Competitive Radical Migrations and Ribose Ring Cleavage in Adenosine and 2'-Deoxyadenosine Cation Radicals

We report a combined experimental and computational study of adenosine cation radicals that were protonated at adenine and furnished with a radical handle in the form of an acetoxyl radical, •CH2COO, that was attached to ribose 5'-O. Radicals were generated by collision-induced dissociation (CID) and characterized by tandem mass spectrometry and UV-vis photodissociation action spectroscopy. The acetoxyl radical was used to probe the kinetics of intramolecular hydrogen transfer from the ribose ring positions that were specifically labeled with deuterium at C1', C2', C3', C4', C5', and in the exchangeable hydroxyl groups. Hydrogen transfer was found to chiefly involve 3'-H with minor contributions by 5'-H and 2'-H, while 4'-H was nonreactive. The hydrogen transfer rates were affected by deuterium isotope effects. Hydrogen transfer triggered ribose ring cleavage by consecutive dissociations of the C4'-O and C1'-C2' bonds, resulting in expulsion of a C6H9O4 radical and forming a 9-formyladenine ion. Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations of unimolecular constants were carried out using the effective CCSD(T)/6-311++G(3d,2p) and M06-2X/aug-cc-pVTZ potential energy surfaces for major isomerizations and dissociations. The kinetic analysis showed that hydrogen transfer to the acetoxyl radical was the rate-determining step, whereas the following ring-opening reactions in ribose radicals were fast. Using DFT-computed energies, a comparison was made between the thermochemistry of radical reactions in adenosine and 2'-deoxyadenosine cation radicals. The 2'-deoxyribose ring showed lower TS energies for both the rate-determining 3'-H transfer and ring cleavage reactions.

Sugar-Pucker Force-Induced Transition in Single-Stranded DNA

The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples range from DNA hybridization, DNA ligand binding, DNA unwinding by helicases, etc. To date, ssDNA elasticity has been studied with different methods in molecules of varying sequence and contour length. A dispersion of results has been reported and the value of the persistence length has been found to be larger for shorter ssDNA molecules. We carried out pulling experiments with optical tweezers to characterize the elastic response of ssDNA over three orders of magnitude in length (60-14 k bases). By fitting the force-extension curves (FECs) to the Worm-Like Chain model we confirmed the above trend:the persistence length nearly doubles for the shortest molecule (60 b) with respect to the longest one (14 kb). We demonstrate that the observed trend is due to the different force regimes fitted for long and short molecules, which translates into two distinct elastic regimes at low and high forces. We interpret this behavior in terms of a force-induced sugar pucker conformational transition (C3'-endo to C2'-endo) upon pulling ssDNA.

Electron-Induced Repair of 2'-Deoxyribose Sugar Radicals in DNA: A Density Functional Theory (DFT) Study

In this work, we used ωB97XD density functional and 6-31++G** basis set to study the structure, electron affinity, populations via Boltzmann distribution, and one-electron reduction potentials (E°) of 2′-deoxyribose sugar radicals in aqueous phase by considering 2′-deoxyguanosine and 2′-deoxythymidine as a model of DNA. The calculation predicted the relative stability of sugar radicals in the order C4′^• > C1′^• > C5′^• > C3′^• > C2′^•. The Boltzmann distribution populations based on the relative stability of the sugar radicals were not those found for ionizing radiation or OH-radical attack and are good evidence the kinetic mechanisms of the processes drive the products formed. The adiabatic electron affinities of these sugar radicals were in the range 2.6–3.3 eV which is higher than the canonical DNA bases. The sugar radicals reduction potentials (E°) without protonation (−1.8 to −1.2 V) were also significantly higher than the bases. Thus the sugar radicals will be far more readily reduced by solvated electrons than the DNA bases. In the aqueous phase, these one-electron reduced sugar radicals (anions) are protonated from solvent and thus are efficiently repaired via the “electron-induced proton transfer mechanism”. The calculation shows that, in comparison to efficient repair of sugar radicals by the electron-induced proton transfer mechanism, the repair of the cyclopurine lesion, 5′,8-cyclo-2′-dG, would involve a substantial barrier.

