Effect of Various Pyrimidines Possessing the 1-[(2-Hydroxy-1-(hydroxymethyl)ethoxy)methyl] Moiety, Able To Mimic Natural 2‘-Deoxyribose, on Wild-type and Mutant Hepatitis B Virus Replication

Hepatitis B virus (HBV) is the most common cause of chronic liver disease worldwide. Development of drug resistance against clinical anti-HBV drug lamivudine due to long-term use and rebound of viral DNA after cessation of treatment has been a major setback of the current therapy. We have synthesized a series of pyrimidine nucleosides possessing a variety of substituents at the C-5 position, and a 1-[(2-hydroxy-1-(hydroxymethyl)ethoxy)methyl] flexible acyclic glycosyl moiety at the N-1 position, that have the ability to mimic the natural 2'-deoxyribosyl moiety. Some of these potential antiviral compounds included variations at both C-5 and C-6 positions of the uracil base. Other variations of the uracil derivatives were the 6-aza congeners. 4-Amino and 4-methoxy pyrimidine derivatives were also made. Compounds in which the base moiety was substituted by 5-chloro- (25), 5-(2-bromovinyl)- (32), or 5-bromo-6-methyl- (37) groups possess significant activity against duck-HBV, wild-type human HBV (2.2.15 cells), and lamivudine-resistant HBV containing single and double mutations. No cytotoxicity was seen in host HepG2 and Vero cells, up to the highest concentration tested. The anti-HBV activity exhibited by compounds 25, 32, and 37 was superior for human HBV and comparable for DHBV to that of the corresponding purine nucleoside, ganciclovir. Further, they were only 10-15-fold less inhibitory against human HBV in 2.2.15 cells than the reference drug, lamivudine. Other compounds in the series were moderately inhibitory against DHBV and wild-type human HBV. The size of the halogen and the electronegativity of the substituents at the 5- and 6-positions are important for antiviral activity toward HBV. These compounds were also evaluated for their antiviral activity for West Nile virus, respiratory syncytial virus, SARS-coronavirus, and hepatitis C virus. They were generally inactive in these antiviral assay systems (at concentrations up to 100 microg/mL). 1-[(2-Hydroxy-1-(hydroxymethyl) ethoxy)methyl]-5-fluorocytosine (34) showed some inhibitory activity against hepatitis C virus. Taken together, these data support our previous observations that the 5-substituted pyrimidine nucleosides containing acyclic glycosyl moieties have potential to serve as a new generation of potent, selective, and nontoxic anti-HBV agents for wild-type and lamivudine-resistant mutant HBV.

Preference for ribose over deoxyribose in loop-closing base pairs of extra stable nucleic acid hairpins

We have investigated the effect of switching ribose to deoxyribose at the closing base-pair of an extra-stable RNA hairpin. Specifically, we studied the sequence 5'-GGAC(UUCG)GUCC, a dodecanucleotide that folds into a well-characterized, "extra stable" RNA hairpin structure. Recently, we showed that hairpins containing a 2',5'-linked (UUCG) loop instead of the native 3',5'-linked loop also exhibit extra-stability (Hannoush and Damha, J. Am. Chem. Soc., 2001, 123, 12368-12374). In this article, we show that the ribose units located at the loop-closing positions (i.e., rC4 and rG9) contribute significantly to the stabilization of RNA hairpins, particularly those containing the 3',5'-UUCG loop. Interestingly, the requirement of rC4 and rG9 is more relaxed for DNA hairpins containing the 2',5'-UUCC loop and, in fact, they may be replaced altogether (ribose--> deoxyribose) without affecting stability. The results broaden our understanding of the behavior of highly stable (UUCG) hairpin loops and how they respond to structural perturbation of the loop-closing base pairs.

