The effects of oxidation and protonation on the N-glycosidic bond stability of 8-oxo-2′-deoxyguanosine: DFT study

This work is an attempt to evaluate the ability of protonation of 8-oxo-2′-deoxyguanosine (8-oxodG) and the effects of oxidation and protonation on its N-glycosidic bond stability by using the density functional theory B3LYP/6-31++G(d, p) method. In all modified forms, the length of the N9–C1′ bond increases as compared to the neutral system 8-oxodG. Especially, the changes are much more obvious for the di-cationic systems. The analysis for the ability of protonation indicates that for the mono-protonated systems, the O8 atom becomes the preferred protonation site in the gas phase. From the dissociation energies of the N-glycosidic bond, it has been found that the homolytic cleavage becomes more difficult upon introducing positive charge in the base ring. In contrast, these systems favor significantly the heterolytic cleavage, especially for the di-cationic systems in which the dissociation energy values are negative. The influence is most prominent with the mono-cation obtained by O8 protonation.     

A label-free ultrasensitive assay of 8-hydroxy-2′-deoxyguanosine in human serum and urine samples via polyaniline deposition and tetrahedral DNA nanostructure

Oxidative damage is an important factor in causing various human disease and injury. As an oxidative DNA damage product, 8-hydroxy-2′-deoxyguanosine (8-OHdG) is a key marker, which is widely used to study oxidative damage mechanism in diseases. Most reported electrochemical methods were based on oxidation current of 8-OHdG. In this work, a simple electrochemical biosensor for ultrasensitive detection of 8-OHdG was proposed based on it triggered polyaniline (PANI) deposition on tetrahedral DNA nanostructure (TDN). TDN was immobilized onto a gold electrode surface based on self-assembly between three thiolated nucleotide sequences. 8-OHdG-aptamer on the top of TDN formed a hemin/G-quadruplex structure in the presence of 8-OHdG and hemin, which have high catalytic activity to trigger PANI deposition. Numerous negative charges on the duplex DNAs contained in hemin/G-quadruplex and TDN supplied exquisite environment for PANI deposition, which improved the detection sensitivity greatly by increasing the DPV current to10-fold (∼3 μA) compared to our previously reported method without TDN. The response signals correlated linearly with the concentration of 8-OHdG ranging from 10 pM to 2 nM, with a detection limit of 1 pM (S/N = 3). The sensitivity was improved to almost 300-fold when compared with most of previously reported electrochemical methods. The method was also simple and reliable, avoiding complex, expensive label procedures and nanomaterial synthesized procedures. The method had been successfully applied to quantify 8-OHdG in urine and human serum samples with satisfactory results.     

8-Aza-2′-deoxyguanosine and Related 1,2,3-Triazolo[4,5-d]pyrimidine 2′-Deoxyribofuranosides

The synthesis of 8-azaguanine N⁹-, N⁸-, and N⁷-(2′-deoxyribonucleosides) 1–3 , related to 2′-deoxyguanosine ( 4 ), is described. Glycosylation of the anion of 5-amino-7-methoxy-3H-1,2,3-triazolo[4,5-d]pyrimidine ( 5 ) with 2-deoxy-3,5-di-O-(4-toluoyl)-α-D -erythro-pentofuranosyl chloride ( 6 ) afforded the regioisomeric glycosylation products 7a/7b, 8a/8b , and 9 (Scheme 1) which were detoluoylated to give 10a, 10b, 11a, 11b , and 12a . The anomeric configuration as well as the position of glycosylation were determined by combination of UV, ¹³C-NMR, and ¹H-NMR NOE-difference spectroscopy. The 2-amino-8-aza-2′-deoxyadenosine ( 13 ), obtained from 7a , was deaminated by adenosine deaminase to yield 8-aza-2′-deoxyguanosine ( 1 ), whereas the N⁷- and N⁸-regioisomers were no substrates of the enzyme. The N-glycosylic bond of compound 1 (0.1 N HCl) is ca. 10 times more stable than that of 2′-deoxyguanosine ( 4 ).     

