Decomposition of 2‐deoxy‐D‐ribose by irradiation with 0.6 keV electrons and by 0.5 keV ultrasoft X‐rays

PURPOSE

To compare the molecular decomposition of 2-deoxy-D-ribose induced by 0.6 keV electron irradiation or by 0.5keV ultrasoft X-ray irradiation.

MATERIALS AND METHODS

A thin film of 2-deoxy-D-ribose was irradiated by two radiation sources: low-energy (approximately 0.6 keV) electrons and ultrasoft X-rays (approximately 0.5 keV). The positive ions that were desorbed from the sample during the irradiation were measured using a quadrupole mass spectrometer. The spectral changes in the X-ray absorption near edge structure (XANES) were also examined after the irradiation.

RESULTS AND DISCUSSION

The ions that were desorbed from 2-deoxy-D-ribose due to electron irradiation were mainly H+, CHx+, C2Hx+, CO+, CHxO+, C3Hx+, C2HxO+ and C3sHO+ (x=1, 2, and 3) ions. These ions were the same as those observed in desorption due to ultrasoft X-ray irradiation. The XANES spectral changes induced by electron irradiation showed C-O bond cleavage in the molecule and C=O bond formation in the surface residues. These results show that intensive molecular decomposition of the furanose ring structure was induced by both types of irradiation. It is inferred that these irradiation products are primarily produced by secondary electrons (several tens of eV), which are thought to be generated by both types of irradiation when they are applied to the 2-deoxy-D-ribose sample.

The multiple Maillard reactions of ribose and deoxyribose sugars and sugar phosphates

Ribose 5-phosphate (R5P) undergoes the Maillard reaction with amines at significantly higher rates than most other sugars and sugar phosphates. The presence of an intramolecular phosphate group, which catalyzes the early stages of the Maillard reaction, provides the opportunity for the R5P molecule to undergo novel reaction paths creating unique Maillard products. The initial set of reactions leading to an Amadori product (phosphorylated) and to an alpha-dicarbonyl phosphate compound follows a typical Maillard reaction sequence, but an observed phosphate hydrolysis accompanying the reaction adds to the complexity of the products formed. The reaction rate for the loss of R5P is partially dependent on the pK(a) of the amine but also is correlated to the protonation of an early intermediate of the reaction sequence. In the presence of oxygen, a carboxymethyl group conjugated to the amine is a major product of the reaction of R5P with N-acetyllysine while little of this product is generated in the absence of oxygen. Despite lacking a critical hydroxyl group necessary for the Maillard reaction, 2-deoxyribose 5-phosphate (dR5P) still generates an Amadori-like product (with a carbonyl on the C-3 carbon) and undergoes phosphate cleavage. Two highly UV-absorbing products of dR5P were amine derivatives of 5-methylene-2-pyrrolone and 2-formylpyrrole. The reaction of dR5P with certain amines generates a set of products that exhibit an interesting absorbance at 340nm and a high fluorescence.

Mechanisms of direct radiation damage in DNA, based on a study of the yields of base damage, deoxyribose damage, and trapped radicals in d(GCACGCGTGC)(2)

Dose-response curves were measured for the formation of direct-type DNA products in X-irradiated d(GCACGCGTGC)(2)prepared as dry films and as crystalline powders. Damage to deoxyribose (dRib) was assessed by HPLC measurements of strand break products containing 3' or 5' terminal phosphate and free base release. Base damage was measured using GC/ MS after acid hydrolysis and trimethylsilylation. The yield of trappable radicals was measured at 4 K by EPR of films X-irradiated at 4 K. With exception of those used for EPR, all samples were X-irradiated at room temperature. There was no measurable difference between working under oxygen or under nitrogen. The chemical yields (in units of nmol/J) for trapped radicals, free base release, 8-oxoGua, 8-oxoAde, diHUra and diHThy were G(total)(fr) = 618 +/- 60, G(fbr) = 93 +/- 8, G(8-oxoGua) = 111 +/- 62, G(8-oxoAde) = 4 +/- 3, G(diHUra) = 127 +/- 160, and G(diHThy) = 39 +/- 60, respectively. The yields were determined and the dose-response curves explained by a mechanistic model consisting of three reaction pathways: (1) trappable-radical single-track, (2) trappable-radical multiple-track, and (3) molecular. If the base content is projected from the decamer's GC:AT ratio of 4:1 to a ratio of 1:1, the percentage of the total measured damage (349 nmol/J) would partition as follows: 20 +/- 16% 8-oxoGua, 3 +/- 3% 8-oxoAde, 28 +/- 46% diHThy, 23 +/- 32% diHUra, and 27 +/- 17% dRib damage. With a cautionary note regarding large standard deviations, the projected yield of total damage is higher in CG-rich DNA because C combined with G is more prone to damage than A combined with T, the ratio of base damage to deoxyribose damage is approximately 3:1, the yield of diHUra is comparable to the yield of diHThy, and the yield of 8-oxoAde is not negligible. While the quantity and quality of the data fall short of proving the hypothesized model, the model provides an explanation for the dose-response curves of the more prevalent end products and provides a means of measuring their chemical yields, i.e., their rate of formation at zero dose. Therefore, we believe that this comprehensive analytical approach, combined with the mechanistic model, will prove important in predicting risk due to exposure to low doses and low dose rates of ionizing radiation.