C5'- and C3'-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2'-deoxyadenosine and its derivatives

We report that photo-excitation of one-electron-oxidized adenine [A(-H)•] in dAdo and its 2′-deoxyribonucleotides leads to formation of deoxyribose sugar radicals in remarkably high yields. Illumination of A(-H)• in dAdo, 3′-dAMP and 5′-dAMP in aqueous glasses at 143 K leads to 80-100% conversion to sugar radicals at C5′ and C3′. The position of the phosphate in 5′- and 3′-dAMP is observed to deactivate radical formation at the site of substitution. In addition, the pH has a crucial influence on the site of sugar radical formation; e.g. at pH ∼5, photo-excitation of A(-H)• in dAdo at 143 K produces mainly C5′• whereas only C3′• is observed at high pH ∼12. ¹³C substitution at C5′ in dAdo yields ¹³C anisotropic couplings of (28, 28, 84) G whose isotropic component 46.7 G identifies formation of the near planar C5′•. A β-¹³C 16 G isotropic coupling from C3′• is also found. These results are found to be in accord with theoretically calculated ¹³C couplings at C5′ [DFT, B3LYP, 6-31(G) level] for C5′• and C3′•. Calculations using time-dependent density functional theory [TD-DFT B3LYP, 6-31G(d)] confirm that transitions in the near UV and visible induce hole transfer from the base radical to the sugar group leading to sugar radical formation.

Hydroxyl radical scavenging reactivity of proton pump inhibitors

In addition to the established control of acid secretion of the class of proton pump inhibitors (PPI) reactivity from the pyridyl methyl sulphinyl benzimidazole type a second independent anti-inflammatory reactivity was observed in vitro. This inhibitory reactivity was clearly noticed using three different assays where the aggressive hydroxyl radicals were successfully trapped in a concentration dependent manner. There is unequivocal evidence that the proton pump inhibitors having the sulphoxide group are able to scavenge hydroxyl radicals which are generated during a Fenton reaction. By way of contrast, the corresponding thioethers were substantially less active. No detectable effect was seen in the superoxide radical scavenging system. In conclusion, pantoprazole as well as the other proton pump inhibitors have a pronounced inhibitory reactivity towards hydroxyl radicals.

The structure of a mixed LNA/DNA:RNA duplex is driven by conformational coupling between LNA and deoxyribose residues as determined from 13C relaxation measurements

A study of the internal dynamics of an LNA/DNA:RNA duplex has been performed to further characterize the conformational changes associated with the incorporation of locked nucleic acid (LNA) nucleotides in a DNA:RNA duplex. In general, it was demonstrated that the LNA/DNA:RNA duplex has a very high degree of order compared to dsDNA and dsRNA duplexes. The order parameters of the aromatic carbon atoms in the LNA/DNA strand are uniformly high, whereas a sharp drop in the degree of order was seen in the RNA strand in the beginning of the AUAU stretch in the middle of the strand. This can be related to a return to normal dsRNA dynamics for the central A:U base pair. The high order of the heteroduplex is consistent with preorganization of the chimera strand for an A-form duplex conformation. These results partly explain the dramatic increase in T(m) of the chimeric heteroduplex over dsDNA and DNA:RNA hybrids of the same sequence.

Dual mechanism of mangiferin protection against iron-induced damage to 2-deoxyribose and ascorbate oxidation

We studied mangiferin effects on the degradation of 2-deoxyribose induced by Fe(III)-EDTA/citrate plus ascorbate, in relation to ascorbate oxidation (measured at 265 nm). Results revealed that mangiferin was equally effective in preventing degradation of both 15 and 1.5 mM 2-deoxyribose. At a fixed Fe(III) concentration, increasing the concentration of ligands (either EDTA or citrate) caused a significant reduction in the protective effects of mangiferin. Interestingly, mangiferin strongly stimulated Fe(III)-EDTA ascorbate oxidation, but inhibited it when citrate was used as iron co-chelator. Mangiferin stimulated O2 consumption due to Fe(II) (formed by Fe(III) ascorbate reduction) autoxidation when the metal ligand was EDTA, but inhibited it when citrate was used. These results suggest that mangiferin removes iron from citrate, but not from EDTA, forming an iron-mangiferin complex that cannot induce ascorbate oxidation effectively, thus inhibiting iron-mediated oxyradical formation. Taken together, these results indicate that mangiferin works mainly by a mechanism different from the classical hydroxyl radical scavengers, keeping iron in its ferric form, by complexing Fe(III), or stimulating Fe(II) autoxidation.