A Bioactive Coating Enhances Bone Allografts in Rat Models of Bone Formation and Critical Defect Repair

Bone allografts are inferior to autografts for the repair of critical-sized defects. Prior studies have suggested that bone morphogenetic protein-2 (BMP-2) can be combined with allografts to produce superior healing. We created a bioactive coating on bone allografts using polycondensed deoxyribose isobutyrate ester (PDIB) polymer to deliver BMP-2 ± the bisphosphonate zoledronic acid (ZA) and tested its ability to enhance the functional utility of allografts in preclinical Wistar rat models. One ex vivo and two in vivo proof-of-concept studies were performed. First, PDIB was shown to be able to coat bone grafts (BGs). Second, PDIB was used to coat structural allogenic corticocancellous BG with BMP-2 ± ZA ± hydroxyapatite (HA) microparticles and compared with PDIB-coated grafts in a rat muscle pouch model. Next, a rat critical defect model was performed with treatment groups including (i) empty defect, (ii) BG, (iii) collagen sponge + BMP-2, (iv) BG + PDIB/BMP-2, and (v) BG + PDIB/BMP-2/ZA. Key outcome measures included detection of fluorescent bone labels, microcomputed tomography (CT) quantification of bone, and radiographic healing. In the muscle pouch study, BMP-2 did not increase net bone volume measured by microCT, however, fluorescent labeling showed large amounts of new bone. Addition of ZA increased BV by sevenfold (p < 0.01). In the critical defect model, allografts were insufficient to promote reliable union, however, union was achieved in collagen/BMP-2 and all BG/BMP-2 groups. Statement of clinical significance: These data support the concept that PDIB is a viable delivery method for BMP-2 and ZA delivery to enhance the bone forming potential of allografts. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:2278-2286, 2019.

Optimized Synthesis of Poly(deoxyribose) Isobutyrate, a Viscous Biomaterial for Bone Morphogenetic Protein-2 Delivery

Injectable and phase-transitioning carriers from natural polysaccharides have great potential for the minimally invasive delivery of therapeutic proteins in the field of bone tissue engineering. In this study, a novel and highly viscous drug carrier was synthesized by a sequential process of deoxyribose polycondensation and esterification. The effect of synthesis parameters on the molecular weight, viscosity, and adhesion of the material was studied and correlated to temperature and time of polycondensation ( T_p and t_p), time and temperature of esterification ( T_e and t_e), and the molar ratio of the monomer ( R). The formulations were evaluated for molecular weight and distribution properties using GPC, chemical structures by FTIR and NMR spectra, and rheological properties using a rheometer. Formulations illustrated a wide range of viscosities (0.736 to 2225 Pa s), adhesion (0.896 to 58.45 N), and molecular weights (637 to 4216 Da), where viscosity was significantly reduced in the presence of low amounts of solvents (10-20%). The sustained release of BSA was observed over 42 days in vitro. The biocompatibility of poly(deoxyribose) isobutyrate (PDIB) as well as its potential as a bone morphogenetic protein delivery system was assessed in vivo using a rat ectopic bone model, where bone nodules were observed at 2 weeks. In summary, PDIB is a promising molecule with multiple applications for protein delivery, including for bone tissue engineering.

Measurement of Leukemic B-Cell Growth Kinetics in Patients with Chronic Lymphocytic Leukemia

Cell proliferation plays a central role in the pathogenesis of every neoplastic disease as well as many other types of illness. Labeling of newly replicated DNA with deuterium (²H), a nonradioactive isotope of hydrogen, administered to the patients in drinking water (²H₂O) is a safe and reliable method to measure the in vivo birth rates of cells. Here, we describe a protocol to measure chronic lymphocytic leukemia B-cell birth/proliferation and death rates over time using this approach.

Antioxidant activity of different species and varieties of turmeric (Curcuma spp): Isolation of active compounds