Recent highlights in modified oligonucleotide chemistry

The synthesis of modified nucleic acids has been the subject of much study ever since the structure of DNA was elucidated by Watson and Crick at Cambridge and Wilkins and Franklin at King's College over half a century ago. This review describes recent developments in the synthesis and application of these artificial nucleic acids, predominantly the phosphoramidites which allow for easy inclusion into oligonucleotides, and is divided into three separate sections. Firstly, modifications to the base portion will be discussed followed secondly by modifications to the sugar portion. Finally, changes in the type of nucleic acid linker will be discussed in the third section. Peptide Nucleic Acids (PNAs) are not discussed in this review as they represent a separate and large area of nucleic acid mimics.

Increased single-nucleotide discrimination in allele-specific polymerase chain reactions through primer probes bearing nucleobase and 2'-deoxyribose modifications

The diagnosis of genetic dissimilarities between individuals is becoming increasingly important due to the discovery that these variations are related to complex phenotypes like the predisposition to certain diseases or compatibility with drugs. The most common among these sequence variations are single-nucleotide polymorphisms (SNPs). The availability of reliable and efficient methods for the interrogation of the respective genotypes is the basis for any progress along these lines. Many methods for the detection of nucleotide variations in genes exist, in which amplification of the target gene is required before analysis can take place. The allele-specific polymerase chain reaction (asPCR) combines target amplification and analysis in a single step. The principle of asPCR is based on the formation of matched or mismatched primer-target complexes. The most important parameter in asPCR is the discrimination of these matched or mismatched pairs. In recent publications we have shown that the reliability of SNP detection through asPCR is increased by employing chemically modified primer probes. In particular, primer probes that bear a polar 4'-C-methoxymethylene residue at the 3' end have superior properties in discriminating single-nucleotide variations by PCR. Here we describe the synthesis of several primer probes that bear nucleobase modifications in addition to the 4'-C-methoxymethylenated 2'-deoxyriboses. We studied the effects of these alterations on single-nucleotide discrimination in allele-specific PCR promoted by a DNA polymerase and completed these results with single-nucleotide-incorporation kinetic studies. Moreover, we investigated thermal denaturing of the primer-probe-template complexes and recorded circular dichroism (CD) spectra for inspecting the thermodynamic and photophysical duplex behaviour of the introduced modifications. In short, we found that primer probes bearing a 4'-C-methoxymethylene residue at the 2'-deoxyribose moiety in combination with a thiolated thymidine moiety have synergistic effects and display significantly increased discrimination properties in asPCR.

