Computational investigation of hydrogen abstraction from 2-aminoethanol by the 1,5-dideoxyribose-5-yl radical: a model study of a reaction occurring in the active site of ethanolamine ammonia lyase

Hydrogen abstraction from 2-aminoethanol by the 5'-deoxyadenosyl radical, which is formed upon Co--C bond homolysis in coenzyme B(12), was investigated by theoretical means with employment of the DFT (B3LYP) and ab initio (MP2) approaches. As a model system for the 5'-deoxyadenosyl moiety the computationally less demanding 1,5-dideoxyribose was employed; two conformers, which differ in ring conformation (C2- and C3-endo), were considered. If hydrogen is abstracted from "free" substrate by the C2-endo conformer of the 1,5-dideoxyribose-5-yl radical, the activation enthalpy is 16.7 kcal mol(-1); with the C3-endo counterpart, the value is 17.3 kcal mol(-1). These energetic requirements are slightly above the activation enthalpy limit (15 kcal mol(-1)) determined experimentally for the rate-determining step of the sequence, that is, hydrogen delivery from 5'-deoxyadenosine to the product radical. The activation enthalpy is lower when the substrate interacts with at least one amino acid from the active site. According to the computations, when a His model system partially protonates the substrate the activation enthalpy is 4.5 kcal mol(-1) for the C3-endo conformer and 5.8 kcal mol(-1) for the C2-endo counterpart. As hydrogen abstraction from the fully as well as the partially protonated substrate is preceded by the formation of quite stable encounter complexes, the actual activation barriers are around 13-15 kcal mol(-1). A synergistic interaction of 2-aminoethanol with two amino acids where His partially protonates the NH(2) group and Asp partially deprotonates the OH group of the substrate results in an activation enthalpy of 12.4 kcal mol(-1) for the C3-endo conformer and 13.2 kcal mol(-1) for the C2-endo counterpart. However, if encounter complexes exist in the active site, the actual activation barriers are much higher (>25 kcal mol(-1)) than that reported for the rate-determining step. These findings together with previous computations suggest that the energetics of the initial hydrogen abstraction decrease with an interaction of the substrate with only a protonating auxiliary, but for the rearrangement of the radical the synergistic effects of two auxiliaries are essential to pull the barrier below the limit of 15 kcal mol(-1).

Parallel DNA double helices incorporating isoG or m5isoC bases studied by FTIR, CD and molecular modeling

FTIR spectroscopy has been used to follow the formation of parallel stranded DNA duplexes incorporating isoG or m5isoC bases and determine their base pairing scheme. The results are discussed in comparison with data concerning anti-parallel duplexes with comparable base composition and sequence. In duplexes containing A-T and isoG-C or m5isoC-G base pairs shifts of the thymine C2=O2 and C4=O4 carbonyl stretching vibrations (to lower and higher wavenumbers, respectively, when compared to their positions in classical cis Watson-Crick (WC) base pairs) reflect the formation of trans Watson-Crick A-T base pairs. All carbonyl groups of cytosines, m5isocytosines, guanines and isoguanines are found to be involved in hydrogen bonds, indicative of the formation of isoG-C and m5isoC-G base pairs with three hydrogen bonds. Molecular modeling shows that both structures form regular right handed helices with C2'endo sugar puckers. The role of the water content on the helical conformation of the parallel duplexes has been studied by FTIR and CD. It is found that a conformational transition similar to the B --> A transition observed for anti-parallel duplexes induced by a decrease of the water content of the samples can occur for these parallel duplexes. Their helical flexibility has been evidenced by FTIR studies on hydrated films by the emergence of absorption bands characteristic of A type geometry, in particular by an S-type --> N-type repuckering of the deoxyribose. All sugars in the parallel duplex with alternating d(isoG-A)/d(C-T) sequence can adopt an N-type geometry in low water content conditions. The conformational transition of the parallel hairpin duplex with alternating d(isoG-A)/d(C-T) sequence was followed by circular dichroism in water/trifluoroethanol solutions and its free energy at 0 degrees C was estimated to be 6.6 +/- 0.3 kcal mol(-1).