5′,8-Cyclopurine-2′-deoxynucleosides: Molecular structure and charge distribution – DFT study in gaseous and aqueous phase

Oxidatively generated damage to DNA frequently appears in the human genome as an effect of aerobic metabolism or as the result of exposure to exogenous oxidizing agents. Due to these facts, it has been decided to present the structural propriety and charge distribution of 5′,8-cyclo-2′-deoxyadenosine/guanosine (cdA, cdG) in their 5′R and 5′S diastereomeric forms. For all points of quantum mechanics studies presented, the density functional theory (DFT) with B3LYP parameters on 6-311++G** basis set level was used. The 2-deoxyribose moiety of cyclopurines has adopted the ₀T¹ conformation in their cationic, neutral and anionic forms. The natural population analysis (NPA) of charge distribution between purine/2-deoxyribose moieties exhibited positive/positive value for cations, positive/negative for neutral molecules. NPA data for anionic forms showed negative/negative values in gas (exclude (5′S)cdG) and positive/negative in water. The dipole moments of 5′,8-cyclopurine-2′-deoxynucleosides were found as follows: 7.83(5′R)cdG, 6.86(5′S)cdG, 3.99(5′R)cdA, 1.99(5′S)cdA in the gaseous phase, 11.29(5′R)cdG, 9.99(5′S)cdG, 6.44(5′R)cdA, 4.14(5′S)cdA in the aqueous phase.     

Synthesis,Base Pairing,and Structural Transitions of Oligodeoxyribonucleotides Containing 8-Aza-2′-deoxyguanosine

The synthesis of oligonucleotides containing 8-aza-2′-deoxyguanosine (z⁸G_d; 1 ) or its N⁸-regioisomer z⁸G_d^* ( 2 ) instead of 2′-deoxyguanosine (G_d) is described. For this purpose, the NH₂ group of 1 and 2 was protected with a (dimethylamino)methylidene residue (→ 5, 6 ), a 4,4′-dimethoxytrityl group was introduced at 5′-OH (→ 7, 8 ), and the phosphonates 3a and 4 as well as the phosphoramidite 3b were prepared. These building blocks were used in solid-phase oligonucleotide synthesis. The oligonucleotides were characterized by enzymatic hydrolysis and melting curves (T_m values). The thermodynamic data of the oligomers 12–15 indicate that duplexes were stabilized when 1 was replacing G_d. The aggregation of d(T-G-G-G-G-T) ( 18 ) was studied by RP 18 HPLC, gel electrophoresis and CD spectroscopy and compared with that of oligonucleotides containing an increasing number of z⁸G_d residues instead of G_d. Similarly to [d(C-G)]₃ ( 12a ), the hexamer d(C-z⁸G-C-z⁸G-C-G) ( 14 ) underwent salt-dependent B-Z transition.     

Structurally characterized group 4 metal alkoxides modified with the pyridyl-based ligands 2-mercapto pyridine n-oxide and 3,3′-dihydroxy-2,2′-bipyridine

An investigation of a series of substituted pyridyl-based ligands was undertaken using 2-mercapto pyridine n-oxide (H-2MPO) and 3,3′-dihydroxy-2,2′-bipyridine (H₂-OBPy) as the modifying reagents of a series of titanium alkoxides. The resultant products were identified as (2MPO)₂Ti(OR)₂ [OR = OCHMe₂ (1), OCH₂CMe₃ (2), OCMe₃ (3)] and [(OR)₂M(μ_c-OBPy)]₃ where MOR = TiOCH₂CMe₃ (4) along with ZrOCMe₃ (5) from Zr(OCMe₃)₄ (μ_c = chelating bridging). The structure of 1–3 were found to adopt similar monomeric structures with octahedrally (Oh) bound Ti metal centers using two terminal OR and two chelating 2MPO derivatives. Switching to the OBPy ligand, cyclic trinuclear species with Oh bound metals that employed two terminal OR and two μ_c-OBPy ligands were isolated. The two rings of the bridging OBPy were rotated such that one O and one N from different rings chelate to a single metal. The synthesis and characterization of these compounds and comparison to appropriate literature species are presented.     

