Light-driven enzymatic catalysis of DNA repair: a review of recent biophysical studies on photolyase

More than 50 years ago, initial experiments on enzymatic photorepair of ultraviolet (UV)-damaged DNA were reported [Proc. Natl. Acad. Sci. U. S. A. 35 (1949) 73]. Soon after this discovery, it was recognized that one enzyme, photolyase, is able to repair UV-induced DNA lesions by effectively reversing their formation using blue light. The enzymatic process named DNA photoreactivation depends on a non-covalently bound cofactor, flavin adenine dinucleotide (FAD). Flavins are ubiquitous redox-active catalysts in one- and two-electron transfer reactions of numerous biological processes. However, in the case of photolyase, not only the ground-state redox properties of the FAD cofactor are exploited but also, and perhaps more importantly, its excited-state properties. In the catalytically active, fully reduced redox form, the FAD absorbs in the blue and near-UV ranges of visible light. Although there is no direct experimental evidence, it appears generally accepted that starting from the excited singlet state, the chromophore initiates a reductive cleavage of the two major DNA photodamages, cyclobutane pyrimidine dimers and (6-4) photoproducts, by short-distance electron transfer to the DNA lesion. Back electron transfer from the repaired DNA segment is believed to eventually restore the initial redox states of the cofactor and the DNA nucleobases, resulting in an overall reaction with net-zero exchanged electrons. Thus, the entire process represents a true catalytic cycle.Many biochemical and biophysical studies have been carried out to unravel the fundamentals of this unique mode of action. The work has culminated in the elucidation of the three-dimensional structure of the enzyme in 1995 that revealed remarkable details, such as the FAD-cofactor arrangement in an unusual U-shaped configuration. With the crystal structure of the enzyme at hand, research on photolyases did not come to an end but, for good reason, intensified: the geometrical structure of the enzyme alone is not sufficient to fully understand the enzyme's action on UV-damaged DNA. Much effort has therefore been invested to learn more about, for example, the geometry of the enzyme-substrate complex, and the mechanism and pathways of intra-enzyme and enzyme ↔DNA electron transfer. Many of the key results from biochemical and molecular biology characterizations of the enzyme or the enzyme-substrate complex have been summarized in a number of reviews. Complementary to these articles, this review focuses on recent biophysical studies of photoreactivation comprising work performed from the early 1990s until the present.     

Study of a Hydridoma Cell Line Producing Monoclonal Antibodies Against Spinach Betaine Aldehyde Dehydrogenase and Its Application

By fusion of mouse myeloma cells (SP2/O-Ag14) and spleen cells derived from BALB/c mice immunized with spinach betaine aldehyde dehydrogenase (BADH) protein, a hybridoma cell line secreting monoclonal antibodies was obtained. The antibody titer of the ascites was about 1 : 103. Not only could the monoclonal antibodes cross react with the BADH of spinach and sugar beet, it could also cross react with the leaf and root crude extracts of barley, rice, sorghum, and wheat. These results indicated the occurrence of BADH in both the photosynthetic tissue and the non-photosynthetic tissue of these graminea spicies.     

应用流行性出血热病毒抗NP和G1、G2单抗检测感染细胞和疫苗内的不同抗原成分

应用出血热病毒的抗核蛋白（ＮＰ）和糖蛋白（Ｇ１、Ｇ２）单克隆抗体的ＥＬＩＳＡ夹心法对感染细胞培养物和灭活疫苗内的ＮＰ和Ｇ１、Ｇ２抗原成分进行检测,结果表明感染Ｖｅｒｏ－Ｅ６细胞内ＮＰ和Ｇ１、Ｇ２含量均高于细胞外培养液上清,前者的抗原滴度分别为≥５１２和２５６,后者仅为６４和１６。比较三种不同疫苗内的抗原成分,显示乳鼠脑纯化疫苗内的ＮＰ抗原最高,滴度达３２０－≥６４０,而二种细胞疫苗（沙鼠肾和地鼠肾细胞）则较低,一般在２０－８０,相反二种细胞疫苗的糖蛋白滴度则高于脑疫苗（８－３２对２－８）该方法可用于疫苗生产过程中检测ＮＰ和Ｇ抗原成分。     