Reevaluating the role of 1,10-phenanthroline in oxidative reactions involving ferrous ions and DNA damage

It is widely believed that the iron chelator 1,10-phenanthroline (phen) is able to fully block the Fenton reaction by forming a complex (Fe(phen)3(2+), also known as ferroin) that cannot react with H2O2. We observed that phen cannot fully prevent 2-deoxyribose (5 mM) degradation induced by Fenton reagents (30 microM Fe(II) plus 100-500 microM H2O2); protection varied from 55% to 66% when the phen/Fe(II) ratio was 3:1 to 20:1. Inhibition of 2-deoxyribose damage was nearly unchanged if phen was pre-incubated with Fe(II). Moreover, preformed Fe(phen)3(2+) complex added to the solution containing H2O2 was able to induce 2-deoxyribose degradation and methane sulfinic acid formation from the oxidation of 5% DMSO. The partially protective effect of phen was unchanged with the use of either phosphate or HEPES as buffers (5 mM, pH 7.2), or in unbuffered media (pH 5.1). Both DMSO oxidation and 2-deoxyribose degradation correlated with the increase in Fe(phen)3(2+) concentration. Strand breaks in plasmid pTARGETtrade mark DNA induced by Fenton reagents (1 microM Fe(II) plus 25 microM H2O2) in HEPES buffer could only be partially prevented by phen, even when the chelator was 16 times more concentrated than Fe(II). In these experiments, Fe(phen)3(2+) and DNA were pre-incubated from 1 to 10 min before addition of H2O2. Moreover, a high level of DNA strand breakage was observed when iron and phen are added to the reaction immediately before H2O2. On the other hand, phen fully prevented 2-deoxyribose degradation induced by the autoxidation of 30 microM Fe(II) in phosphate-buffered (3 to 30 mM) media. Our data provide evidence that the Fe(phen)3(2+) complex induces in vitro oxidative damage in the presence of H2O2 (possibly by means of Fe(phen)3(2+) dissociation into Fe(phen)2(2+)), but they show that the complex cannot undergo autoxidation.

[Effect of some nonsteroid antiinflammatory drugs on Fenton-reaction initiated degradation of 2-deoxy-D-ribose]

The authors examined the possible interactions of some nonsteroidal anti-inflammatory drugs with hydroxyl radicals by means of the test based on degradation of 2-deoxy-D-ribose initiated by hydroxyl radicals. The method is based on spectrophotometric measurement of thiobarbituric acid (TBA)-reactive carbonyl compounds that are formed in the degradation reaction of 2-deoxy-D-ribose by hydroxyl radicals (HO*) generated in the Fenton-reaction between iron(II)-ions and hydrogen peroxide (H2O2). The authors studied the degradation-inhibitory effect of phenacetin, paracetamol (acetaminophen), indomethacin, ibuprofen, diclofenac sodium, salicylic acid and salicylamide used in 100 microM and 200 microM concentrations, in the present or without addition of EDTA. In the short term (10 minute) studies paracetamol and salicylic acid proved to show the most effective degradation inhibitory effect. In the longer-time (120 minute) studies after the early inhibitory effect of paracetamol, indometacine and salicylic acid, an increase of the TBA-reactive compounds could be observed.

Reaction of 2'-deoxyribonucleosides with cis- and trans-1,4-dioxo-2-butene

cis-1,4-Dioxo-2-butene is a toxic metabolite of furan, while the trans-isomer is a product of deoxyribose oxidation in DNA. It has recently been reported that both cis- and trans-1,4-dioxo-2-butene react with the 2'-deoxynucleosides dC, dG, and dA to form novel diastereomeric oxadiazabicyclo(3.3.0)octaimine adducts. We have now extended these studies with kinetic and spectroscopic analyses of the reactions of cis- and trans-1,4-dioxo-2-butene, as well as the identification of novel adducts of dA. The reaction of dC with trans-1,4-dioxo-2-butene was observed to be nearly quantitative and produced two interchanging diastereomers with a second-order rate constant of 3.66 x 10(-2)M(-1)s(-1), which is nearly 10-fold faster than the reaction with the cis-isomer (3.74 x 10(-3)M(-1)s(-1)). HPLC analyses of reactions of 1,4-dioxo-2-butene with both dA and 9-methyladenine (pH 7.4, 37 degrees C) revealed multiple products including a novel pair of closely eluting fluorescent species of identical mass ([M+H] m/z 420), each of which contains two molecules of 1,4-dioxo-2-butene, and a more abundant but unstable and non-fluorescent species ([M+H] m/z 414). Partial structural characterization of the fluorescent adducts of dA revealed the presence of the oxadiazabicyclo(3.3.0)octaimine ring system common to the dC adducts. These results support the genotoxic potential of furan metabolites and products of deoxyribose oxidation.