Antioxidant Activity of Four Endemic Stachys Taxa

Methanol extracts of aerial flowering parts of four endemic Stachys taxa: S. anisochila VIS. et PANCIC, S. beckeana DORFLER & HAYEK, S. plumosa GRISEB. and S. alpina L. ssp. dinarica MURB. were investigated on their antioxidant activity. The extracts were studied for total antioxidant activity (TAA), along with 1,1-diphenyl 2-picryl hydrazyl (DPPH) and OH radical scavenging activity, and lipid peroxidation (LP). High correlations between total phenolics content, TAA and scavenging DPPH radical indicate that polyphenols are the main antioxidants. All Stachys extracts, with the exception of S. plumosa, exhibited high anti-DPPH activity (IC50<50 microg/ml). In concentration range from 6.25 to 50 microg/ml, all extracts scavenged OH radical above 40%, with maximal inhibitions for S. anisochila, S. alpina ssp. dinarica and S. beckeana extracts of 50.22%, 50.94% and 64.97%, respectively. Only S. plumosa extract achieved maximal activity of 60.67% at 100 microg/ml. As for LP, IC50 values for S. beckeana and S. alpina ssp. dinarica extracts were 25.07 and 49.00 microg/ml, respectively, while S. anisochila and S. plumosa extracts did not reach 50% of LP inhibition.

10–100 eV Ar+ ion induced damage to d-ribose and 2-deoxy-d-ribose molecules in condensed phase

We report that 10-100 eV Ar+ ion irradiation induces severe damage to the biologically relevant sugar molecules D-ribose and 2-deoxy-D-ribose in the condensed phase on a polycrystalline Pt substrate. Ar+ ions with kinetic energies down to 15 eV induce effective decomposition of both sugar molecules, leading to the desorption of abundant cation and anion fragments, including CH3+, C2H3+, C3H3+, H3O+, CHO+, CH3O+, C2H3O+, H-, O-, and OH-, etc. Use of isotopically labelled molecules (5- 13C D-ribose and 1-D D-ribose) reveals the site specificity for some of the fragment origins, and thus the nature of the chemical bond breaking. It is found that all of the chemical bonds in both molecules are vulnerable to ion impact at energies down to 15 eV, particularly both the endo- and exocyclic C-O bonds. In addition to molecular fragmentation, several chemical reactions are also observed. A small amount of O-/O fragments abstract hydrogen to form OH-. It is found that the formation of the H3O+ ion is related to the hydroxyl groups of the sugar molecules, and is associated with additional hydrogen loss from the parent or adjacent molecules via hydrogen abstraction or proton transfer. The formation of several other cation fragments also requires hydrogen abstraction from its parent or an adjacent molecule. These fragmentations and reactions are likely to occur in a real biomedium during ionizing radiation treatment of tumors and thus bear significant radiobiological relevance.

Quantification of ion-induced molecular fragmentation of isolated 2-deoxy-d-ribose molecules

Recent experiments on low energy ion-induced damage to DNA building blocks indicate that ion induced DNA damage is dominated by deoxyribose disintegration (Phys. Rev. Lett., 2005, 95, 153201). We have studied interactions of keV H+ and He(q+) with isolated deoxyribose molecules by means of high resolution time-of-flight spectrometry. Extensive statistical fragmentation of the molecules is observed. The fragment distribution is found to follow a power law dependence. The exponent can be used to characterize and quantify the molecular damage.

Antioxidant and pro-oxidant activities of aqueous extracts and crude polyphenolic fractions of rooibos (Aspalathus linearis)

Unfermented rooibos tea is known to contain higher levels of total polyphenols and flavonoids than its fermented counterpart, making it the obvious choice for the preparation of flavonoid-enriched fractions. Evaluation of aqueous extracts and crude polyphenolic fractions of unfermented and fermented rooibos showed anti- and/or pro-oxidant activities, using a linoleic acid-Tween-buffer emulsion for lipid peroxidation and the deoxyribose degradation assay, based on a Fenton reaction model system containing FeCl3-EDTA and H2O2 for the generation of hydroxyl radicals. Except for the ethyl acetate fraction, with the highest total polyphenol (TP) content and offering the least protection presumably due to pro-oxidant activity, the inhibition of lipid peroxidation by the samples correlated moderately with their TP content in a linear relationship (r = 0.896, P < 0.01). Using the deoxyribose degradation assay, the pro-oxidant activity of the aqueous extracts and their crude polymeric fractions (0.1 mg/mL in the reaction mixture) was linear with respect to their dihydrochalcone (aspalathin and nothofagin) (r = 0.977, P = 0.023) and flavonoid (r = 0.971, P = 0.029) content. Pro-oxidant activity was demonstrated for pure aspalathin. Using the same assay, but with ascorbate added to regenerate Fe3+ to Fe2+, the aqueous extract and crude polymeric fraction of fermented rooibos displayed hydroxyl radical scavenging activity. Fermentation (i.e., oxidation) of rooibos decreased the pro-oxidant activity of aqueous extracts, which was contributed to a decrease in their dihydrochalcone content. The in vitro pro-oxidant activity displayed by flavonoid-enriched fractions of rooibos demonstrates that one must be aware of the potential adverse biological properties of potent antioxidant extracts utilized as dietary supplements.