There are >80 species of turmeric (Curcuma spp.) and some species have multiple varieties, for example, Curcuma longa (C. longa) has 70 varieties. They could be different in their chemical properties and biological activities. Therefore, we compared antioxidant activity, total phenolic and flavonoid content of different species and varieties of turmeric namely C. longa [variety: Ryudai gold (RD) and Okinawa ukon], C. xanthorrhiza, C. aromatica, C. amada, and C. zedoaria. The antioxidant activity was determined using the 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activity, oxygen radical absorbance capacity (ORAC), reducing power and 2-deoxyribose (2-DR) oxidation assay. Our results suggested that RD contained significantly higher concentrations of total phenolic (157.4 mg gallic acid equivalent/g extract) and flavonoids (1089.5 mg rutin equivalent/g extract). RD also showed significantly higher DPPH radical-scavenging activity (IC₅₀: 26.4 μg/mL), ORAC (14,090 μmol Trolox equivalent/g extract), reducing power absorbance (0.33) and hydroxyl radical scavenging activity (IC₅₀: 7.4 μg/mL). Therefore, RD was chosen for the isolation of antioxidant compounds using silica gel column, Toyopearl HW-40F column, and high-performance liquid chromatography. Structural identification of the compounds was conducted using ¹H NMR, ¹³C NMR, and liquid chromatography-tandem mass spectrometry. The purified antioxidant compounds were bisabolone-9-one (1), 4-methyllene-5-hydroxybisabola-2,10-diene-9-one (2), turmeronol B (3), 5-hydroxy-1,7-bis(4-hydroxy-3-methoxyphenyl)-1-hepten-3-one (4), 3-hydroxy-1,7-bis(4-hydroxyphenyl)-6-hepten-1,5-dione (5), cyclobisdemethoxycurcumin (6), bisdemethoxycurcumin (7), demethoxycurcumin (8) and curcumin (9). The IC₅₀ for DPPH radical-scavenging activity were 474, 621, 234, 29, 39, 257, 198, 47 and 18 μM and hydroxyl radical-scavenging activity were 25.1, 24.4, 20.2, 2.1, 5.1, 17.2, 7.2, 3.3 and 1.5 μM for compound 1, 2, 3, 4, 5, 6, 7, 8 and 9, respectively. Our findings suggested that the RD variety of C. longa, developed by the University of the Ryukyus, Okinawa, Japan, is a promising source of natural antioxidants.

Polymorphism of G4 associates: from stacks to wires via interlocks

We examined the assembly of DNA G-quadruplexes (G4s) into higher-order structures using atomic force microscopy, optical and electrophoretic methods, NMR spectroscopy and molecular modeling. Our results suggest that parallel blunt-ended G4s with single-nucleotide or modified loops may form different types of multimers, ranging from stacks of intramolecular structures and/or interlocked dimers and trimers to wires. Decreasing the annealing rate and increasing salt or oligonucleotide concentrations shifted the equilibrium from intramolecular G4s to higher-order structures. Control antiparallel and hybrid G4s demonstrated no polymorphism or aggregation in our experiments. The modification that mimics abasic sites (1',2'-dideoxyribose residues) in loops enhanced the oligomerization/multimerization of both the 2-tetrad and 3-tetrad G4 motifs. Our results shed light on the rules that govern G4 rearrangements. Gaining control over G4 folding enables the harnessing of the full potential of such structures for guided assembly of supramolecular DNA structures for nanotechnology.

Risky repair: DNA-protein crosslinks formed by mitochondrial base excision DNA repair enzymes acting on free radical lesions

Oxygen is both necessary and dangerous for aerobic cell function. ATP is most efficiently made by the electron transport chain, which requires oxygen as an electron acceptor. However, the presence of oxygen, and to some extent the respiratory chain itself, poses a danger to cellular components. Mitochondria, the sites of oxidative phosphorylation, have defense and repair pathways to cope with oxidative damage. For mitochondrial DNA, an essential pathway is base excision repair, which acts on a variety of small lesions. There are instances, however, in which attempted DNA repair results in more damage, such as the formation of a DNA-protein crosslink trapping the repair enzyme on the DNA. That is the case for mitochondrial DNA polymerase γ acting on abasic sites oxidized at the 1-carbon of 2-deoxyribose. Such DNA-protein crosslinks presumably must be removed in order to restore function. In nuclear DNA, ubiquitylation of the crosslinked protein and digestion by the proteasome are essential first processing steps. How and whether such mechanisms operate on DNA-protein crosslinks in mitochondria remains to be seen.

Modification of the deoxyribose test to detect strong iron binding

Deoxyribose test has been widely used for determination of reactivities of various compounds for the hydroxyl radical. The test is based on the formation of hydroxyl radical by Fe²⁺ complex in the Fenton reaction. We propose a modification of the deoxyribose test to detect strong iron binding, inhibiting participation of Fe²⁺ in the Fenton reaction, on the basis of examination of concentration dependence of deoxyribose degradation on Fe²⁺ concentration, at a constant concentration of a chelating agent.