Theoretical studies on the structural and optical properties of a series of Os(II) diimine complexes [Os(NN)(CO)2I2] (NN = 2,2′-bipyridine(bpy), 4,4′-di-tert-butyl-2,2′-bipyridine(dbubpy), 4,4′-dichlorine-2,2′-bipyridine(dclbpy))

The ground- and excited-state structures for a series of Os(II) diimine complexes [Os(NN)(CO)₂I₂] (NN = 2,2′-bipyridine (bpy) (1), 4,4′-di-tert-butyl-2,2′-bipyridine (dbubpy) (2), and 4,4′-dichlorine-2,2′-bipyridine (dclbpy) (3)) were optimized by the MP2 and CIS methods, respectively. The spectroscopic properties in dichloromethane solution were predicted at the time-dependent density functional theory (TD-DFT, B3LYP) level associated with the PCM solvent effect model. It was shown that the lowest-energy absorptions at 488, 469 and 539 nm for 1–3, respectively, were attributed to the admixture of the [d_xy (Os) → π^*(bpy)] (metal-to-ligand charge transfer, MLCT) and [p(I) → π^*(bpy)] (interligand charge transfer, LLCT) transitions; their lowest-energy phosphorescent emissions at 610, 537 and 687 nm also have the ³MLCT/³LLCT transition characters. These results agree well with the experimental reports. The present investigation revealed that the variation of the substituents from H → t-Bu → Cl on the bipyridine ligand changes the emission energies by altering the energy level of HOMO and LUMO but does not change the transition natures.     

Resonance Raman spectra of metalloporphyrins. On the methine-bridge vibrations of ferric octaethylporphyrins and its α′, β′, γ′, and δ′ deutero derivatives

Raman spectra of Fe³⁺ and Pd²⁺ octaethylporphyrin (OEP) and their α′, β′, γ′, and δ′ deutero derivatives were measured with the 5145, 4880 and 4765 Å lines of an Ar ion laser. Raman bands due to methine-bridge stretching vibrations were assigned and their vibrational amplitudes were calculated from the observed frequency shifts on deuterium substitution of methine-bridge hydrogens. These vibrations correspond to the spin-state sensitive Raman bands of heme proteins. On the basis of symmetry considerations and the observed polarizations, vibrational assignments of other Raman bands were made.     

Kinetic study of the complex reaction between copper(II) and 2-(2′-hydroxy-3′-methoxyphenyl)benzothiazole

2-(2′-Hydroxy-3′-methoxyphenyl)benzothiazole reacts with copper(II) in an ethanol/water mixture to form an O,S chelate which exhibits the remarkable property of changing the chelation site above a pH of ca. 5.0, to the O,N site. The detailed kinetics of this reaction in an ethanol/water mixture (3:1) at a temperature of 25 °C was investigated using a stopped-flow spectrophotometric technique employing a wavelength of 400 nm. The initial complex, Cu(O,S), is formed via a fast, reversible second-order complex formation step whereupon the formation of the Cu (O,N) follows first order kinetics. The Cu(O,N) complex is, however, unstable towards internal electron exchange and after the reaction is complete, a black polymeric material very slowly precipitates out of solution. Rate and equilibrium constants for the postulated reactions are presented and discussed.     

Rapid extraction and spectrophotometric determination of vanadium(V) with 2′-hydroxy-4-methoxy-5′-methyl chalkone oxime (HMMCO)

2′-Hydroxy-4-methoxy-5′-methyl chalkone oxime (HMMCO) is used for the extraction and spectrophotometric determination of microgram quantities of vanadium. HMMCO forms a green colored complex with vanadium at 9 M HCl extracted into chloroform. The complex absorbs maximum at 630 nm. Beer's law holds good over the concentration range of 2.7 to 94.0 μg of vanadium per ml. The Ringbom plot shows the effective working range of 4.5 to 67.0 μg of vanadium per ml. The extracted species shows the composition to be 1:2 (V:HMMCO). Vanadium can be extracted quantitatively without any serious interference of the foreign ions. It is possible to extract and determine vanadium quantitatively from binary mixtures that contain niobium, tantalum, or titanium. The method is also applicable to some ores.     