Unique properties of purine/pyrimidine asymmetric PNA.DNA duplexes: differential stabilization of PNA.DNA duplexes by purines in the PNA strand

PNA.DNA duplexes are significantly stabilized by purine nucleobases in the PNA strand. To elucidate and understand the effect of switching the backbone in a nucleic acid duplex, we now report a thermodynamics study along with a solution conformations study of two purine/pyrimidine strand asymmetric duplexes and a strand symmetrical control by comparing the behavior of all four possible PNA/DNA combinations. In essence, we are comparing an identical basepair stack connected by either an aminoethyl glycine PNA or a deoxyribose DNA backbone. We show that the PNA.DNA duplexes containing purine-rich PNA strands are stabilized with regard to the thermal melting temperature and free energy as well as enthalpy (and concomitantly relatively less entropically disfavored). Based on our data, we find it unlikely that differences in counterion binding (identical ionic-strength dependence was observed), hydration (identical and insignificant water release was observed), or single-strand conformation can be responsible for the difference in duplex stability. The only consistent difference observed between the purine-rich PNA versus the pyrimidine-rich PNA in isosequential PNA.DNA duplexes is the significant increase in both binding enthalpy and entropy for the PNA.DNA duplexes containing pyrimidine-rich PNA in organic solvent, which would indicate that these duplexes are relatively enthalpically disfavored in water. Although our results so far do not allow us to identify the origin of the different stabilities of homopurine/homopyrimidine PNA.DNA duplexes, the evidence does point to a significant structural component, which involves enthalpic contributions both within the duplex structure and also from bound water molecules.

Hydroxyl radical scavenging effects of guaiacol used in traditional dental pulp sedation: reaction kinetic study

Guaiacol, which is a phenolic compound with a methoxy group and used in traditional dental pulp sedation, has the property of inducing cell proliferation. To clarify these mechanisms of guaiacol, this study examined the hydroxyl radical (*OH) scavenging effects of guaiacol in vitro. Generation of *OH was carried out by the Fenton reaction using mixture of ascorbic acid, H2O2, and Fe(III)-EDTA, and *OH was detected by measuring the *OH-mediated production of degradation products of deoxyribose, which reacts with 2-thiobarbituric acid (TBA) and is relatively stable for a long time. At concentrations of 10(-10) M to 10(-3) M, guaiacol inhibited the TBA reactive substance (TBA-RS) formation in a dose-dependent manner. Phenol and formaldehyde were also found to inhibit the TBA-RS formation, but their inhibitory activities were lower than that of guaiacol. The concentrations of guaiacol, phenol, and formaldehyde needed to cause 50% inhibition of TBA-RS formation were approximately 5 x 10(-6), 5 x 10(-5), and 2 x 10(-3) M, respectively. In this reaction system, guaiacol showed no chelating reaction with ferrous ion and did not directly react with H2O2. Guaiacol also exhibited radical scavenging activity on 1,1-diphenyl-2-picrylhydrazyl (DPPH) stable free radical, but its scavenging activity was lower than that toward *OH. These results suggest that guaiacol is a potent scavenger of reactive oxygen radicals and that its radical scavenging activity may be associated with its effect on cell proliferation.

Formation of M1G-dR from endogenous and exogenous ROS-inducing chemicals

The present study provides fundamental information regarding the production of M1G-dR by ROS. To investigate the production of M1G-dR from deoxyribose damage as caused by ROS, calf thymus DNA (CT-DNA) was incubated with NAD(P)H, CuCl2, and various concentrations of hydrogen peroxide (H2O2). The incubation of CT-DNA with H2O2 resulted in concentration-dependent increases in the number of M1G-dR adducts. In subsequent experiments, 1,4-tetrachlorobenzoquinone or catechol estrogens were evaluated for their effects on M1G-dR formation. In addition, the role of lipid peroxidation in the formation of M1G-dR was verified using an in vitro lipid peroxidation model which consisted of methyl esters of either fish oil or purified fatty acids found in cellular membranes. This experiment confirmed that M1G-dR is a major DNA adduct produced by lipid peroxidation. Furthermore, the number of double bonds in polyunsaturated fatty acids was found to be the key factor in the formation of M1G-dR. The findings obtained from this study provide important information regarding the molecular pathways for M1G-dR formation by ROS, which is an essential element in understanding and evaluating the genotoxicity of a variety of ROS-inducing chemicals.