A high-throughput screen for detection of compound-dependent phosphodiester bond cleavage at abasic sites

We have employed a DNA molecular beacon with a real abasic site, namely a 2-deoxyribose, in a fluorescent high-throughput assay to identify artificial nucleases that cleave at abasic sites. We screened a 1280 compound chemical library and identified a compound that functions as an artificial nuclease. We validated a key structure-activity relationship necessary for abasic site cleavage using available analogs of the identified artificial nuclease. We also addressed the activity of the identified compound with dose titrations in the absence and presence of a source of non-specific DNA. Finally, we characterized the phosphodiester backbone cleavage at the abasic site using denaturing gel electrophoresis. This study provides a useful template for researchers seeking to rapidly identify new artificial nucleases.

When DNA repair goes wrong: BER-generated DNA-protein crosslinks to oxidative lesions

Free radicals generate an array of DNA lesions affecting all parts of the molecule. The damage to deoxyribose receives less attention than base damage, even though the former accounts for ∼20% of the total. Oxidative deoxyribose fragments (e.g., 3'-phosphoglycolate esters) are removed by the Ape1 AP endonuclease and other enzymes in mammalian cells to enable DNA repair synthesis. Oxidized abasic sites are initially incised by Ape1, thus recruiting these lesions into base excision repair (BER) pathways. Lesions such as 2-deoxypentos-4-ulose can be removed by conventional (single-nucleotide) BER, which proceeds through a covalent Schiff base intermediate with DNA polymerase β (Polβ) that is resolved by hydrolysis. In contrast, the lesion 2-deoxyribonolactone (dL) must be processed by multinucleotide ("long-patch") BER: attempted repair via the single-nucleotide pathway leads to a dead-end, covalent complex with Polβ cross- linked to the DNA by an amide bond. We recently detected these stable DNA-protein crosslinks (DPC) between Polβ and dL in intact cells. The features of the DPC formation in vivo are exactly in keeping with the mechanistic properties seen in vitro: Polβ-DPC are formed by oxidative agents in line with their ability to form the dL lesion; they are not formed by non-oxidative agents; DPC formation absolutely requires the active-site lysine-72 that attacks the 5'-deoxyribose; and DPC formation depends on Ape1 to incise the dL lesion first. The Polβ-DPC are rapidly processed in vivo, the signal disappearing with a half-life of 15-30min in both mouse and human cells. This removal is blocked by inhibiting the proteasome, which leads to the accumulation of ubiquitin associated with the Polβ-DPC. While other proteins (e.g., topoisomerases) also form DPC under these conditions, 60-70% of the trapped ubiquitin depends on Polβ. The mechanism of ubiquitin targeting to Polβ-DPC, the subsequent processing of the expected 5'-peptidyl-dL, and the biological consequences of unrepaired DPC are important to assess. Many other lyase enzymes that attack dL can also be trapped in DPC, so the processing mechanisms may apply quite broadly.

Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study

Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2'-position attribute special properties to nucleic acids when compared to other modifications. 2'-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2'-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2'-O-methyl modified counterparts to investigate the effect of 2'-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes.

Ameliorative effect of polyphenols from Padina boergesenii against ferric nitrilotriacetate induced renal oxidative damage: With inhibition of oxidative hemolysis and in vitro free radicals

The aim of this study was to evaluate the antioxidant activities of diethyl ether (DEE) and methanol (M) extracts from brown alga Padina boergesenii using in vitro and in vivo antioxidant assay, which may help to relate the antioxidant properties with the possible outline of its ameliorative effect. M extract showed higher radical scavenging activity through ferric reducing antioxidant power 139.11 µmol tannic acid equivalent/g; DPPH 71.32 ± 0.56%; deoxyribose radical 88.31 ± 0.47%, and total antioxidant activity 0.47 ± 0.02 mg ascorbic acid equivalents/g. Oxidative red blood cell (RBC) hemolysis inhibition rate was significantly higher in M extract (150 mg/kg body weight) in reference to total phenolic content (r = 0.935). Rats administered with DEE and M extracts (150 mg/kg body weight) for seven days before the administration of ferric nitrilotriacetate (9 mg of Fe/mg/kg bodyweight). Rats pretreated with extracts significantly changed the level of renal microsomal lipid peroxidation, glutathione, and antioxidant enzymes in post-mitochondrial supernatant (P < 0.05). Ameliorative effect of extracts against renal oxidative damage was evident in rat kidney through changes in necrotic and epithelial cells. HPTLC technique has identified the presence of rutin with reference to retardation factor (Rf ) in both the extracts. These findings support the source of polyphenols (rutin) from P. boergesenii had potent antioxidant activity; further work on isolation of bioactive compounds can be channeled to develop as a natural antioxidant.