Synthesis of a 1'-aminomethylthymidine and oligodeoxyribonucleotides with 1'-acylamidomethylthymidine residues

Reported here is a 10-step synthesis of a phosphoramidite building block of 1'-aminomethylthymidine that starts from 2-deoxyribose. The framework of the branched aminonucleoside was elaborated from a known 1-cyano-1-bromo glycosyl donor, whose reaction with the silylated nucleobase furnished the 1'-cyanide, which was reduced to the desired aminomethylnucleoside. The N-allyloxycarbonyl (Alloc)-protected nucleoside was converted to a phosphoramidite building block and incorporated into the oligonucleotides 5'-GCAT*TATTAC-3', and 5'-GCAT*TAT*TAC-3', where T* denotes 1'-acylamidomethylthymidine residues. Removal of the Alloc protecting group and acylation with the residue of pyrene-1-yl-butanoic acid were achieved on support, using microwave irradiation to ensure full conversion. The UV-melting point of the duplex of the singly and doubly modified decamers with their fully complementary target sequence is 0.1-6.9 degrees C higher than that of the unmodified control duplex, depending on the salt concentration. This suggests that the aminomethyl linker may allow for the placing of a functional "payload" in the minor groove of DNA duplexes without disrupting the helix. Oligonucleotides thus endowed with functional modifications may become useful for biomedical applications.

Application of the C4'-alkylated deoxyribose primer system (CAPS) in allele-specific real-time PCR for increased selectivity in discrimination of single nucleotide sequence variants

This study describes a quantitative real-time PCR-based approach for discrimination of single nucleotide sequence variants, called CAPS (C4' alkylated primer system). To increase the discrimination potential of DNA polymerases against competing sequence variants of single nucleotides, 3'-terminally modified primers were designed carrying a methyl residue bound to the C4' of the thymidylate deoxyribose. In a model sequence system positional dependencies of modified thymidylate (at -1, -2, -3) were tested for their influence on discrimination. Highest discrimination factors were obtained with the modification at the ultimate 3'-position. In a comparison between Taq and Pwo DNA polymerases, substantial better results were obtained by Taq DNA polymerase. In contrast to conventional PCR methods for discrimination of sequence variants, achieving a maximum discrimination potential of about 20, CAPS is capable of obtaining sequence-specific amplifications of a desired target among discriminated templates with a dynamic range of 1:100. Therefore, CAPS is a method able to quantitatively discriminate two sequence variants only differing in a single base (e.g., SNP alleles or point mutations). The range of applications of this easy to perform, fast and reliable technique reaches from medical diagnostics, transplantation medicine, molecular and cell biology to human genetics. Targeting of SNPs assures a universal exertion of this method, since these markers are gender-independent, highly abundant and ubiquitous.

Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection

In vitro selections performed in the presence of Mg(2+) generated DNA sequences capable of cleaving an internal ribonucleoside linkage. Several of these, surprisingly, displayed intermolecular catalysis and catalysis independent of Mg(2+), features that the selection protocol was not explicitly designed to select. A detailed physical organic analysis was applied to one of these DNAzymes, termed 614. First, the progress curve for the reaction was dissected to identify factors that prevented the molecule from displaying clean first-order transformation kinetics and 100% conversion. Several factors were identified and quantitated, including (a) competitive intra- and intermolecular rate processes, (b) alternative reactive and unreactive conformations, and (c) mutations within the catalyst. Other factors were excluded, including "approach to equilibrium" kinetics and product inhibition. The possibility of complementary strand inhibition was demonstrated but was shown to not be a factor under the conditions of these experiments. The rates of the intra- and intermolecular processes were compared, and saturation models for the intermolecular process were built. The rate-limiting step for the intermolecular reaction was found to be the association/folding of the enzyme with the substrate and not the cleavage step. The DNAzyme 614 is more active in trans than in cis and more active at temperatures below the selection temperature than at the selection temperature. Many of these properties have not been reported in similar systems; these results therefore expand the phenomenology known for this class of DNA-based catalysts. A brief survey of other catalysts arising from this selection found other Mg(2+)-independent DNAzymes and provided a preliminary view of the ruggedness of the landscape, relating function to structure in sequence space. Hypotheses are suggested to account for the fact that a selection in the presence of Mg(2+) did not exploit this Mg(2+). This study of a specific catalytically active DNAzyme is an example of studies that will be necessary generally to permit in vitro selection to help us understand the distribution of function in sequence space.