Understanding How the Herpes Thymidine Kinase Orchestrates Optimal Sugar and Nucleobase Conformations To Accommodate Its Substrate at the Active Site: A Chemical Approach

The herpes virus thymidine kinase (HSV-tk) is a critical enzyme for the activation of anti-HSV nucleosides. However, a successful therapeutic outcome depends not only on the activity of this enzyme but also on the ability of the compound(s) to interact effectively with cellular kinases and with the target viral or cellular DNA polymerases. Herein, we describe the synthesis and study of two nucleoside analogues built on a conformationally locked bicyclo[3.1.0]hexane template designed to investigate the conformational preferences of HSV-tk for the 2'-deoxyribose ring. Intimately associated with the conformation of the 2'-deoxyribose ring is the value of the C-N torsion angle chi, which positions the nucleobase into two different domains (syn or anti). The often-conflicting sugar and nucleobase conformational parameters were studied using North and South methanocarbadeoxythymidine analogues (6 and 7), which forced HSV-tk to make a clear choice in the conformation of the substrate. The results provide new insights into the mechanism of action of this enzyme, which cannot be gleaned from a static X-ray crystal structure.

UVA-visible photo-excitation of guanine radical cations produces sugar radicals in DNA and model structures

This work presents evidence that photo-excitation of guanine radical cations results in high yields of deoxyribose sugar radicals in DNA, guanine deoxyribonucleosides and deoxyribonucleotides. In dsDNA at low temperatures, formation of C1′• is observed from photo-excitation of G•⁺ in the 310–480 nm range with no C1′• formation observed ≥520 nm. Illumination of guanine radical cations in 2′dG, 3′-dGMP and 5′-dGMP in aqueous LiCl glasses at 143 K is found to result in remarkably high yields (∼85–95%) of sugar radicals, namely C1′•, C3′• and C5′•. The amount of each of the sugar radicals formed varies dramatically with compound structure and temperature of illumination. Radical assignments were confirmed using selective deuteration at C5′ or C3′ in 2′-dG and at C8 in all the guanine nucleosides/tides. Studies of the effect of temperature, pH, and wavelength of excitation provide important information about the mechanism of formation of these sugar radicals. Time-dependent density functional theory calculations verify that specific excited states in G•⁺ show considerable hole delocalization into the sugar structure, in accord with our proposed mechanism of action, namely deprotonation from the sugar moiety of the excited molecular radical cation.

Assessment of the antioxidant activities of Brazilian extracts of propolis alone and in topical pharmaceutical formulations

The antioxidant activity of extracts of propolis and of formulations added with these extracts were measured by scavenging different radicals in different systems. For the ethanolic extract of propolis (EEP) and the glycolic extract of propolis (GEP) the IC50 observed were respectively of 0.024 and 0.035 microL/mL in scavenging hydroxyl radical, 0.016 and 0.012 microL/mL in inhibiting lipid peroxidation, 0.22 and 0.24 microL/mL in inhibiting chemiluminescence produced in the H2O2/luminol/horseradish peroxide (HRP) system and about 0.005 microL/mL for both extracts in inhibiting chemiluminescence produced in the xanthine/luminol/xanthine oxidase (XOD) system. The antioxidant activity of extracts of propolis in the formulations was not able to be assessed neither using the deoxyribose assay, since the formulation components interfered in the assay measurements, nor using chemiluminescence in the H2O2/luminol/HRP system, since this method did not show to be sensitive for the extract of propolis evaluation. However, the antioxidant activity of extracts of propolis could be successfully evaluated in the formulations using both lipid peroxidation and chemiluminescence generated in the xanthine/luminol/XOD system inhibitions.