Antioxidant activity of Caesalpinia digyna root

The antioxidant properties of three successive extracts of Caesalpinia digyna Rottler root and the isolated compound, bergenin, were tested using standard in vitro and in vivo models. The amount of the total phenolic compounds present was also determined. The successive methanol extract of Caesalpinia digyna root (CDM) exhibited strong scavenging effect on 2,2-diphenyl-2-picryl hydrazyl (DPPH) free radical, 2,2'-azino-bis(3-ethylbenzo-thiazoline-6-sulphonic acid) diammonium salt (ABTS) radical cation, hydrogen peroxide, nitric oxide, hydroxyl radical and inhibition of lipid peroxidation. The free radical scavenging effect of CDM was comparable with that of reference antioxidants. The CDM having the highest content of phenolic compounds and strong free radical scavenging effect when administered orally to male albino rats at 100, 200 and 400mg/kg body weight for 7 days, prior to carbontetrachloride (CCl(4)) treatment, caused a significant increase in the levels of catalase (CAT) and superoxide dismutase (SOD) and significant decrease in the levels of lipidperoxidation (LPO) in serum, liver and kidney in a dose dependent manner, when compared to CCl(4) treated control. These results clearly indicate the strong antioxidant property of Caesalpinia digyna root. The study provides a proof for the ethnomedical claims and reported biological activities. The plant has, therefore, very good therapeutic potential.

Dissociative electron attachment to furan, tetrahydrofuran, and fructose

We study dissociative electron attachment to furan (FN) (C(4)H(4)O), tetrahydrofuran (THF) (C(4)H(8)O), and fructose (FRU) (C(6)H(12)O(6)) using crossed electron/molecular beams experiments with mass spectrometric detection of the anions. We find that FN and THF are weak electron scavengers and subjected to dissociative electron attachment essentially in the energy range above 5.5 eV via core excited resonances. In striking contrast to that, FRU is very sensitive towards low energy electrons generating a variety of fragment ions via a pronounced low energy feature close to 0 eV. These reactions are associated with the degradation of the ring structure and demonstrate that THF cannot be used as surrogate to model deoxyribose in DNA with respect to the attack of electrons at subexcitation energies (<3 eV). The results support the picture that in DNA the sugar moiety itself is an active part in the initial molecular processes leading to single strand breaks.

2-deoxyribose as a rich source of chiral 5-carbon building blocks

We have developed concise routes to a number of useful chiral 5-carbon synthetic building blocks using readily available O-1-methyl-2-deoxyribose as starting material. Novel transformations include the use of indium triflate to catalyze the oxidation of a methyl furanoside to the corresponding lactone with MCPBA and the Vasella-type fragmentation of a 5-iodo furanoside using chromium(II) chloride when zinc proved ineffective. In addition, 3,4-disubstituted piperidine derivatives were prepared without hydroxyl group protection via a simple reductive amination reaction.

First observation of luminescence from tris(2,2'-bipyridine)ruthenium(II) triggered by anodic oxidation of oligodeoxyribonucleotide

Anodic oxidation of oligodeoxyribonucleotide in an alkaline aqueous medium containing tris(2,2'-bipyridine)ruthenium(II) (Ru(bpy)3(2+)) was shown to cause luminescence around +1.3 V (vs. Ag/AgCl) with a maximal intensity at approximately 600 nm, possibly originating from Ru(bpy)3(2+) in the d-pi* triplet state. A pivotal initial stage in the light production path was postulated to be the anodic oxidation of 2-deoxyribose residue. This reaction seems to be available for the determination of sub-micromol dm(-3) levels of oligodeoxyribonucleotide.

Evaluation of antioxidant potential of ethyl acetate extract/fractions of Acacia auriculiformis A. Cunn

The present study estimates the free radical scavenging activity of the ethyl acetate extract/fractions of Acacia auriculiformis A. Cunn in different assays viz. 1'-1' diphenyl-2'picrylhydrazyl (DPPH), deoxyribose (site specific and non-site specific), relative reducing power, chelating power and lipid peroxidation. The bark powder of the plant was extracted with different solvents by maceration method in the order of increasing and decreasing polarity. The crude ethyl acetate extract was partitioned with ethyl acetate and water (Flow Chart 1 and 2). The scavenging activity of fractions was found to be more as compared to the crude extract. The percent inhibition with water fraction of ethyl acetate extract was observed to be 71.2%, 73.66%, 83.37%, 75.63% and 72.92% in DPPH, chelating power, lipid peroxidation, site specific and non-site specific deoxyribose scavenging assays respectively at maximum concentration tested. l-ascorbic acid and BHT were used as reference compounds for comparing the activity of plant extract/fractions. Studies are in progress to evaluate the effect of extract/fractions in other antioxidant assays and identify the factors responsible for the activity.