A comprehensive comparison of DNA replication past 2-deoxyribose and its tetrahydrofuran analog in Escherichia coli

Apurinic/apyrimidinic (AP) sites are alkali labile lesions that, when encountered during DNA replication, can block polymerases or potentially result in mutagenic events. Owing to the instability of 2-deoxyribose lesions (AP), a chemically stable tetrahydrofuran analog (F) is often used as a model of abasic sites. A comparison of the two lesions in Saccharomyces cerevisiae revealed that the model lesion and 2-deoxyribose have distinct in vivo effects. Comprehensive comparative analyses of F and AP have not been carried out in Escherichia coli. We conducted a side-by-side investigation of F and AP in E.coli to compare their biological effects and interactions with SOS polymerases. Both lesions were examined in SOS-induced and uninduced cells. Our studies reveal that in uninduced E.coli the effects of individual polymerases in the replication of plasmids containing F or AP are distinct. However, when cells are SOS-induced, the biological effects of F and AP are similar.

Partial B-to-A DNA transition upon minor groove binding of protein Sac7d monitored by Raman spectroscopy

Members of the Sso7d/Sac7d protein family and other related proteins are believed to play an important role in DNA packaging and maintenance in archeons. Sso7d/Sac7d are small, abundant, basic, and nonspecific DNA-binding proteins of the hyperthermophilic archeon Sulfolobus. Structures of several complexes of Sso7d/Sac7d with DNA octamers are known. These structures are characterized by sequence unspecific minor groove binding of the proteins and sharp kinking of the double helix. Corresponding Raman vibrational signatures have been identified in this study. A Raman spectroscopic analysis of Sac7d binding to the oligonucleotide decamer d(GAGGCGCCTC)(2) reveals large conformational perturbations in the DNA structure upon complex formation. Perturbed Raman bands are associated with the vibrational modes of the sugar phosphate backbone and frequency shifts of bands assigned to nucleoside vibrations. Large changes in the DNA backbone and partial B- to A-form DNA transitions are indicated that are closely associated with C2'-endo/anti to C3'-endo/anti conversion of the deoxyadenosyl moiety upon Sac7d binding. The major spectral feature of Sac7d binding is kinking of the DNA. Raman markers of minor groove binding do not largely contribute to spectral differences; however, clear indications for minor groove binding come from G-N2 and G-N3 signals that are supported by Trp24 features. Trp24 is the only tryptophan present in Sac7d and binds to guanine N3, as has been demonstrated clearly in X-ray structures of Sac7d-DNA complexes. No changes of the Sac7d secondary structure have been detected upon DNA binding.

Synthesis and characterization of oligonucleotides containing a 4'-keto abasic site

DNA strand breaks can result as a direct or indirect consequence of oxidative damage to the nucleic acid bases and/or deoxyribose sugars. Ionizing radiation and the antitumor agents, the bleomycins (BLMs) and enediynes, share in common the ability to indirectly cause DNA strand scission after C4' hydrogen atom abstraction from the deoxyribose moiety. In the case of extensively studied BLMs, the C4' radical generated under anaerobic conditions results in production of a 4'-keto abasic site after C4' oxidation to a cation and H(2)O addition. To study the structure, stability, and repair of this lesion, a general method is reported for its homogeneous preparation in any sequence context. 4'-Azido-2'-deoxyuridine-5'-triphosphate is incorporated into duplex DNA using a primer, a template containing a restriction enzyme (NgoM IV) cleavage site at its 3'-end, and HIV-1 reverse transcriptase. The two strands of the duplex are separated based on size after cleavage with the restriction enzyme. The single-stranded (ss) DNA containing 4'-azido-2'-deoxyuridine, when treated with uracil-DNA glycosylase, results in quantitative release of uracil, azide, and generation of a ss-DNA containing the 4'-keto abasic site. This lesion is characterized directly by MALDI-TOF MS and indirectly by subsequent reduction, enzymatic digestion, and GC/MS. The stability of duplex DNA containing a 4'-keto abasic site relative to an abasic site in the same sequence context is reported under physiological conditions.

Oxidation of 2-deoxyribose by benzotriazinyl radicals of antitumor 3-amino-1,2,4-benzotriazine 1,4-dioxides

Tirapazamine (3-amino-1,2,4-benzotriazine 1,4-dioxide) is the lead bioreductive drug in clinical trials as an anticancer agent to kill refractory hypoxic cells of solid tumors. It has long been known that, upon metabolic one-electron reduction, tirapazamine induces lethal DNA double strand breaks in hypoxic cells. These strand breaks arise from radical damage to the ribose moiety of DNA, and in this pulse radiolysis and product analysis study we examine mechanistic aspects of the dual function of tirapazamine and analogues in producing radicals of sufficient power to oxidize 2-deoxyribose to form radicals, as well as the ability of the compounds to oxidize the resulting deoxyribose radicals to generate the strand breaks. Both the rate of oxidation of 2-deoxyribose and the radical yield increase with the one-electron reduction potentials of the putative benzotriazinyl radicals formed from the benzotriazine 1,4-dioxides. Subsequent oxidation of the 2-deoxyribose radicals by the benzotriazine 1,4-dioxides and 1-oxides proceeds through adduct formation followed by breakdown to form the radical anions of both species. The yield of the radical anions increases with increasing one-electron reduction potentials of the compounds. We have previously presented evidence that oxidizing benzotriazinyl radicals are formed following one-electron reduction of the benzotriazine 1,4-dioxides. The reactions reported in this work represent the kinetic basis of a short chain reaction leading to increased oxidation of 2-deoxyribose, a process which is dependent on the one-electron reduction potential of the benzotriazinyl radicals that are above a threshold value of ca. 1.24 V.

