing data and previous investigations. DNA constituents inosine, adenosine, uracil, uridine, and thymine form 1?:?1 and 1?:?2 complexes and the binding sites are assigned. Inosine 5′-monophosphate, guanosine 5′-monophosphate, adenosine 5′-monophosphate and adenine form protonated species in addition to 1?:?1 and 1?:?2 complexes. The protonation sites and tin-binding sites were elucidated. Cytosine and cytidine do not form complexes with dipropyltin(IV) due to low basicity of the donor sites. The stepwise formation constants of the complexes formed in solution were calculated using the non-linear least-square program MINIQUAD-75. The concentration distribution of the various complex species was evaluated as a function of pH.     

Radiation Chemical Studies of Protein Reactions: Effect of Amino Acids and Vitamins on the Breaking of Secondary Bonding in Protein

The radiation protective effect of the breaking of secondary bonding in protein was examined with such amino acids as disodium inosine-5′ -monophosphate and disodium guanosine-5′ -monophosphate and vitamins such as thiamine and λ-ascorbic acid. The behavior of the viscosity change closely resembles that found with the sodium 1-glutamate as shown by a similar dependence on concentration.     

Pd纳米粒子敏化的纳米单层TiO_2-Ru(Ⅱ)螯合物修饰电极对单磷酸鸟苷的电催化氧化行为

利用LB膜技术可控制备了纳米单层的二氧化钛-有机钌螯合物杂化膜,并研究了上述无机-有机杂化膜修饰电极在Pd纳米粒子敏化后对单磷酸鸟苷(GMP)的电催化氧化行为.实验结果表明:(1)纳米单层TiO2/[Ru(phen)2(dC18bpy)]2+(简称为TiO2-Ru)杂化膜的平均厚度为(3.2±0.5)nm;(2)在光照条件下TiO2-Ru杂化膜能有效催化还原[Pd(NH3)4]2+形成粒径位于20～200nm之间的Pd纳米粒子;(3)纳米单层TiO2-Ru/Pd杂化膜能高效催化氧化具有供电子能力的单磷酸鸟苷(GMP),与纳米单层TiO2-Ru杂化膜修饰的ITO电极(ITO/TiO2-Ru)相比,当工作电压为1200mV时,ITO/TiO2-Ru/Pd电极在含有1×10-3molL-1GMP的磷酸盐缓冲液中,单位面积的催化氧化电流提高了约36倍;(4)Pd纳米粒子的引入消除了金属钌螯合物中配体对电子传递的阻碍作用,改变了电子传递途径,从而有效减少了电子空穴对的复合,提高了杂化膜修饰电极(ITO/TiO2-Ru/Pd)的电子传递效率.     

A rapid and simple chemical method for the preparation of Ag colloids for surface-enhanced Raman spectroscopy using the Ag mirror reaction

Colloidal silver (Ag) nanoparticles (AgNP) have been widely used for surface-enhanced Raman spectroscopy (SERS) applications. We report a simple, rapid and effective method to prepare AgNP colloids for SERS using the classic organic chemistry Ag mirror reaction with Tollens’ reagent. The AgNP colloid prepared with this process was characterized using SEM, and the reaction conditions further optimized using SERS measurements. It was found that Ag mirror reaction conditions that included 20 mM AgNO₃, 5 min reaction time, and 0.5 M glucose produced AgNP colloids with an average size of 319.1 nm (s.d ± 128.1). These AgNP colloids exhibited a significant SERS response when adenine was used as the reporter molecule. The usefulness of these new AgNP colloids was demonstrated by detecting the nucleotides adenosine 5′-mono-phosphate (AMP), guanosine 5′-monophosphate (GMP), cytidine 5′-monophosphate (CMP), and uridine 5′-monophosphate (UMP). A detection limit of 500 nM for AMP was achieved with the as-prepared AgNP colloid. The bacterium Mycoplasma pneumoniae was also easily detected in laboratory culture with these SERS substrates. These findings attest to the applicability of this AgNP colloid for the sensitive and specific detection of both small biomolecules and microorganisms.     