Nile Red nucleoside: novel nucleoside analog with a fluorophore replacing the DNA base

A solvatochromic dye is very useful in studies of local polarity and dynamics in biological systems. A novel solvatochromic chromophore, Nile Red beta-C-2'-deoxyriboside, has been synthesized to act as a photophysical probe, and incorporated site-selectively into an oligodeoxynucleotide. The absorption and fluorescence spectra of Nile Red nucleoside showed a remarkable sensitivity to the solvent polarity.

Mid-Infrared Study of Deoxyadenosine at High Pressures: Evidence of Phase Transitions

Room temperature mid-infrared experiments between 500 and 1800 cm(-1) have been performed on crystalline deoxyadenosine as a function of pressure up to about 10 GPa. Discontinuities observed near 2 and 4 GPa indicate that two separate phase transitions occur at these pressures. Changes in the spectra suggest that both transitions involve a rearrangement of the pucker of the deoxyribose moiety. The wavenumbers of the vibrational modes shift to higher values with applied pressure. Our results for deoxyadenosine are compared to similar measurements on adenosine. Assignments for the observed modes are made on the basis of work published in the literature.

Characterization of Adducts Formed in the Reaction of Glutaraldehyde with 2‘-Deoxyadenosine

Glutaraldehyde (1,5-pentanedial) is a widely used industrial chemical that has been found to be mutagenic in bacteria and mammalian cells. In this study, we examined the reaction of glutaraldehyde with 2'-deoxyadenosine and calf thymus DNA in aqueous buffered solutions. The 2'-deoxyadenosine adducts were isolated by reversed phase HPLC and characterized by their UV absorbance and 1H and 13C NMR spectroscopic and mass spectrometric features. The reaction produced three major adducts. The adduct dA567 was derived from two 2'-deoxyadenosine units bound together with a piperidine unit, and its yield was 10.4%. The carbons of the piperidine ring originated from glutaraldehyde, whereas the nitrogen of the ring originated from the exocyclic amino group of one of the 2'-deoxyadenosine units. The adduct dA451d (yield 0.6%) was similar in structure to dA567, but one of the deoxyribose moieties from 2'-deoxyadenosine was missing. The third adduct, dA334, consisted of a hydroxy-tetrahydropyridine moiety derived from glutaraldehyde and N6 of 2'-deoxyadenosine (yield 4.0%). Furthermore, LC-ESI-MS/MS analysis of the reaction mixture revealed the formation of compounds with ion peaks of m/z = 352. None of these compounds were sufficiently stable for preparative isolation. They were tentatively identified as a pair of diastereomers of 2,6-dihydroxypiperidine derivatives, which are likely precursors to dA334. Plausible mechanisms for the formation of the adducts are presented. In the reaction of glutaraldehyde with single and double stranded calf thymus DNA, the dA334 adduct was formed.

Vinylogous Amadori rearrangement: Implications in food and biological systems

The 4-hydroxy-alkenals are important lipid peroxidation products and are known to play a major role both in the development of degenerative diseases in biological systems and off-flavors, or rancidity in food systems. The 4-hydroxy-alkenals can also be formed in nonlipid systems from 2-deoxy-sugar moieties such as 2-deoxy-ribose. FTIR spectroscopic evidence was provided for such a transformation catalyzed by amino acids through monitoring the decrease in intensity of the aldehydic band centered at 1716 cm(-1) of the open form of 2-deoxy-ribose and increase in the intensity of the formed conjugated aldehydic band centered at 1672 cm(-1). Furthermore, 4-hydroxy-alkenals can react with nitrogen nucleophiles such as amino acids and proteins to form Schiff base adducts that are able to undergo vinylogous Amadori rearrangement (vARP) and subsequently cyclize to generate a pyrrole moiety. This cyclization is prevented in the case of secondary amino acids such as proline to form a stable vinylogous Amadori rearrangement product (vARP). Monitoring this reaction of proline with 4-hydroxy-2-nonenal (HNE) has indicated that within 15 min at 28 degrees C the 1685 cm(-1) band of HNE completely disappears and that at 50 degrees C, vARP is formed within 5 min, as indicated by the formation of a characteristic band at 1709 cm(-1).