Evaluation of antioxidant capacity of cereal brans

Several oat brans (crunchy oat bran, oat bran alone, and oat breakfast cereal) and wheat brans (wheat bran alone, wheat bran powder, wheat bran with malt flavor, bran breakfast cereal, tablet of bran, and tablet of bran with cellulose) used as dietary fiber supplements by consumers were evaluated as alternative antioxidant sources (i) in the normal human consumer, preventing disease and promoting health, and (ii) in food processing, preserving oxidative alterations. Products containing wheat bran exhibited higher peroxyl radical scavenging effectiveness than those with oat bran. Wheat bran powder was the best hydroxyl radical (OH*) scavenger. In terms of hydrogen peroxide (H2O2) scavenging, wheat bran alone was the most effective, while crunchy oat bran, oat bran alone, and oat breakfast cereal did not scavenge H2O2. The shelf life of fats (obtained by the Rancimat method for butter) increased most in the presence of crunchy oat bran. When the antioxidant activity during 28 days of storage was measured by the linoleic acid assay, all of the oat and wheat bran samples analyzed showed very good antioxidant activities. The Trolox equivalent antioxidant capacity (TEAC) assay was used to provide a ranking order of antioxidant activity. The wheat bran results for TEAC (6 min), in decreasing order, were wheat bran powder > wheat bran with malt flavor > or = wheat bran alone > or = bran breakfast cereal > tablet of bran > tablet of bran with cellulose. The products made with oat bran showed lower TEAC values. In general, avenanthramide showed a higher antioxidant level than each of the following typical cereal components: ferulic acid, gentisic acid, p-hydroxybenzoic acid, protocatechuic acid, syringic acid, vanillic acid, vanillin, and phytic acid.

Modeling deoxyribose radicals by neutralization-reionization mass spectrometry. Part 2. Preparation, dissociations, and energetics of 3-hydroxyoxolan-3-yl radical and cation

The title radical (1) is generated in the gas-phase by collisional neutralization of carbonyl-protonated oxolan-3-one. A 1.5% fraction of 1 does not dissociate and is detected following reionization as survivor ions. The major dissociation of 1 (approximately 56%) occurs as loss of the hydroxyl H atom forming oxolan-3-one (2). The competing ring cleavages by O[bond]C-2 and C-4[bond]C-5 bond dissociations combined account for approximately 42% of dissociation and result in the formation of formaldehyde and 2-hydroxyallyl radical. Additional ring-cleavage dissociations of 1 resulting in the formation of C(2)H(3)O and C(2)H(4)O cannot be explained as occurring competitively on the doublet ground (X) electronic state of 1, but are energetically accessible from the A and higher electronic states accessed by vertical electron transfer. Exothermic protonation of 2 also produces 3-oxo-(1H)-oxolanium cation (3(+)) which upon collisional neutralization gives hypervalent 3-oxo-(1H)-oxolanium radical (3). The latter dissociates spontaneously by ring opening and expulsion of hydroxy radical. Experiment and calculations suggest that carbohydrate radicals incorporating the 3-hydroxyoxolan-3-yl motif will prefer ring-cleavage dissociations at low internal energies or upon photoexcitation by absorbing light at approximately 590 and approximately 400 nm.

Modeling deoxyribose radicals by neutralization-reionization mass spectrometry. Part 1. Preparation, dissociations, and energetics of 2-hydroxyoxolan-2-yl radical, neutral isomers, and cations