An Fe2+- and α-Ketoglutarate-Dependent Halogenase Acts on Nucleotide Substrates

While halogenated nucleosides are used as common anticancer and antiviral drugs, naturally occurring halogenated nucleosides are rare. Adechlorin (ade) is a 2′-chloro nucleoside natural product first identified from Actinomadura sp. ATCC 39365. However, the installation of chlorine in the ade biosynthetic pathway remains elusive. Reported herein is a Fe²⁺-α-ketoglutarate halogenase AdeV that can install a chlorine atom at the C2′ position of 2′-deoxyadenosine monophosphate to afford 2′-chloro-2′-deoxyadenosine monophosphate. Furthermore, 2′,3′-dideoxyadenosine-5′-monophosphate and 2′-deoxyinosine-5′-monophosphate can also be converted, albeit 20-fold and 2-fold, respectively, less efficiently relative to the conversion of 2′-deoxyadenosine monophosphate. AdeV represents the first example of a Fe²⁺-α-ketoglutarate-dependent halogenase that converts nucleotides into chlorinated analogues.     

Determination of inosine 5′-monophosphate and guanosine 5′-monophosphate in pig feed by capillary zone electrophoresis

A capillary zone clectrophoresis method was developed for the determination of IMP and GIMP, commonly used as flavor enhancers in poultry feed, in a real sample of complex composition. A baseline separation of inosine 5′-monophosphate and guanosine 5′-monophosphate was achieved within 10 min and the other components in the sample did not interfere with the separation. Quantitative results obtained from pig feed samples are presented. The separation conditions and experimental reproducibility are also discussed.     

3-Acetyloxy-2-cyano-2-(alkylaminocarbamoyl)propyl groups as biodegradable protecting groups of nucleoside 5´-mono-phosphates

Thymidine 5′-bis[3-acetyloxy-2-cyano-2-(2-phenylethylcarbamoyl)propyl]phosphate (1) has been prepared and the removal of phosphate protecting groups by hog liver carboxyesterase (HLE) at pH 7.5 and 37 °C has been followed by HPLC. The first detectable intermediates are the (R(P))- and (S(P))-diastereomers of the monodeacetylated triester 14, which subsequently undergo concurrent retro-aldol condensation to diester 4 and enzyme-catalyzed hydrolysis to the fully deacetylated triester 15. The former pathway predominates, representing 90% of the overall breakdown of 14. The diester 4 undergoes the enzymatic deacetylation 700 times less readily than the triester, but gives finally thymidine 5′-monophosphate as the desired main product. To elucidate the potential toxicity of the electrophilic 2-cyano-N-(2-phenylethyl)acrylamideby-product 17 released upon the deprotection, the hydrolysis of 1 has also been studied in the presence of glutathione (GSH).     

Synthesis, characterization, antitumor activity of nickel(Ⅱ) and cobalt (Ⅱ) complexes of 2,2''''-diamino-4,4''''-bithiazole and their interaction with dGMP

New complexes,of bis(2,2'-diamino-4,4'-bithiazole)sulfate nickel(Ⅱ) and bis(2,2'-diami-no-4,4'-bithiazole)sulfate cobalt(Ⅱ),have been prepared.The complexes were characterized by infrared and UV-Vis spectroscopy,1H NMR,elemental analyses and molar conductivity.The effect of these complexes on the DNA synthesis of sarcoma 180 cells has been studied by the technique of isotopic liquid scintillation.The results indicated that complexes show ability to inhibit DNA synthesis of the tumor cells.In order to provide a molecular basis for understanding the biological effects,the probe,[trana-en2Os(η2-H2)](CF3SO3)2 (en,ethylenediamine) as a monitor was first used to explore interaction of the complexes with 2'-deoxyguanosine-5'-monophosphate (dGMP).     

Perturbation theory analysis for electronic response of DNA base pairs

The electronic responses of duplex B-DNA sequences are investigated using perturbation theory analyses. The electronic polarizability and effective mass are computed for base pair doublets and triplets and the electronic structures are calculated according to density functional theory. High polarizability and a light effective mass are obtained in a sequence such as 5′-GGG-3′. The results indicate that the concentration of GC base pairs causes a high response of the electronic states, and molecular orbitals that are very responsive to the electric field tend to be reactive with other orbitals or conducting hole carriers. Furthermore, the interaction between the electronic states and a positively charged wavepacket is discussed, assuming hole injection in the DNA sequences. The sequence of 5′-GGG-3′ responds sensitively to the external hole approach, which is presumably injected to a guanine site.     