In vitro protection of reactive oxygen species-induced degradation of lipids, proteins and 2-deoxyribose by tea catechins

Both the anti- and pro-oxidant effects of tea catechins, have been implicated in the alterations of cellular functions which determine their chemoprotective and therapeutic potentials in toxicity and diseases. Here, we have studied the protective mechanism (s) of three main green tea catechins namely, epicatechin (EC), epicatechin gallate (ECG) and epigallocatechin gallate (EGCG) on free radical induced oxidative degradation of membrane lipids and proteins under in vitro conditions using isolated cell free fractions from rat liver. In addition, we have also studied the effects of the tea catechins on 2-deoxyribose degradation in the presence of Fenton and Haber-Weiss oxidants. Glutathione S-transferase and cytochrome P450 2E1 activities and lipid peroxidation were found to be markedly inhibited by tea catechins. These catechins also inhibited the reactive oxygen species formation and oxidative carbonylation of subcellular proteins induced by a physiological oxidant, 4-hydroxynonenal. EGCG and the other catechins showed a time and concentration-dependent effects on the degradation of 2-deoxyribose in the presence of Fenton oxidants. Our results indicate that tea catechins prevent molecular degradation in oxidative stress conditions by directly altering the subcellular ROS production, glutathione metabolism and cytochrome P450 2E1 activity. These results may have implications in determining the chemotherapeutic use of tea catechins in oxidative stress related diseases.

Low energy electron-induced reactions in gas phase 1,2,3,5-tetra-O-acetyl-β-D-ribofuranose: A model system for the behavior of sugar in DNA

Dissociative electron attachment to 1,2,3,5-tetra-O-acetyl-beta-D-ribofuranose (TAR) is studied in a crossed electron-molecular beam experiment with mass spectrometric detection of the observed fragment ions. Since in TAR acetyl groups are coupled at the relevant positions to the five membered ribose ring, it may serve as an appropriate model compound to study the response of the sugar unit in DNA towards low energy electrons. Intense resonances close to 0 eV are observed similar to the pure gas phase sugars (2-deoxyribose, ribose, and fructose). Further strong resonances appear in the range of 1.6-1.8 eV (not present in the pure sugars). Based on calculations on transient anions adopting the stabilization method, this feature is assigned to a series of closely spaced shape resonances of pi* character with the extra electron localized on the acetyl groups outside the ribose ring system. Further but weaker resonant contributions are observed in the range of 7-11 eV, representing core excited resonances and/or sigma* shape resonances. The decomposition processes involve single bond ruptures but also more complex reactions associated with substantial rearrangement. The authors hence propose that the sugar unit in DNA plays an active role in the molecular mechanism towards single strand breaks induced by low energy electrons.

Synchrotron radiation circular dichroism spectroscopy of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides

Synchrotron radiation circular dichroism (SRCD) spectra of ribose and deoxyribose sugars, adenosine, AMP and dAMP nucleotides and cyclic derivatives were measured in the vacuum ultraviolet region (down to 168 nm for sugars and 175 nm for adenine derivatives) and at different pH values (3, 6-7, 9-10) and temperatures (between 5 and 45 degrees C). The information content in the VUV region is important since the CD bands strongly depend on the chemical structure of the sugar, the presence and orientation of a phosphate group and the protonation state of adenine. On the other hand, single or double deprotonation of the phosphoric acid group has no influence on the spectra. We assign the vacuum ultraviolet (VUV) CD bands of the nucleoside and nucleotides to be due mainly to n-->pi* transitions in the adenine nucleobase based on a comparison with the absorption spectra. The CD bands of the sugars are due to n(O -->sigma*) transitions and are much smaller than the CD signal from the nucleotides in the VUV region. Bands are assigned to both pyranose and open-chain forms.

The role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA

The role of 2'-hydroxyl groups in stabilizing the tightly kinked geometry of the kink-turn (K-turn) has been investigated. Individual 2'-OH groups have been removed by chemical synthesis, and the kinking of the RNA has been studied by gel electrophoresis and fluorescence resonance energy transfer. The results have been analyzed by reference to a database of 11 different crystallographic structures of K-turns. The potential hydrogen bonds fall into several classes. The most important are those in the core of the turn and ribose-phosphate interactions around the bulge. Of these the single most important hydrogen bond is one donated from the 2'-OH of the 5' nucleotide of the bulge to the N1 of the adenine of the kink-proximal A*G pair. This is present in all known K-turn structures, and removal of the 2'-OH completely prevents metal ion-induced folding. Hydrogen bonds formed in the minor grooves of the helical stems are less important, and removal of the participating 2'-OH groups leads to reduced impairment of folding. These interactions are generally more polymorphic, and hydrogen bonds probably form where possible, as permitted by the global structure.