Antioxidant Activity of Caffeic Acid against Iron-Induced Free Radical Generation--A Chemical Approach

Caffeic acid (CA) is a phenolic compound widely found in coffee beans with known beneficial effects in vivo. Many studies showed that CA has anti-inflammatory, anti-mutagenic, antibacterial and anti-carcinogenic properties, which could be linked to its antioxidant activity. Taking in consideration the reported in vitro antioxidant mechanism of other polyphenols, our working hypothesis was that the CA antioxidant activity could be related to its metal-chelating property. With that in mind, we sought to investigate the chemical antioxidant mechanism of CA against in vitro iron-induced oxidative damage under different assay conditions. CA was able to prevent hydroxyl radical formation promoted by the classical Fenton reaction, as determined by 2-deoxyribose (2-DR) oxidative degradation and DMPO hydroxylation. In addition to its ability to prevent hydroxyl radical formation, CA had a great inhibition of membrane lipid peroxidation. In the lipid peroxidation assays CA acted as both metal-chelator and as hydrogen donor, preventing the deleterious action promoted by lipid-derived peroxyl and alkoxyl radicals. Our results indicate that the observed antioxidant effects were mostly due to the formation of iron-CA complexes, which are able to prevent 2-DR oxidation and DMPO hydroxylation. Noteworthy, the formation of iron-CA complexes and prevention of oxidative damage was directly related to the pH of the medium, showing better antioxidant activity at higher pH values. Moreover, in the presence of lipid membranes the antioxidant potency of CA was much higher, indicating its enhanced effectiveness in a hydrophobic environment. Overall, our results show that CA acts as an antioxidant through an iron chelating mechanism, preventing the formation of free hydroxyl radicals and, therefore, inhibiting Fenton-induced oxidative damage. The chemical properties of CA described here—in association with its reported signaling effects—could be an explanation to its beneficial effects observed in vivo.

[EFFECT OF BIOACTIVE ALDEHYDES ON GELATIN PROPERTIES]

Bioactive aldehydes are among main factors of proteins postsynthetic modifications, which are the cause and consequence of many diseases. Comparative study of some aldehydes modifying action on gelatin was carried out in vitro. Gelatin samples (20 mM) were incubated with: ribose, deoxyribose, glyoxal, methylglyoxal, formaldehyde, acrolein (20 mM each) and their combinations in 0.1 M Naphosphate buffer (pH 7.4) containing 0.02% sodium azide at 37 °C in the dark for 30 days. We investigated the fluorescent properties of these samples and their molecular weight distribution by electrophoresis. It has been revealed that formed adducts had different fluorescence spectra. According to fluorescence intensity these aldehydes were put in order: formaldehyde < methylglyoxal < acrolein <ribose < deoxyribose < glyoxal. The electrophoresis results showed fragments of gelatin molecular weight redistribution. By this index, the aldehydes rating was as follows: ribose < deoxyribose < acrolein < glyoxal < formaldehyde < methylglyoxal. Comparison of these two ratings indicates that aldehydes with a lower ability to form fluorescent adducts have higher ability to form intermolecular crosslinks. Therefore, the traditional clinical fluorescent test of a patients' skin surface for collagen crosslinks determination has to be verified by other tests for proteins postsynthetic modifications.