Avoiding One-Electron Oxidation of Biomolecules by 3,4-Dihydroxy-L-Phenylalanine (DOPA)†

It has been proposed that 3,4-dihydroxy-L-phenylalanine (DOPA) has antioxidant properties, and thus, the objective of this work was to evaluate the effect of adding DOPA during the photosensitized oxidation of tyrosine (Tyr), tryptophan (Trp), histidine (His), 2′-deoxyguanosine 5′-monophosphate (dGMP) and 2′-deoxyadenosine 5′-monophosphate (dAMP). It was observed that, upon pterin-photosensitized degradation of a given biomolecule in acidic aqueous solutions, the rate of the biomolecule consumption decreases due to the presence of DOPA. Although DOPA deactivates the excited states of pterin (Ptr), biomolecules do as well, being the bimolecular quenching constants in the diffusional control limit, indicating that DOPA antioxidant mechanism is not a simple deactivation of Ptr excited states. Laser flash photolysis experiments provide evidence of the formation of DOPA radical (DOPA(–H)^•, λ_MAX 310 nm), which is formed in a timescale longer than Ptr triplet excited state (³Ptr*) lifetime, ruling out its formation in a reaction between DOPA and ³Ptr*. The experimental results presented in this work indicate that the observed decrease on the rate of each biomolecule consumption due to the presence of DOPA is through a second one-electron transfer reaction from DOPA to the biomolecule radicals.     

Carbocyclic Analogs of Nucleosides. Part 3. Synthesis of a new sulfone analog of cyclic adenosine 3′,5′-monophosphate

The novel uncharged analog 2 of adenosine 3′,5′ -monophosphate (1) was prepared in its racemic form. To increase membrane permeability, the phosphate diester monoanion group of 1 was replaced by a dimethylene sulfone unit ( = methanosulfonylmethano group), and the 2′-OH group was removed. To decrease lability against acid-catalyzed depurination, the ring O-atom was replaced by a CH₂ group. All three modifications are also expected to increase the stability of analog 2 towards enzymatic degradation. The carbocyclic skeleton of 2 was constructed from trinorbornenecarbaldehyde 3 (see Scheme 1–3), and the adenine precursor 6-chloropurine was introduced in the carbocyclic unit via an S_N2 reaction based on Mitsunobu chemistry (Schemes 4 and 5).     

Ion trap collisional activation of the deprotonated deoxymononucleoside and deoxydinucleoside monophosphates

Deoxymononucleoside and deoxydinucleoside monophosphate anions formed by electrospray have been subjected to ion trap collisional activation. The threshold for decomposition via loss of base is significantly lower for the deoxymononucleoside 3′-monophosphates than for the corresponding 5′-monophosphates, which indicates that the presence of a charged 3′ phosphate group facilitates base loss. The behavior of the bases among each class of isomers shows slight variation in threshold and tandem mass spectrometry efficiency with tile notable exception of 2′-deoxyguanosine 5′-monophosphate. This ion is exceptionally stable toward decomposition via base loss, which reflects a strong hydrogen bonding interaction between the base and the phosphate group. All dinucleotides fragment via similar mechanisms, but the propensity for neutral base loss relative to loss of a charged base is highly dependent on the identities of both the 5′ and 3′ bases. The behavior of the dinucleotides under collisional activation conditions supports the proposal that base loss proceeds via a proton-bound dimer intermediate in which loss of the charged base directly competes with loss of the neutral base. Application of the kinetic method allows for quantitative predictions of the differences of the gas-phase acidities of the dimer components.     