Differential oxidation of deoxyribose in DNA by gamma and alpha-particle radiation

Emerging evidence points to the importance of deoxyribose oxidation in the toxicity of oxidative DNA damage, including the formation of protein-DNA crosslinks and base adducts. With the goal of understanding the differences in deoxyribose oxidation chemistry known to occur with different oxidants, we have compared the formation of one product of 3'-oxidation of deoxyribose in DNA, 3'-phosphoglycolaldehyde (PGA) residues, in isolated DNA and cells exposed to ionizing radiations. A recently developed gas chromatography/negative chemical ionization mass spectrometry method was used to quantify PGA residues in purified DNA and in human TK6 lymphoblastoid cells exposed to gamma radiation (60Co) and alpha particles (241Am). The level of PGA residues was then correlated with the total quantity of deoxyribose oxidation determined by plasmid topoisomer analysis. Alpha-particle irradiation (0-100 Gy) of purified DNA in 50 mM potassium phosphate (pH 7.4) produced a linear dose response of 0.13 PGA residues per 10(6) nucleotides per gray. When normalized to an estimate of the total number of deoxyribose oxidation events (2.0 per 10(6) nucleotides per gray), PGA formation occurred in 7% (+/-0.5) of deoxyribose oxidation events produced by alpha-particle radiation. In contrast, the efficiency of PGA formation in gamma-irradiated DNA was found to be 1% (+/-0.02), which indicates a shift in the chemistry of deoxyribose oxidation, possibly as a result of the different track structures of the two types of ionizing radiation. Studies with gamma radiation were extended to TK6 cells, in which it was observed that gamma radiation produced a linear dose response of 0.0019 PGA residues per 10(6) nucleotides per gray. This is consistent with an approximately 1000-fold quenching effect in cells, similar to the results of other published studies of oxidative DNA damage in vivo.

Arc Repressor−Operator DNA Interactions and Contribution of Phe10 to Binding Specificity

Solution properties of Arc repressors (wild-type and F10H variant) from Salmonella bacteriophage P22 and their complexes with operator DNA (Arc-wt-DNA and Arc-F10H-DNA) were characterized by circular dichroism, fluorescence, and Raman difference spectroscopy and compared with the crystal structures of free and DNA-bound Arc repressors (wild-type and F10V variant). From the crystal structure of Arc-wt-operator DNA complex, it is known that amino acids Phe10/10' flip out of the hydrophobic protein core, and in the Arc-F10V-DNA complex, the methyl groups of Val10/10' rotate toward the DNA. Arc-wt and Arc-F10H significantly perturb the Raman signatures of the operator DNA upon complex formation. The two proteins induce similar changes in the DNA spectra. Raman markers in the difference spectra (spectrum of the complex minus spectra of DNA and Arc) indicate binding of Arc in the major groove, several direct contacts, e.g., hydrogen bonds of protein residues with bases, and slight perturbations of the deoxyribose ring systems that are consistent with bending of the operator DNA. Trp14, the only one tryptophan of Arc repressor monomers, serves as a very sensitive tool for changes of the hydrophobic core of the protein. The Raman spectra identify in the free Arc-F10H variant a largely different chi(2,1) rotation angle of Trp14 compared to that in wild-type Arc. In the Arc-wt-DNA and Arc-F10H-DNA complexes, however, the Trp14 chi(2,1) rotation angles are similar in both proteins. Furthermore, in both complexes, a strengthening of the van der Waals interactions of the aromatic ring of Trp14 is indicated compared to these interactions in the free proteins. According to the fluorescence and Raman data, His10 is buried in the hydrophobic core of free Arc-F10H, resembling the "core" conformation of Phe10 in Arc-wt, but His10 is looped out in the complex with DNA resembling the "bound" conformation of Phe10 in the Arc-wt-operator DNA complex.

Probing the Watson−Crick, Wobble, and Sugar-Edge Hydrogen Bond Sites of Uracil and Thymine

