Photoreactivity of UV-b damage in bacteriophage phi X174 DNA

Abstract— The fraction of biological damage in isolated single-strand and double-strand forms of bac-teriophage DNA resulting from pyrimidine dimers following exposure to germicidal UV (254 nm) and UV-B (280-320. nm) radiation has been compared. Radiation from a Westinghouse FS-40 sunlamp filtered through a cellulose acetate sheet was used as the UV-B radiation source. Biological damage from pyrimidine dimers was determined by measuring the survival of the viral DNA with and without photoreactivation, an enzymatic process specific for repair of pyrimidine dimers. The same fraction of biological damage in the single strand and double–strand forms of φX174 DNA is repairable by photo-reactivation following exposures to germicidal UV and UV-B radiation.     

Dithionite adducts of pyridinium salts: regioselectivity of formation and mechanisms of decomposition

¹H and ¹³C NMR spectroscopy has been used to detect and to characterize the adducts formed, in alkaline solutions, by the attack of dithionite anion on 3-carbamoyl or 3-cyano substituted pyridinium salts. In all studied cases, only 1,4-dihydropyridine-4-sulfinates, formed by attack of dithionite oxyanion on the carbon 4 of pyridinium ring, were found. This absolute regioselectivity seems to suggest a very specific interaction between the pyridinium cation and the dithionite through the formation of a rigidly oriented ion pair, determining the position of attack. In weak alkaline solution, the adducts decompose according to two mechanisms S_Ni and S_Ni′: the S_Ni path is operative in all studied cases and preserves the 1,4-dihydro structure yielding the corresponding 1,4-dihydropyridines, whereas the S_Ni′ path involves the shift of 2,3 or 5,6 double bonds yielding 1,2- or 1,6-dihydropyridines, respectively. The formation of 1,2- or 1,6-dihydropyridines, in addition to 1,4-dihydro isomers, depends on their respective thermodynamic stabilities.     

Inhibition of restriction enzyme's DNA sequence recognition by PUVA treatment

Applying various restriction enzymes on a specially designed 1.5 kb DNA fragment revealed that the inhibitory effects of psoralens + UVA irradiation (PUVA) treatment on restriction endonuclease activities are caused by recognition inhibition. In this study restriction enzymes that have a 5'-TpA sequence at the cleaving site (KpnI, XbaI, PmeI and DraI), and the noncleaving site (PacI) in recognition sites, or have two 5'-TpA sequences at the recognition site, and a nonspecific sequence between the recognition and the cleaving sites (BciVI), were inhibited by PUVA treatment. Most of the other restriction enzymes used in this study, which do not have a 5'-TpA sequence at their restriction site, were not inhibited by PUVA treatment, although a 5'-TpA sequence is located adjacent (SmaI) or very close (BamHI, SacI and PstI) to the recognition and cleaving sites for these enzymes. Because SphI, which does not have 5'-TpA at its restriction site, was strongly inhibited by PUVA treatment, the 5'-CpA sequence is suggested to be a new binding site of psoralens after UVA irradiation.     

Novel 1:1 adducts from the reaction of hexafluoroacetone azine with various olefins and 1,3-dienes; Diels-Alder adducts as intermediates in the formation of criss-cross 2:1 adducts

Hexafluoroacetone azine¹ (I) has been reported^2,3 to react thermally (160–180°) with electron-rich olefins of type H₂CCHR (R  H, Me, or Et) to give “criss-cross” (1,3-:4,2-) adducts (II). In contrast, cis- or trans-but-2-ene and cyclohexene react under comparable conditions to give nitrogen and products derived formally from addition and insertion reactions of bis(trifluoromethyl)-carbene, although it is doubtful if the free carbene is involved^2,4. The reaction of azine (I) with alkanes is reported⁵ to involve a radical mechanism in which the diazo compound (CF₃)₂CN₂, and thence the carbene (CF₃)₂C:, is formed by a secondary process.     