Factors determining the deriving force of DNA formation: geometrical differences of base pairs, dehydration of bases, and the arginine assisting

The mechanism of the fidelity synthesis of DNA associated with the process of dGTP combination to the DNA template was explored. The exclusion of water molecules from the hydrated DNA bases can amplify the energy difference between the correct and incorrect base pairs, but the effect of the water molecules on the Gibbs free energy of formation is dependent on the binding sites for the water molecules. The water detachment from the incoming dNTP is not the only factor but the first step for the successful replication of DNA. The second step is the selection of the DNA polymerase on the DNA base pair through the comparison between the correct DNA base and the incorrect DNA base. The bonding of the Arg668 with the incoming dNTP can enlarge the Gibbs free energies of formation of the base pairs, especially the correct base pairs, thus increasing the driving force of DNA formation. When the DNA base of the primer terminus is correct, the extension of the guanine and the adenine is quicker than that of the cytosine and the thymine because of the hydrogen bonding fork formation of Arg668 with the minor groove of the primer terminus and the ring oxygen of the deoxyribose moiety of the incoming dNTP. Because of the geometry differences of the incorrect base pairs with the correct base pairs, the effect from the DNA polymerase is smaller on the incorrect base pair than on the correct base pair, and the extension of a mispair is slower than that of a correct base pair. This decreases the extension rate of the base pair and thus allows proofreading exonuclease activity to excise the incorrect base pair. Arg668 cannot prevent the extension of the GT mispair, as well as the GC correct base pair, and GA and GG mispairs. This may be attributed to the small geometry difference between the GT base pair and the correct AT base pair.

Formation of 1,4-dioxo-2-butene-derived adducts of 2'-deoxyadenosine and 2'-deoxycytidine in oxidized DNA

Oxidation of deoxyribose in DNA produces a variety of electrophilic residues that are capable of reacting with nucleobases to form adducts such as M(1)dG, the pyrimidopurinone adduct of dG. We now report that deoxyribose oxidation in DNA leads to the formation of oxadiazabicyclo(3.3.0)octaimine adducts of dC and dA. We previously demonstrated that these adducts arise in reactions of nucleosides and DNA with trans-1,4-dioxo-2-butene, the beta-elimination product of the 2-phosphoryl-1,4-dioxobutane residue arising from 5'-oxidation of deoxyribose in DNA, and with cis-1,4-dioxo-2-butene, a metabolite of furan. Treatment of DNA with enediyne antibiotics capable of oxidizing the 5'-position of deoxyribose (calicheamicin and neocarzinostatin) led to a concentration-dependent formation of oxadiazabicyclo(3.3.0)octaimine adducts of dC and dA, while the antibiotic bleomycin, which is capable of performing only 4-oxidation of deoxyribose, did not give rise to the adducts. The nonspecific DNA oxidant, gamma-radiation, also produced the adducts that represented approximately 0.1% of the 2-phosphoryl-1,4-dioxobutane residues formed during the irradiation. These results suggest that the oxadiazabicyclo(3.3.0)octaimine adducts of dC and dA could represent endogenous DNA lesions arising from oxidative stresses that also give rise to other DNA adducts.

Towards elucidation of the mechanism of UV1C, a deoxyribozyme with photolyase activity

Among the unexpected chemistries that can be catalyzed by nucleic acid enzymes is photochemistry. We have reported the in vitro selection of a small, cofactor-independent deoxyribozyme, UV1C, capable of repairing thymine dimers in a DNA substrate, most optimally with light at a wavelength of >300 nm. We hypothesized that a guanine quadruplex functioned both as a light antenna and an electron source for the repair of the substrate within the enzyme-substrate complex. Here, we report structural and mechanistic investigations of that hypothesis. Contact-crosslinking and guanosine to inosine mutational studies reveal that the thymine dimer and the guanine quadruplex are positioned close to each other in the deoxyribozyme-substrate complex, and permit us to refine the structure and topology of the folded deoxyribozyme. In exploring the substrate utilization capabilities of UV1C, we find it to be able to repair uracil dimers as well as thymine dimers, as long as they are present in an overall deoxyribonucleotide milieu. Some surprising similarities with bacterial CPD photolyase enzymes are noted.