The nucleobases uracil (U) and thymine (T) offer three hydrogen-bonding sites for double H-bond formation via neighboring N-H and C=O groups, giving rise to the Watson-Crick, wobble and sugar-edge hydrogen bond isomers. We probe the hydrogen bond properties of all three sites by forming hydrogen bonded dimers of U, 1-methyluracil (1MU), 3-methyluracil (3MU), and T with 2-pyridone (2PY). The mass- and isomer-specific S1 <-- S0 vibronic spectra of 2PY.U, 2PY.3MU, 2PY.1MU, and 2PY.T were measured using UV laser resonant two-photon ionization (R2PI). The spectra of the Watson-Crick and wobble isomers of 2PY.1MU were separated using UV-UV spectral hole-burning. We identify the different isomers by combining three different diagnostic tools: (1) Selective methylation of the uracil N3-H group, which allows formation of the sugar-edge isomer only, and methylation of the N1-H group, which leads to formation of the Watson-Crick and wobble isomers. (2) The experimental S1 <-- S0 origins exhibit large spectral blue shifts relative to the 2PY monomer. Ab initio CIS calculations of the spectral shifts of the different hydrogen-bonded dimers show a linear correlation with experiment. This correlation allows us to identify the R2PI spectra of the weakly populated Watson-Crick and wobble isomers of both 2PY.U and 2PY.T. (3) PW91 density functional calculation of the ground-state binding and dissociation energies De and D0 are in agreement with the assignment of the dominant hydrogen bond isomers of 2PY.U, 2PY.3MU and 2PY.T as the sugar-edge form. For 2PY.U, 2PY.T and 2PY.1MU the measured wobble:Watson-Crick:sugar-edge isomer ratios are in good agreement with the calculated ratios, based on the ab initio dissociation energies and gas-phase statistical mechanics. The Watson-Crick and wobble isomers are thereby determined to be several kcal/mol less strongly bound than the sugar-edge isomers. The 36 observed intermolecular frequencies of the nine different H-bonded isomers give detailed insight into the intermolecular force field.

DNA Cleavage by the Photolysis of Cyclopentadienyl Metal Complexes: Mechanistic Studies and Sequence Selectivity of Strand Scission by CpW(CO)3CH3

[Reaction: see text]. The photolysis of CpW(CO)3Me has been shown to produce methyl radicals and to cleave DNA in a single-stranded manner, and preliminary evidence implicated a carbon-centered radical in this process. In this work, the mechanism of strand scission in this reaction was determined to occur by hydrogen atom abstraction from the 4'- and 5'-positions of the deoxyribose moiety of the backbone of DNA. Additionally, in a side reaction that does not lead to frank strand scission, all four bases of DNA are methylated under these conditions; however, none of these base or backbone modifications lead to the formation of abasic sites.

Inhibition of induced DNA oxidative damage by beers: correlation with the content of polyphenols and melanoidins

Beers are a source of dietary flavonoids; however, there exist differences in composition, alcohol concentration, and beneficial activities. To characterize these differences, three kinds of lager beer of habitual consumption in Spain, dark, blond, and alcohol-free, were assayed for total phenolic content, antioxidant activity, superoxide and hydroxyl radical scavenging activities, and in vitro inhibitory effect on DNA oxidative damage. Furthermore, their melanoidin content and correlation with antioxidant activity were evaluated. Dark beer contained the highest total phenolic (489 +/- 52 mg/L) and melanoidin (1.49 +/- 0.02 g/L) contents with a 2-fold difference observed when compared to the alcohol-free beer. For the three kinds of beer, the antioxidant activity measured as N,N-dimethyl-p-phenylenediamine dihydrochloride concentration was strongly correlated with the total polyphenol content (R(2) = 0.91102, p < 0.005) and with the melanoidin content (R(2) = 0.7999, p < 0.05). The results support a positive effect of beers on the protection of DNA oxidative damage, by decreasing the deoxyribose degradation, DNA scission (measured by electrophoresis), and inhibition of 8-hydroxydeoxyguanosine (8-OH-dG) formation. Furthermore, a correlation between the total melanoidin content (R(2) = 0.7309, p < 0.01) and inhibition of 8-OH-dG was observed.

An extremely stable and orthogonal DNA base pair with a simplified three-carbon backbone

A nucleotide C3HQ with a minimal three-carbon backbone displays unprecedented pairing strength and orthogonality in a homopair C3HQ:C3HQ in the presence of one equivalent of Cu2+. The pairing stability in DNA even exceeds the related base pair having the regular 2'-deoxyribose backbone. This discovery of a synergy between an artificial backbone and base-pairing scheme opens new avenues for the economical design of modified oligonucleotides with tailored properties.