Singlet oxygen generation in PUVA therapy studied using electronic structure calculations

The ability of furocoumarins to participate in the PUVA (Psoralen + UV-A) therapy against skin disorders and some types of cancer, is analyzed on quantum chemical grounds. The efficiency of the process relies on its capability to populate its lowest triplet excited state, and then either form adducts with thymine which interfere DNA replication or transfer its energy, generating singlet molecular oxygen damaging the cell membrane in photoactivated tissues. By determining the spin–orbit couplings, shown to be the key property, in the intersystem crossing yielding the triplet state of the furocoumarin, the electronic couplings in the triplet–triplet energy transfer process producing the singlet oxygen, and the reaction rates and lifetimes, the efficiency in the phototherapeutic action of the furocoumarin family is predicted as: khellin < 5-methoxypsoralen (5-MOP) < 8-methoxypsoralen (8-MOP) < psoralen < 4,5′,8-trimethylpsoralen (TMP) < 3-carbethoxypsoralen (3-CPS), the latter being the most efficient photosensitizer and singlet oxygen generator.     

Theoretical investigations on the formation of nitrobenzanthrone-DNA adducts

3-Nitrobenzanthrone (3-NBA) is a potent mutagen and suspected human carcinogen identified in diesel exhaust. The thermochemical formation cascades were calculated for six 3-NBA-derived DNA adducts employing its arylnitrenium ion as precursor using density functional theory (DFT). Clear exothermic pathways were found for four adducts, i.e., 2-(2'-deoxyadenosin-N(6)-yl)-3-aminobenzanthrone, 2-(2'-deoxyguanosin-N(2)-yl)-3-aminobenzanthrone, N-(2'-deoxyguanosin-8-yl)-3-aminobenzanthrone and 2-(2'-deoxyguanosin-8-yl)-3-aminobenzanthrone. All four have been observed to be formed in cell-free experimental systems. The formation of N-(2'-deoxyadenosin-8-yl)-3-aminobenzanthrone is predicted to be not thermochemically viable explaining its absence in either in vitro or in vivo model systems. However, 2-(2'-deoxyadenosin-8-yl)-3-aminobenzanthrone, can be formed, albeit not as a major product, and is a viable candidate for an unknown adenine adduct observed experimentally. 2-nitrobenzanthrone (2-NBA), an isomer of 3-NBA, was also included in the calculations; it has a higher abundance in ambient air than 3-NBA, but a much lower genotoxic potency. Similar thermochemical profiles were obtained for the calculated 2-NBA-derived DNA adducts. This leads to the conclusion that enzymatic activation as well as the stability of its arylnitrenium ion are important determinants of 2-NBA genotoxicity.     

Differential survival of Escherichia coli uvrA,uvrB, and uvrC mutants to psoralen plus UV-A (PUVA): Evidence for uncoupled action of nucleotide excision repair to process DNA adducts

The nucleotide excision repair mechanism (NER) of Escherichia coli is responsible for the recognition and elimination of more than twenty different DNA lesions. Herein, we evaluated the in vivo role of NER in the repair of DNA adducts generated by psoralens (mono- or bi-functional) and UV-A light (PUVA) in E. coli. Cultures of wild-type E. coli K12 and mutants for uvrA, uvrB, uvrC or uvrAC genes were treated with PUVA and cell survival was determined. In parallel, kinetics of DNA repair was also evaluated by the comparison of DNA sedimentation profiles in all the strains after PUVA treatment. The uvrB mutant was more sensitive to PUVA treatment than all the other uvr mutant strains. Wild-type strain, and uvrA and uvrC mutants were able to repair PUVA-induced lesions, as seen by DNA sedimentation profiles, while the uvrB mutant was unable to repair the lesions. In addition, a quadruple fpg nth xth nfo mutant was unable to nick PUVA-treated DNA when the crude cell-free extract was used to perform plasmid nicking. These data suggest that DNA repair of PUVA-induced lesions may require base excision repair functions, despite proficient UvrABC activity. These results point to a specific role for UvrB protein in the repair of psoralen adducts, which appear to be independent of UvrA or UvrC proteins, as described for the classical UvrABC endonuclease mechanism.     