Collisional neutralization of several isomeric C(4)H(7)O(2) cations is used to generate radicals that share some structural features with transient species that are thought to be produced by radiolysis of 2-deoxyribose. The title 2-hydroxyoxolan-2-yl radical (1) undergoes nearly complete dissociation when produced by femtosecond electron transfer from thermal organic electron donors dimethyl disulfide and N,N-dimethylaniline in the gas phase. Product analysis, isotope labeling ((2)H and (18)O), and potential energy surface mapping by ab initio calculations at the G2(MP2) and B3-PMP2 levels of theory and in combination with Rice-Ramsperger-Kassel-Marcus (RRKM) kinetic calculations are used to assign the major and some minor pathways for 1 dissociations. The major (approximately 90%) pathway is initiated by cleavage of the ring C-5[bond]O bond in 1 and proceeds to form ethylene and *CH(2)COOH as main products, whereas loss of a hydrogen atom forms 4-hexenoic acid as a minor product. Loss of the OH hydrogen atom forming butyrolactone (2, approximately 9%) and cleavage of the C-3[bond]C-4 bonds (<1%) in 1 are other minor pathways. The major source of excitation in 1 is by Franck-Condon effects that cause substantial differences between the adiabatic and vertical ionization of 1 (5.40 and 6.89 eV, respectively) and vertical recombination in the precursor ion 1(+) (4.46 eV). (+)NR(+) mass spectra distinguish radical 1 from isomeric radicals 2-oxo-(1H)oxolanium (3), 1,3-dioxan-2-yl (9), and 1,3-dioxan-4-yl (10) that were generated separately from their corresponding ion precursors.

Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution

DNA polymerases recognize their substrates with exceptionally high specificity, restricting the use of unnatural nucleotides and the applications they enable. We describe a strategy to expand the substrate range of polymerases. By selecting for the extension of distorting 3' mismatches, we obtained mutants of Taq DNA polymerase that not only promiscuously extended mismatches, but had acquired a generic ability to process a diverse range of noncanonical substrates while maintaining high catalytic turnover, processivity and fidelity. Unlike the wild-type enzyme, they bypassed blocking lesions such as an abasic site, a thymidine dimer or the base analog 5-nitroindol and performed PCR amplification with complete substitution of all four nucleotide triphosphates with phosphorothioates or the substitution of one with the equivalent fluorescent dye-labeled nucleotide triphosphate. Such 'unfussy' polymerases have immediate utility, as we demonstrate by the generation of microarray probes with up to 20-fold brighter fluorescence.

Analysis of 3'-phosphoglycolaldehyde residues in oxidized DNA by gas chromatography/negative chemical ionization/mass spectrometry

Deoxyribose oxidation in DNA represents a biologically important facet of oxidative DNA damage that gives rise to protein-DNA cross-links and base adducts. Toward the goal of quantifying deoxyribose oxidation chemistry in cells, we report a method for the quantification of 3'-phosphoglycolaldehyde (PGA) residues, which likely arise from 3'-oxidation of deoxyribose in DNA. The method exploits the aldehyde moiety in PGA by derivatization as a stable oxime with pentafluorobenzylhydroxylamine, followed by solvent extraction and gas chromatography/negative chemical ionization/mass spectrometry. A stable isotopically labeled [(13)C(2)]PGA was synthesized and used as an internal standard. The assay showed a linear response over the range of 30 fmol to 300 pmol, and its precision was verified by analysis of a synthetic, PGA-containing oligodeoxynucleotide. The limit of detection in the presence of DNA was 30 fmol per sample, corresponding to two molecules of PGA in 10(6) nucleotides for 170 microg of DNA. Samples were exposed to 0-100 Gy of (60)Co gamma-radiation, which resulted in a linear dose-response of 1.5 PGA residues per 10(6) nucleotides per Gy and a radiation chemical yield (G-value) of 0.0016 micromol/J. When compared to the total quantity of deoxyribose oxidation occurring under the same conditions (141 oxidation events per 10(6) nucleotides per Gy; determined by plasmid topoisomer analysis), PGA formation occurs in 1% of deoxyribose oxidation events. This small fraction is consistent with current models of limited solvent accessibility of the 3'-position of deoxyribose, although partitioning of 3'-chemistry could lead to other damage products that would increase the fraction of oxidation at this site in deoxyribose.

Deciphering the function of an ORF: Salmonella enterica DeoM protein is a new mutarotase specific for deoxyribose

We identified in Salmonella enterica serovar Typhi a cluster of four genes encoding a deoxyribokinase (DeoK), a putative permease (DeoP), a repressor (DeoQ), and an open reading frame encoding a 337 amino acid residues protein of unknown function. We show that the latter protein, called DeoM, is a hexamer whose synthesis is increased by a factor over 5 after induction with deoxyribose. The CD spectrum of the purified recombinant protein indicated a dominant contribution of betatype secondary structure and a small content of alpha-helix. Temperature and guanidinium hydrochloride induced denaturation of DeoM indicated that the hexamer dissociation and monomer unfolding are coupled processes. DeoM exhibits 12.5% and 15% sequence identity with galactose mutarotase from Lactococcus lactis and respectively Escherichia coli, which suggested that these three proteins share similar functions. Polarimetric experiments demonstrated that DeoM is a mutarotase with high specificity for deoxyribose. Site-directed mutagenesis of His183 in DeoM, corresponding to a catalytically active residue in GalM, yielded an almost inactive deoxyribose mutarotase. DeoM was crystallized and diffraction data collected for two crystal systems, confirmed its hexameric state. The possible role of the protein and of the entire gene cluster is discussed in connection with the energy metabolism of S. enterica under particular growth conditions.