Synthesis and structure of mixed-metal thiolate complex Cp′Cr(CO)2(μ-SBu)Pt(PPh3)2: Side-on-coordination of Cr–S double bond with platinum

The reaction of [Cp′Cr(CO)₂(μ-SBu)]₂ (1) (Cp′ = MeC₅H₄) with (PPh₃)₂Pt(PhCCPh) gives Cp′Cr(CO)₂(μ-SBu)Pt(PPh₃)₂ (2) which could be regarded as a product of the substitution of acetylene ligand at platinum by a monomeric chromium–thiolate fragment. According to the X-ray diffraction analysis 2 contains single Cr–Pt (2.7538(15)) and Pt–S (2.294(2) Å) bonds while Cr–S bond (2.274(3) Å) is shortened in comparison with ordinary Cr–S bonds (2.4107(4)–2.4311(4) Å) in 1. The bonding between Cr–S fragment and platinum atom is similar to the olefine coordination in their platinum complexes.     

8-Aza-7-deaza-2′-deoxyguanosine: Phosphoramidite synthesis and properties of octanucleotides

Base-modified octanucleotides derived from d(G1–G2–A–A–T–T–C–C–) ( 11 ) but containing 8-aza-7-deaza-2′-deoxyguanosine ( 2 ) instead of 2′-deoxyguanosine ( 1 ) have been prepared by solid-phase synthesis employing P(III) chemistry. Isobutyrylation of 2 , followed by 4, 4′-dimethoxytritylation and subsequent phosphitylation yielded the methyl or the cyanoethyl phosphoramidites 6a or 6b , respectively. They were used as building blocks in automated DNA synthesis. The resulting octanucleotides 12–14 containing 2 showed increased T_m values compared to the parent oligomer 11 . The oligomers 11 – 14 were employed as sequence-specific probes in endo-deoxyribonuclease Eco RI oligonucleotide recognition. Whereas displacement of dG-2 (enzymic cleavage site of 11 ) abolished phosphodiester hydrolysis, replacement of dG-1 enhanced the cleavage rate compared to 11 .     

Selective 5′-desilylation of 3′,5′-disilyi AraU derivatives under basic conditions

3′,5′-di-tert-butyldimethylsilyl-2,2′-anhydrouridine 3 was hydrolyzed under basic conditions to yield selectively 3′-tert-butyldimethylsilylarabinouridine 5 in 85 % yield. 3′,5′-disilyl-arabinouridine derivatives 4 and 6 also led selectively to 5 under the same conditions. These reactions suggest an intramolecular participation of the 2′-hydroxyl group in the desilylation and can be used to prepare rapidly and in high yield 3′-silylaraU derivatives.     

超高效液相色谱-串联质谱法测定氧化损伤标志物8-羟基脱氧鸟苷

发展了一种超高效液相色谱-串联质谱法(UPLC-MS/MS)检测脱氧核糖核酸(DNA)分子中8-羟基脱氧鸟苷(8-OHdG)的方法。DNA分子在酶解过程中,脱氧鸟苷(dG)易被氧化形成8-OHdG,从而使得8-OHdG的检测结果不准确。通过加入甲磺酸去铁铵作为保护剂,有效地避免了酶解过程造成的dG氧化。酶解液通过超滤膜(截留相对分子质量为3 000的分子)处理,有效去除大量蛋白分子后,直接进行UPLC-MS/MS测定。采用外标法定量,在17.6～1 400fmol范围内,8-OHdG的峰面积与其物质的量具有良好的线性关系,相关系数为0.999 8。利用本方法测定了小牛胸腺DNA中8-OHdG的含量(用比值8-OHdG/106dG表示)为12.9±2.35,与前人报道的检测结果一致。本方法也可以应用于评价各种氧化因素引起的DNA氧化损伤。     

A computational study and fragment analysis of the back-bonding in Titanocenyl Complexes containing a five-member L,L′-cyclic ligand, L,L′ = O,O′; S,S′ or Se,Se′

A DFT computational study is performed on different Cp₂Ti^IV(L,L′-BID) complexes with L,L′-BID = dioxolene, dithiolene or diselenolene. A fragment analysis of the titanocene-ligand bonding in the DFT optimized geometries showed that out of plane folding for maximum Ti ← L π donation increases Cp₂Ti^IV(O,O′-BID) (35°) < Cp₂Ti^IV(S,S′-BID) (43–49°) < Cp₂Ti^IV(Se,Se′-BID) (48–53°).     