5'-(2-phosphoryl-1,4-dioxobutane) as a product of 5'-oxidation of deoxyribose in DNA: elimination as trans-1,4-dioxo-2-butene and approaches to analysis

Oxidation of deoxyribose in DNA leads to the formation of a spectrum of electrophilic products unique to each position in the sugar. For example, chemical reactions following abstraction of the C5'-hydrogen atom partition to form either a nucleoside 5'-aldehyde residue attached to the 5'-end of the DNA strand or a 5'-formyl phosphate residue attached to the 3'-end of the DNA strand that is accompanied by a four-carbon fragment on the 5'-end. We now present two approaches that both identify the latter fragment as 5'-(2-phosphoryl-1,4-dioxobutane) and provide a means to quantify the formation of this residue by different oxidizing agents. The first approach involves oxidation of DNA followed by reaction with O-benzylhydroxylamine to form stable dioxime derivatives of the putative 5'-(2-phosphoryl-1,4-dioxobutane) residues. The beta-elimination product of this dioxime proved to be the expected trans-1,4-dioxo-2-butene, as judged by gas chromatographic and mass spectrometric (GC/MS) comparison to authentic dioximes of cis- and trans-1,4-dioxo-2-butene, which revealed a unique pattern of three signals for each isomer, and by X-ray crystallography. Using a benzylhydroxylamine dioxime derivative of [2H4]-labeled cis-1,4-dioxo-2-butene as an internal standard, the dose-response for the formation of 5'-(2-phosphoryl-1,4-dioxobutane) was determined to be linear for gamma-radiation, with approximately 6 lesions per 10(6) nt per Gy, and nonlinear for Fe2+-EDTA. A comparison of 5'-(2-phosphoryl-1,4-dioxobutane) formation to total deoxyribose oxidation suggests that gamma-radiation produces approximately 0.04 lesions per deoxyribose oxidation event. As a positive control for 5'-oxidation of deoxyribose, the enediyne calicheamicin was observed to produce 5'-(2-phosphoryl-1,4-dioxobutane) at the rate of approximately 9 lesions per 10(6) nt per microM. A second approach to identifying and quantifying the sugar residue involved derivatization with hydrazine and beta-elimination to form pyridazine followed by quantification of the pyridazine by GC/MS. Using this approach, it was observed that the enediyne, neocarzinostatin, produced a linear dose-response for pyridazine formation, as expected given the ability of this oxidant to cause 1'-, 4'-, and 5'-oxidation of deoxyribose in DNA. The antitumor antibiotic, bleomycin, on the other hand, produced pyridazine at a 10-fold lower rate, which is consistent with 4'-chemistry as the predominant mode of deoxyribose oxidation by this agent. These results provide novel insights into the chemistry of deoxyribose oxidation in DNA and two approaches to quantifying the 5'-(2-phosphoryl-1,4-dioxobutane) precursor of trans-1,4-dioxo-2-butene, an electrophile known to react with nucleobases to form novel DNA adducts.

Free radical reactions and antioxidant activities of sesamol: pulse radiolytic and biochemical studies

Sesamol (from Sesamum indicum) is a dietary compound, which is soluble in aqueous as well as lipid phases. Free radical scavenging reactions of sesamol, 5-hydroxy-1,3-benzodioxole, have been studied using a nanosecond pulse radiolysis technique. Sesamol efficiently scavenges hydroxyl, one-electron oxidizing, organo-haloperoxyl, lipid peroxyl, and tryptophanyl radicals. Its antioxidant activity has also been evaluated with cyclic voltammetry. In biochemical studies, it has been found to inhibit lipid peroxidation, hydroxyl radical-induced deoxyribose degradation, and DNA cleavage. These antioxidant and free radical scavenging activities of sesamol have been reported in the paper.

Changing selectivity of DNA oxidation from deoxyribose to Guanine by ligand design and a new binuclear copper complex

A dinuclear copper complex [CuII2(PD'O)(H2O)2]3+ (1) (where PD'OH is a pyridylalkylamine containing binucleating ligand) promotes guanine oxidation in single-stranded DNA in the presence of 3-mercaptopropionic acid and dioxygen. This reaction is detected after subsequent piperidine treatment. Little spontaneous strand scission indicative of deoxyribose oxidation is observed in contrast to the results known for other copper complexes. Chemical characterization and nanospray ionization mass spectrometry analysis of oligodeoxynucleotides treated with 1 suggest conversion of guanine residues to their 2,6-diamino-5-formamidino-4-hydroxypyrimidine (+18 amu) and possibly 5,8-dihydroxy-7,8-dihydroguanine (+34 amu) derivatives. The selectivity toward nucleobase rather than deoxyribose oxidation is discussed in terms of the specific nature of the dicopper (hydro)peroxo species formed with the PD'OH ligand versus the intermediates formed in the presence of other binucleating ligands.