Ion Desorption from DNA Components Irradiated with 0.5 keV Ultrasoft X-Ray Photons

Positive ion desorption from thin films of DNA components, 2-deoxy-d-ribose, thymine, thymidine (dThd), and thymidine 5'-monophosphate (dTMP) was investigated in the oxygen K- shell edge excitation region using synchrotron ultrasoft X rays (538 eV). A large number of molecular fragments, H(+), CH(x)(+), C(2)H(x)(+), CO(+), CH(x)O(+), C(3)H(x)(+), C(2)H(x)O(+) and C(3)H(x)O(+) (x = 1, 2 and 3), were observed as desorbed ions from 2-deoxy-d-ribose. Some of these ions are related to simultaneous bond scission at particular C-C and C-O (or C-C) bonds in the furanose ring structure in the 2-deoxy-d-ribose molecule, indicating that the impact of photons on the oxygen atom and the impact of ejected secondary electrons (e.g. Auger electrons) cause an intense destruction of the furanose ring structure. In thymine thin films, H(+), CH(x)(+), CO(+), CH(x)O(+), C(2)H(x)N(+) and CH(x)NO(+) (x = 1, 2 and 3) fragments were observed. The yields of these ions were smaller than the yields from 2-deoxy-d-ribose. The desorption of CH(3)(+) from thymine might induce a molecular conversion from thymine to uracil. The mass patterns of dThd and dTMP, and especially that of dTMP, were similar to that of 2-deoxy-d-ribose, indicating that a number of ions were generated at the sugar site, even in the nucleotide molecule. It is therefore predicted that the sugar moiety is more fragile than the thymine base.

Deoxyribonucleotides: the unusual chemistry and biochemistry of DNA precursors

Deoxyribonucleotides, monomers of macromolecular DNA and the chemical matter of genes, have received surprisingly little attention among chemists and molecular biologists alike, although their origin, properties, and mechanism of enzyme-catalyzed formation bear unique chemical traits which are the basis of DNA replication. Apart from providing insights in bioorganic free radical chemistry, present interest in deoxyribonucleotides stems from the expected demand of hundreds of kilograms per year for DNA chips and antisense constructs used in gene therapy, difficult to produce by conventional methods. A novel approach towards deoxyribonucleotide, and hence DNA formation in a putative primordial 'RNA world' has also recently emerged.

Antioxidant properties of aqueous extracts from selected lamiaceae species grown in Turkey

Water-soluble extracts from black thyme (Thymbra spicata L.), savory (Satureja cuneifolia Ten.), Spanish oregano (Coridothymus capitatus (L.) Reichb. f.), sweet marjoram (Majorana hortensis Moench), Syrian oregano (Origanum syriacum L.), Toka oregano (Origanum minutiflorum O. Schwarz et P. H. Davis), and Turkish oregano (Origanum onites L.) were screened for antioxidant properties in a battery of six in vitro assays. Total phenol content and qualitative-quantitative compositional analyses were also carried out. The extracts demonstrated varying degrees of efficacy in each screen. The savory extract was the most effective at reducing iron(III), scavenging 1,1-diphenyl-2-picrylhydrazyl radicals, inhibiting ascorbate-iron(III)-catalyzed hydroxyl radical-mediated brain phospholipid peroxidation, and site-specific hydroxyl radical-mediated 2-deoxy-d-ribose degradation. The Syrian oregano extract was the most effective chelator of iron(II), while Spanish and Turkish oregano extracts were the most effective inhibitors of nonsite-specific hydroxyl radical-mediated 2-deoxy-d-ribose degradation. All the extracts contained Folin-Ciocalteu reagent-reactive substances, which was confirmed by the presence of polar phenolic analytes (i.e., hydroxybenzoates, hydroxycinnamates, and flavonoids).