Abasic phosphorothioate oligomers inhibit HIV-1 reverse transcription and block virus transmission across polarized ectocervical organ cultures

In the absence of universally available antiretroviral (ARV) drugs or a vaccine against HIV-1, microbicides may offer the most immediate hope for controlling the AIDS pandemic. The most advanced and clinically effective microbicides are based on ARV agents that interfere with the earliest stages of HIV-1 replication. Our objective was to identify and characterize novel ARV-like inhibitors, as well as demonstrate their efficacy at blocking HIV-1 transmission. Abasic phosphorothioate 2' deoxyribose backbone (PDB) oligomers were evaluated in a variety of mechanistic assays and for their ability to inhibit HIV-1 infection and virus transmission through primary human cervical mucosa. Cellular and biochemical assays were used to elucidate the antiviral mechanisms of action of PDB oligomers against both lab-adapted and primary CCR5- and CXCR4-utilizing HIV-1 strains, including a multidrug-resistant isolate. A polarized cervical organ culture was used to test the ability of PDB compounds to block HIV-1 transmission to primary immune cell populations across ectocervical tissue. The antiviral activity and mechanisms of action of PDB-based compounds were dependent on oligomer size, with smaller molecules preventing reverse transcription and larger oligomers blocking viral entry. Importantly, irrespective of molecular size, PDBs potently inhibited virus infection and transmission within genital tissue samples. Furthermore, the PDB inhibitors exhibited excellent toxicity and stability profiles and were found to be safe for vaginal application in vivo. These results, coupled with the previously reported intrinsic anti-inflammatory properties of PDBs, support further investigations in the development of PDB-based topical microbicides for preventing the global spread of HIV-1.

DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar

Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π-π stacking, π-π T-shaped or sugar-π contacts. Three hundred forty-four nucleobase-amino acid π-π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA-protein sugar-π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C-H···π and/or lone-pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π-π and sugar-π interactions display a range of relative monomer orientations and therefore interaction energies (up to -50 (-70) kJ mol(-1) for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA-protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered.

Non-intercalative, deoxyribose binding of boric acid to calf thymus DNA

The present study characterizes the effects of the boric acid binding on calf thymus DNA (ct-DNA) by spectroscopic and calorimetric methods. UV-Vis absorbance spectroscopy, circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM), isothermal titration calorimetry (ITC), and Fourier transform infrared (FT-IR) spectroscopy were employed to characterize binding properties. Changes in the secondary structure of ct-DNA were determined by CD spectroscopy. Sizes and morphologies of boric acid-DNA complexes were determined by transmission electron microscopy (TEM). The kinetics of boric acid binding to calf thymus DNA (ct-DNA) was investigated by isothermal titration calorimetry (ITC). ITC results revealed that boric acid exhibits a moderate affinity to ct-DNA with a binding constant (K a) of 9.54 × 10(4) M(-1). FT-IR results revealed that boric acid binds to the deoxyribose sugar of DNA without disrupting the B-conformation at tested concentrations.

Propagation of chirality in mixtures of natural and enantiomeric DNA oligomers

Concentrated solutions of ultrashort duplex-forming DNA oligomers may develop various forms of liquid crystal ordering among which is the chiral nematic phase, characterized by a macroscopic helical precession of molecular orientation. The specifics of how chirality propagates from the molecular to the mesoscale is still unclear, both in general and in the case of DNA-based liquid crystals. We have here investigated the onset of nematic ordering and its chiral character in mixtures of natural D-DNA oligomers forming right-handed duplex helices and of mirror symmetric (L-DNA) molecules, forming left-handed helices. Since the nematic ordering of DNA duplexes is mediated by their end-to-end aggregation into linear columns, by controlling the terminals of both enantiomers we could study the propagation of chirality in solutions where the D and L species form mixtures of homochiral columns, and in solutions of heterochiral columns. The two systems behave in markedly different fashion. By adopting a simple model based on nearest-neighbor interactions, we account for the different observed dependence of the chirality of these two systems on the enantiomeric ratio.

[Ultrasonic cleavage of DNA in complexes with Ag(I), Cu(II), Hg(II)]

We investigated a phenomenon of ultrasonic cleavage of DNA complexed with transition metal cations Ag(I), Cu(II) and Hg(II). We found the statistically significant dependence of relative intensity of cleavage on cation type and concentration. Each cation may cause two different types of distortion in the DNA double-helix depending on whether it binds to major or minor DNA groove. The intensity of ultrasonic cleavage decreases if cation binds to the major DNA groove; the intensity of cleavage increases if cation binds to the minor DNA groove and disturbs the hydrogen bonds of complementary base pairs or it intercalates between bases. Both types of DNA distortion can affect the intensity of N-S interconversion of deoxyribose.