Synthesis of oligonucleotides containing 7-(2-deoxy-β-d-erythro-pentofuranosyl)guanine and 8-amino-2′-deoxyguanosine

The synthesis of oligonucleotides containing 7-(2-deoxy-β-D-erythro-pentofuranosyl)guanine and 8-amino-2′-deoxyguanosine was accomplished. The viable intermediate N²-isobutyryl-7-(2-deoxy-β-D-erythro-pentofuranosyl)guanine ( 6 ) was prepared via a four step deoxygenation procedure from 7-β-D-ribofuranosylguanine ( 1 ). The 5′-hydroxyl group of 6 was protected as 4,4′-dimethoxytrityl ether and then converted to the target phosphoramidite ( 8 ) via conventional phosphitylation procedure. The amino groups of 8-amino-2′-deoxyguanosine ( 9 ) were protected in the form of N-(dimethylainino)methylene functions to give the protected nucleoside 10 , which was subsequently converted to the target phosphoramidite 12 via dimethoxytritylation followed by phosphitylation. The phosphoramidites 8 and 12 were incorporated into a 26-mer and a 31-mer G-rich oligonucleotide using solid-support, phosphoramidite methodology. Analysis of antiparallel triplex formation by the oligonucleotides containing 7-(2-deoxy-β-D-erythro-pentofura-nosyl)guanine in place of 2′-deoxyguanosine showed no enhancement in triple helix formation.     

A divergent synthesis of - and -carbocyclic 4′-fluoro-2′,3′-dideoxynucleosides as potential antiviral agents

- and -Carbocyclic 4′-fluoro-2′,3′-dideoxynucleosides have been synthesized from 2, which can be conveniently prepared from 1,2:5,6-di-O-isopropylidene- -mannitol 1 in eight steps. Ruthenium-catalyzed ring-closing metathesis has been employed in the synthesis of -nucleosides, whereas the -series have been obtained through an intramolecular nucleophilic substitution reaction. The Mitsunobu condensation was used as a general tool for the synthesis of both purine and pyrimidine nucleosides.     

Radioprotection by DMSO in nitrogen-saturated mammalian cells exposed to helium ion beams

The contribution of OH radical-mediated indirect action by particle beams under hypoxic irradiation condition was investigated by using a radical scavenger. V79 cells were irradiated with 150 MeV/nucleon helium ions at an LET of 2.2 keV/μm in the presence or absence of DMSO, and their colony survivals were determined. The contribution of indirect action to cell killing under hypoxic condition was estimated to be 52±9%. We conclude that OH radical-mediated indirect action still has a half in total contribution on cell killing under hypoxic condition.     

Approaches to wired terpyridine: Bithienyl alkynyl derivatives of 2,2′:6′,2″-terpyridine and their ruthenium(II) complexes

Two approaches to the formation of ruthenium(II) complexes containing ligands with conjugated 2,2′:6′,2″-terpyridine (tpy), alkynyl and bithienyl units have been investigated. Bromination of 4′-(2,2′-bithien-5′-yl)-2,2′:6′,2″-terpyridine leads to 4′-(5-bromo-2,2’-bithien-5′-yl)-2,2′:6′,2″-terpyridine (1), the single crystal structure of which has been determined. The complexes [Ru(1)₂][PF₆]₂ and [Ru(tpy)(1)][PF₆]₂ have been prepared and characterized. Sonogashira coupling of the bromo-substituent with (TIPS)CCH did not prove to be an efficient method of preparing the corresponding complexes with pendant alkynyl units. The reaction of 4′-ethynyl-2,2′:6’,2″-terpyridine with 5-bromo-2,2′-bithiophene under Sonogashira conditions yielded ligand 2, and the heteroleptic ruthenium(II) complex [Ru(2)(tpy)][PF₆]₂ has been prepared and characterized.