Structures of Purine 2‘-Deoxyribosyltransferase, Substrate Complexes, and the Ribosylated Enzyme Intermediate at 2.0 Å Resolution,

The structure of class I N-deoxyribosyltransferase from Lactobacillus helveticus was determined by X-ray crystallography. Unlike class II N-deoxyribosyltransferases, which accept either purine or pyrimidine deoxynucleosides, class I enzymes are specific for purines as both the donor and acceptor base. Both class I and class II enzymes are highly specific for deoxynucleosides. The class I structure reveals similarities with the previously determined class II enzyme from Lactobacillus leichmanni [Armstrong, S. A., Cook, W. J., Short, S. A., and Ealick, S. E. (1996) Structure 4, 97-107]. The specificity of the class I enzyme for purine deoxynucleosides can be traced to a loop (residues 48-62), which shields the active site in the class II enzyme. In the class I enzyme, the purine base itself shields the active site from the solvent, while the smaller pyrimidine base cannot. The structure of the enzyme with a bound ribonucleoside shows that the nucleophilic oxygen atom of Glu101 hydrogen bonds to the O2' atom, rendering it unreactive and thus explaining the specificity for 2'-deoxynucleosides. The structure of a ribosylated enzyme intermediate reveals movements that occur during cleavage of the N-glycosidic bond. The structures of complexes with substrates and substrate analogues show that the purine base can bind in several different orientations, thus explaining the ability of the enzyme to catalyze alternate deoxyribosylation at the N3 or N7 position.

Density functional theory studies of electron interaction with DNA: can zero eV electrons induce strand breaks?

The discovery of DNA strand breaks induced by low energy secondary electrons sparks a necessity to elucidate the mechanism. Through theoretical studies based on a sugar-phosphate-sugar model that mimics a backbone section of the DNA strand, it is found that bond cleavages at 3' or 5'C-O sites after addition of an electron are possible with a ca. 10 kcal/mol activation barrier. Moreover, the potential energy surfaces show that dissociation at both sites is highly favorable thermodynamically. Although the phosphate group in DNA is not a favored site for electron attachment because of competitive electron transfer to the bases, any electrons which attach to phosphates on first encounter may induce strand breaks even when the electron energy is near zero eV. These findings have profound implication as low energy secondary electrons are abundantly generated in all types of ionization radiation.

Conversion of 2-deoxy-D-ribose into 2-amino-5-(2-deoxy-beta-D-ribofuranosyl)pyridine, 2'-deoxypseudouridine, and other C-(2'-deoxyribonucleosides)

The synthesis of 2-amino-5-(2-deoxy-beta-D-ribofuranosyl)pyridine 2a, 2-amino-5-(2-deoxy-alpha-D-ribofuranosyl)-pyridine 23, 2-amino-5-(2-deoxy-beta-D-ribofuranosyl)-3-methylpyridine 2b, 2-amino-5-(2-deoxy-alpha-D-ribofuranosyl)-3-methylpyridine 29 and 5-(2-deoxy-beta-D-ribofuranosyl)-2,4-dioxopyrimidine [2'-deoxypseudouridine] 30a is described. These C-nucleosides are prepared either from 2-deoxy-3,5-O-(1,1,3,3-tetraisopropyldisiloxan-1,3-diyl)-D-ribofuranose 15 or from 2-deoxy-3,5-O-(1,1,3,3-tetraisopropyldisiloxan-1,3-diyl)-D-ribono-1,4-lactone 16, which are themselves prepared from 2-deoxy-D-ribose 13. The sugar derivatives are first allowed to react with the appropriate 5-lithio-pyridine or 5-lithio-pyrimidine derivatives, which are prepared from 5-bromo-2-(dibenzylamino)pyridine 12a, 5-bromo-2-[bis(4-methoxybenzyl)amino]pyridine 12b, 5-bromo-2-dibenzylamino-3-methylpyridine 25 and 5-bromo-2,4-bis(4-methoxybenzyloxy)pyrimidine 33. The products from the reactions between the lithio-derivatives and the lactol 15 are cyclized under Mitsunobu conditions; the products from the reactions between the lithio-derivatives and the lactone 16 are first reduced with L-Selectride before cyclization, also under Mitsunobu conditions. In all cases, the beta-anomers of the protected C-nucleosides are the predominant products. Finally, the separation of the alpha- and beta-anomers and the removal of all of the protecting groups are described.

Synthesis and properties of oligonucleotides involving a perylene unit linked to a 2'-deoxyribose residue

We report here the synthesis and binding properties of oligonucleotides involving a perylene unit linked to the anomeric position of a 2'-deoxyribose residue. Both anomers were separated and incorporated separately at either the 5'-end or the internal position of a pyrimidine sequence. In any case the presence of the perylene unit stabilizes the complexes formed with either the single or the double-stranded target.