Antioxidant effect of Stryphnodendron rotundifolium Martius extracts from Cariri-Ceará State (Brazil): potential involvement in its therapeutic use

Stryphnodendron rotundifolium is a phytotherapic used in the northeast of Brazil for the treatment of inflammatory processes which normally are associated with oxidative stress. Consequently, we have tested the antioxidant properties of hydroalcoholic (HAB) and aqueous extracts (AB) from the bark and aqueous extract (AL) from the leaves of Stryphnodendron rotundifolium to determine a possible association between antioxidant activity and the popular use of this plant. Free radical scavenger properties were assessed by the quenching of 1',1'-diphenil-2-picrylhydrazyl (DPPH) and the calculated IC(50) were: HAB = 5.4 ± 0.7, AB = 12.0 ± 2.6, and AL = 46.3 ± 12.3 µg/mL. Total phenolic contents were: HAB = 102.7 ± 2.8, AB = 114.4 ± 14.6, and AL = 93.8 ± 9.1 µg/mg plant). HPLC/DAD analyses indicated that gallic acid, catechin, rutin and caffeic acid were the major components of the crude extracts of S. rotundifolium. Plant extracts inhibited Fe(II)-induced lipid peroxidation in brain homogenates. Iron chelation was also investigated and only HBA exhibited a weak activity. Taken together, the results suggest that S. rotundifolium could be considered an effective agent in the prevention of diseases associated with oxidative stress.

Molecular structure of humin and melanoidin via solid state NMR

Sugar-derived humins and melanoidins figure significantly in food chemistry, agricultural chemistry, biochemistry, and prebiotic chemistry. Despite wide interest and significant experimental attention, the amorphous and insoluble nature of the polymers has made them resistant to conventional structural characterization. Here we make use of solid-state NMR methods, including selective (13)C substitution, (1)H-dephasing, and double quantum filtration. The spectra, and their interpretation, are simplified by relying exclusively on hydronium for catalysis. The results for polymers derived from ribose, deoxyribose, and fructose indicate diverse pathways to furans, suggest a simple route to pyrroles in the presence of amines, and reveal a heterogeneous network-type polymer in which sugar molecules cross-link the heterocycles.

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.

Evaluation of the antioxidant activity of soybean extract by different in vitro methods and investigation of this activity after its incorporation in topical formulations

Chemoprevention by natural products is an emerging therapeutic approach for free radical-mediated diseases including cancer. This is a consequence of its wide applicability and acceptance. In the present study, the antioxidant activity of the soybean extract (Isoflavin Beta) and of formulations added with this extract were evaluated using stable free radical 2,2-diphenyl-1-pycrylhydrazyl (DPPH*) and deoxyribose as well as the lipid peroxidation inhibition assays. For all the assays the extract showed a dose-dependent activity, and IC50 of 21.03 microg/mL in lipid peroxidation inhibition, 161.8 microg/mL in DPPH*, and 33.5 ng/mL in hydroxyl radical scavenging assay. The antioxidant activity of the extract added in the formulations could not be assessed using the deoxyribose assay. However, the lipid peroxidation inhibition and DPPH* scavenging assays could be successfully applied for the antioxidant activity evaluation of the formulations added with soybean extract to protect the skin against free radicals, which can be generated by the ultraviolet radiation exposure.

Folic Acid as a Fenton-modulator: Possible Physiological Implication

Acting as a redox switch, folic acid (1) might be a promising iron modulator to protect cellular machinery against oxidative stress and iron overload. The vitamin 1 can directly control the iron concentration by oxidizing it even if present in chelated forms. In addition, during its role as a reducing agent for the biologically relevant reactive oxygen species (ROS), it furnishes 6-formyl pterin. This folate-derived intermediate possesses a stronger Fe2+-oxidizing capacity than 1. Thus, compound 1 can reduce the iron toxicity in two ways. Although, the Fe2+-oxidizing capacity is nullified in the presence of a strong biological reductant like ascorbic acid, this property may play a predominant role during pathogenesis when the cellular ascorbic acid levels deplete significantly. The iron-modulatory property of 1 was also confirmed with the L929 mouse fibroblast cell line.