A Pro-Chelator Triggered by Hydrogen Peroxide Inhibits Iron-Promoted Hydroxyl Radical Formation

The synthesis and structural characterization of a new pro-chelating agent, isonicotinic acid [2-(4,4,5,5-tetramethyl-[1,3,2]dioxaborolan-2-yl)-benzylidene]-hydrazide (BSIH), are presented. BSIH only weakly interacts with iron unless hydrogen peroxide (H2O2) is present to remove the boronic ester protecting group to reveal a phenol that is a key metal-binding group of tridentate salicylaldehyde isonicotinoyl hydrazone (SIH). BSIH prevents deoxyribose degradation caused by hydroxyl radicals that are generated from H2O2 and redox-active iron by sequestering Fe3+ and preventing iron-promoted hydroxyl radical formation. The rate-determining step for iron sequestration is conversion of BSIH to SIH, followed by rapid Fe3+ complexation. The pro-chelate approach of BSIH represents a promising strategy for chelating a specific pool of detrimental metal ions without disturbing healthy metal ion distribution.

Inelastic electron interaction (attachment/ionization) with deoxyribose

We have investigated experimentally the formation of anions and cations of deoxyribose sugar (C(5)H(10)O(4)) via inelastic electron interaction (attachment/ionization) using a monochromatic electron beam in combination with a quadrupole mass spectrometer. The ion yields were measured as a function of the incident electron energy between about 0 and 20 eV. As in the case of other biomolecules (nucleobases and amino acids), low energy electron attachment leads to destruction of the molecule via dissociative electron attachment reactions. In contrast to the previously investigated biomolecules dehydrogenation is not the predominant reaction channel for deoxyribose; the anion with the highest dissociative electron attachment (DEA) cross section of deoxyribose is formed by the release of neutral particles equal to two water molecules. Moreover, several of the DEA reactions proceed already with "zero energy" incident electrons. In addition, the fragmentation pattern of positively charged ions of deoxyribose also indicates strong decomposition of the molecule by incident electrons. For sugar the relative amount of fragment ions compared to that of the parent cation is about an order of magnitude larger than in the case of nucleobases. We determined an ionization energy value for C(5)H(10)O(4) (+) of 10.51+/-0.11 eV, which is in good agreement with ab initio calculations. For the fragment ion C(5)H(6)O(2) (+) we obtained a threshold energy lower than the ionization energy of the parent molecular ion. All of these results have important bearing for the question of what happens in exposure of living tissue to ionizing radiation. Energy deposition into irradiated cells produces electrons as the dominant secondary species. At an early time after irradiation these electrons exist as ballistic electrons with an initial energy distribution up to several tens of electron volts. It is just this energy regime for which we find in the present study rather characteristic differences in the outcome of electron interaction with the deoxyribose molecule compared to other nucleobases (studied earlier). Therefore, damage induced by these electrons to the DNA or RNA strands may start preferentially at the ribose backbone. In turn, damaged deoxyribose is known as a key intermediate in producing strand breaks, which are the most severe form of lesion in radiation damage to DNA and lead subsequently to cell death.

C4' sugar oxidation of deoxyribonucleotide triphosphates by chromium(V) complexes

The Cr(V) complexes, bis(2-ethyl-2-hydroxybutyrato)oxochromate(V) ([OCr(V)(ehba)(2)](-)) and (2,2-bis(hydroxymethyl)-2-(bis(2-hydroxyethyl)amino)ethanolato)oxochromate(V) ([OCr(V)(BT)](2-)), were reacted with a series of deoxyribonucleotide triphosphates. Oxidation of deoxyribose at C4' was observed by measuring the amount of thiobarbituric acid reactive species (TBARS) produced in these reactions. For both compounds, the TBARS obtained with purine nucleotides was between 2.25 and 3.5 times greater than what was observed with pyrimidine nucleotide. This result suggests that the identity of the nucleic acid base can influence the hydrogen atom abstraction at C4'. Overall, the amount of product obtained with [OCr(V)(BT)](2-) was significantly less than what was observed with [OCr(V)(ehba)(2)](-), indicating that these two Cr(V) model complexes may oxidize DNA differently.