Nucleotides part XXX Chemical synthesis of adenylyl-(2′ → 5′)-adenylyl-(2′ → 5′)-8-azidoadenosine,and activation and photoaffinity labelling of RNase L by [32P]p5′A2′p5′A2′p5′N38A

The chemical synthesis of adenylyl-(2′–5′)-adenylyl-(2′–5′)-8-azidoadenosine ( 15 ) was performed by the phosphotriester approach. Enzymatic phosphorylation of 15 by [γ-³²P]ATP led to the corresponding labelled 5′-monophosphate 16 . Photoinsertion of 16 took place on UV irradiation by covalent cross linking to a protein of M_r 80 K known to be RNase L. Radiobinding and core-cellulose assays as well as photoaffinity labelling experiments with 16 are described.     

Ru(II) polypyridine complexes with a high oxidation power. Comparison between their photoelectrochemistry with transparent SnO2 and their photochemistry with desoxyribonucleic acids

The compounds which are discussed in the present review are highly oxidizing Ru(II) complexes, based on various polyazaaromatic ligands, and acting as efficient electron acceptors in the excited state. The photoinduced charge transfer process and the following associated kinetic steps are characterized for the whole series of complexes by quite different techniques and methods. Thus their behaviour in the presence of reductants such as hydroquinone and mononucleotides (guanosine-5′-monophosphate and adenosine-5′-monophosphate) are examined by flash photolysis, spectroelectrochemistry and photoelectrochemistry. It is explained how the light-initiated electron transfer process can be applied for spectral supersensitization of wide band gap SnO₂ semiconductor electrodes. Moreover, it is shown that such a knowledge of the behaviour of these photoredox reactions leads to interesting applications of these oxidizing complexes in a biological area, i.e. for the study of nucleic acids. Thus it is illustrated how these compounds can be used as promising photoreagents of DNA. The easy modulation of their size and shape, and their irreversible anchoring on the DNA bases, triggered by the reductive photoelectron transfer process from the guanine bases to the excited complex, allow one to regard these complexes as attractive molecular tools for DNA study and maybe as future possible drugs activatable under visible light.     

Nucleotides. Part XXVI.. A new synthesis of 9-(′-D-ribofuranosyl)uric acid and its 5′-monophosphate

Syntheses for 9-(β-D -ribofuranosyl)uric acid ( 16 ) and its 5′-monophosphate 14 have been achieved starting from guanosine and applying the 2-(p-nitrophenyl)ethyl group for protection of the aglycon moiety as well as the phosphate function. A more efficient and direct approach to 14 uses O⁶, O⁸-dibenzyl protection and phosphorylation by the Yoshikawa procedure. The various protected intermediates have been characterized by spectroscopic means and elemental analysis.     

Charge hopping in DNA.

The efficiency of charge migration through stacked Watson-Crick base pairs is analyzed for coherent hole motion interrupted by localization on guanine (G) bases. Our analysis rests on recent experiments, which demonstrate the competition of hole hopping transitions between nearest neighbor G bases and a chemical reaction of the cation G(+) with water. In addition, it has been assumed that the presence of units with several adjacent stacked G bases on the same strand leads to the additional vibronic relaxation process (G(+)G...G) --> (GG...G)(+). The latter may also compete with the hole transfer from (G(+)G...G) to a single G site, depending on the relative positions of energy levels for G(+) and (G(+)G...G). A hopping model is proposed to take the competition of these three rate steps into account. It is shown that the model includes two important limits. One corresponds to the situation where the charge relaxation inside a multiple guanine unit is faster than hopping. In this case hopping is terminated by several adjacent G bases located on the same strand, as has been observed for the GGG triple. In the opposite, slow relaxation limit the GG...G unit allows a hole to migrate further in accord with experiments on strand cleavage exploiting GG pairs. We demonstrate that for base pair sequences with only the GGG triple, the fast relaxation limit of our model yields practically the same sequence- and distance dependencies as measurements, without invoking adjustable parameters. For sequences with a certain number of repeating adenine:thymine pairs between neighboring G bases, our analysis predicts that the hole transfer efficiency varies in inverse proportion to the sequence length for short sequences, with change to slow exponential decay for longer sequences. Calculations performed within the slow relaxation limit enable us to specify parameters that provide a reasonable fit of our numerical results to the hole migration efficiency deduced from experiments with sequences containing GG pairs. The relation of the results obtained to other theoretical and experimental studies of charge transfer in DNA is discussed. We propose experiments to gain a deeper insight into complicated kinetics of charge-transfer hopping in DNA.