Photosensitization and phototherapy with furocoumarins: A quantum-chemical study

The effect of electromagnetic radiation on biological objects extends from heating to complex photochemistry, and includes DNA alteration, that properly modified in damaged cells may entail beneficial effects. In this regard, psoralen + UV-A (PUVA) therapy, in which furocoumarins, psoralen-like chromophores, are used as photosensitizers and photoreactants with DNA bases, is one of the most promising strategies against a plethora of diseases. Understanding the underlying photochemical mechanisms is crucial to design effective drugs without undesired side effects. We have undertaken a quantum-mechanical study on the photophysics and photochemistry of furocoumarins, analyzing firstly the most efficient way in which the lowest excited triplet state, as protagonist of the photosensitizing action, is populated from the initially promoted singlet states, and secondly the basics of the formation of furocoumarin–DNA photoadducts.     

Photoreactivity of fluoroquinolones: nature of aryl cations generated in water

The nature of stabilized aryl cations generated from photodehalogenations of fluoroquinolones in aqueous media has been studied by comparing the photophysical and photochemical behavior of lomefloxacin (LFX) and its N(4')-acetylated form (ALFX). Photoproduct studies, laser flash photolysis, and emission measurements have shown that this small peripheral modification produces important changes in the properties of the singlet aryl cations generated. Also, in basic medium, a new photodehalogenation pathway for 6,8-dihalogenated fluoroquinolones has been observed.     

Rendering Photoreactivity to Ceria: The Role of Defects

The photoreactivity of ceria, a photochemically inert oxide with a large band gap, can be increased to competitive values by introducing defects. This previously unexplained phenomenon has been investigated by monitoring the UV‐induced decomposition of N₂O on well‐defined single crystals of ceria by using infrared reflection‐absorption spectroscopy (IRRAS). The IRRAS data, in conjunction with theory, provide direct evidence that reducing the ceria(110) surface yields high photoreactivity. No such effects are seen on the (111) surface. The low‐temperature photodecomposition of N₂O occurs at surface O vacancies on the (110) surface, where the electron‐rich cerium cations with a significantly lowered coordination number cause a local lowering of the huge band gap (ca. 6 eV). The quantum efficiency of strongly reduced ceria(110) surfaces in the photodecomposition of N₂O amounts to 0.03 %, and is thus comparable to that reported for the photooxidation of CO on rutile TiO₂(110).     

Stability and iron coordination in DNA adducts of Anthracycline based anti-cancer drugs

There is evidence that the interaction of the α-ketol group of the Doxorubicin and Epirubicin anti-cancer drugs with Fe(iii) generates hydroxyl radicals under aerobic conditions, causing cardiotoxicity in patients. Considering that the formation of DNA adducts is one of the main targets of Anthracycline drugs, we have in the present study characterized several [Anthracycline-DNA]Fe(iii) complexes with respect to their stability and Fe(iii) coordination, by means of MD simulations. Iron is found to coordinate well to the drugs containing an α-ketol group, this being the only group of the drug that binds to the metal. The complexes containing an α-ketol group, [Doxorubicin-DNA]Fe(iii) and [Epirubicin-DNA]Fe(iii), thus show greater stability than those not containing it, i.e., [Daunorubicin-DNA]Fe(iii), [Idarubicin-DNA]Fe(iii) and [5-Imino-Daunorubicin]Fe(iii). Metal attachment to the α-ketol group is furthermore facilitated by the phosphate groups of DNA. The coordination to iron in the [Doxorubicin-DNA]Fe(iii) system is smaller than that found for the [Epirubicin-DNA]Fe(iii) system, and the corresponding number of coordinating waters in the former is larger than in the latter. This may in turn result in higher hydroxyl radical production, thus explaining the increased cardiotoxicity noted for Doxorubicin.     

Topology effect for DNA structure of cisplatin: topological transformation of cisplatin-closed circular DNA adducts by DNA topoisomerase I.

The reaction of cis-Pt(NH3)2Cl2(cis-DDP)-closed circular DNA adducts with DNA topoisomerse I(topo I) were studied by electron microscopy. We identified unique topoisomers such as a singly-linked catenane (2(1)2), trefoil (3(1), and dimetric catenane (2(1)2), etc., by analysis with electron micrographs. These unique recombination products resulted from cis-DDP-intra-twisting looped DNA adducts by DNA topo I, and the products could be explained a new mechanism based on an odd-even number rule. Our results suggest a new model on the working mechanisms for DNA topology of cis-DDP which enhances the recombination of DNA. Based on our results, we propose the topological idea that the yields of a mini closed circular DNA and pseudo trefoil DNA, etc., can be expected by reaction of cis-DDP-DNA-histone complexes with DNA topo I in the body.     

Structures of oxaliplatin‐oligonucleotide adducts from DNA

Oxaliplatin, [(1R,2R)‐cyclohexane‐1,2‐diamine](ethanedioato‐O,O')platinum(II) shows a great efficiency against colorectal cancer. Although the mode of action of oxaliplatin is not yet understood, it is commonly accepted that binding of oxaliplatin to DNA prevents DNA synthesis and alters protein to DNA binding. In order to elucidate the modified DNA–protein interaction and thus to understand the mechanisms leading to cellular misinterpretation of DNA information and apoptosis, we have identified the preferential binding sites and the dynamics of the oxaliplatin‐DNA intrastrand and interstrand adducts at the oligomer level using high‐performance liquid chromatography/electrospray ionization‐tandem mass spectrometry (HPLC/ESI‐MS/MS) and HPLC/inductively coupled plasma‐MS for quantitative studies. We used a combination of benzonase, alkaline phosphatase and Nuclease S1 for digestion. This digestion procedure allows the study of platinated oligomeric nucleotides and more complex interstrand adducts. The digestion products were mostly chromatographically separated and characterized using HPLC/ESI‐ion trap MS/MS experiments. We could show that the adducts to guanine and adenine are quite dynamic; that is, the ratios are changing for several days. In addition, the resulting adducts provide evidence for the action of the digesting enzymes and indicate that the adduct spectrum at the oligomeric level is different to that at the commonly studies dinucleotide level. Copyright © 2012 John Wiley & Sons, Ltd.     

Reversing the stereoselectivity of the intermolecular Pauson-Khand reaction: formation of endo-fused norbornadiene adducts

[reaction: see text] An unprecedented endo-selective and regioselective intermolecular Pauson-Khand reaction takes place when heterobimetallic (Mo-Co) complexes derived from N-(2-alkynoyl)oxazolidinones or sultams are heated in the presence of norbornadiene.     

Thermodynamics of metal-ligand bond formation: XVI. Base adducts of some organotin compounds

Thermodynamic data have been obtained by calorimetric titration in benzene solution at 30° for reaction of organotin compounds with Lewis bases; data are reported for forty acid/base systems.Ph₃SnCl forms $\text{1}\text{1}$ adducts of low stability with pyridine (py) or 4-methyl-pyridine (4-mepy). Ph₂SnCl₂, Me₂SnCl₂, Bu₂SnCl₂ and Bu₂Sn(NCS)₂ form simultaneously $\text{1}\text{1}$ and $\text{1}\text{2}$ adducts with py or 4-mepy and $\text{1}\text{1}$ adducts with 2,2′-bipyridine or 1,10-phenanthroline (phen); the enthalpies of formation of the phen adducts are similar to those of $\text{1}\text{2}$ adducts with 4-mepy. With BuSnCl₃ and PhSnCl₃ it was not possible to obtain data for each step in addition of pyridine or 4-mepy. Adduct stabilities increase with increasing chloride substitution and in the order Bu < Me < Ph; adducts of Bu₂Sn(NCS)₂ are more stable than those of Bu₂SnCl₂.Tributylphosphine does not react with Ph₃SnCl but gives $\text{1}\text{1}$ adducts with the other tin compounds; only PhSnCl₃ adds a second molecule of this base. The $\text{1}\text{1}$ adducts are more stable than those with heterocyclic bases. Tributylamine brings about disproportionation of the compounds R₂SnX₂ to R₄Sn and SnX₄NBu₃.