Ultraviolet photoproducts at the ochre suppressor mutation site in the glnU gene of Escherichia coli: relevance to "mutation frequency decline"

Summary Ochre suppressor mutations induced by UV in the Escherichia coli glnU tRNA gene are CG to TA transitions at the first letter of the anticodon-encoding triplet, CAA. Premutational UV photoproducts at this site have long been known to exhibit an excision repair anomaly (mutation frequency decline or MFD), whereby post-irradiation inhibition of protein synthesis enhances their excision and reduces suppressor mutation yields ten-fold. We sought to clarify the basis of this unique repair response by determining the spectrum of UV photoproducts on both strands of a 36 by region of glnU which includes the anticodon-encoding triplet. We found that four different photolesions are produced within the 3 by sequence corresponding to the tRNA anticodon: (i) on the transcribed strand, TC (6–4) photoproducts and TC cyclobutane dimers are formed in equal numbers at the site of the C to T transition, indicating that this site is a hotspot for the usually less frequent (6–4) photoproduct; (ii) on the nontranscribed strand, TT dimers are found opposite the second and third letters of the anticodon-encoding triplet, adjacent to the mutation site; and (iii) on the nontranscribed strand, an alkali-sensitive lesion other than a (6–4) photoproduct is formed, apparently at the G in the mutation site. We suggest that mutation frequency decline may reflect excision repair activity at closely spaced UV lesions on opposite strands, resulting in double-strand breaks and the death of potential mutants.     

Preparation and Characterization of Monoclonal Antibodies Specific for Lauroylated Isoform of Bovine Transducin α-Subunit: Immunohistochemical Analysis of Bovine Retinas

Abstract: The photoreceptor G protein transducin [α- and βγ-subunits (Tα/Tβγ)] plays a central role in the visual transduction process. The amino-terminus of bovine Tα is modified by one of four distinct fatty acids—laurate (C12:0), myristate (C14:0), C14:1 (5- cis ), and C14:2 (5- cis , 8- cis )—but the biological significance and the localization of the four isoforms of Tα are poorly understood. To investigate the cellular distribution of each isoform, we prepared monoclonal antibodies against a synthetic C12:0-, C14:0-, C14:1-, or C14:2-nonapeptide corresponding to the N-terminal region of Tα. Among several types of antibodies isolated, only one type, represented by LA4, reacted specifically with the C12:0-peptide as well as purified Tα but not with the other proteins in bovine retinal homogenate, including recoverin, indicating that the epitope comprises both C12:0 and the N-terminal amino acids of Tα. Immunohistochemical analyses of bovine retinal sections by LA4 showed the uniform distribution of C12:0-Tα in almost all the rod outer segments. Hence, it seemed unlikely that each isoform of Tα was localized in specific cells. This observation, together with evidence for a possible functional diversity among the isoforms, suggests that the four isoforms of Tα in a single rod cell may contribute simultaneously to a fine tuning of the photon-signal transduction process.     

Synthesis of new C3 symmetric amino acid‐ and aminoalcohol‐containing chiral stationary phases and application to HPLC enantioseparations

We recently reported a new C3‐symmetric (R)‐phenylglycinol N‐1,3,5‐benzenetricarboxylic acid‐derived chiral high‐performance liquid chromatography (HPLC) stationary phase (CSP 1) that demonstrated better results as compared to a previously described N‐3,5‐dintrobenzoyl (DNB) (R)‐phenylglycinol‐derived CSP. Over a decade ago, (S)‐leucinol, (R)‐phenylglycine, and (S)‐leucine derivatives were used as the starting materials of 3,5‐DNB‐based Pirkle‐type CSPs for chiral separation. In this study, three new C3‐symmetric CSPs (CSP 2, 3, and 4) were prepared by combining the ideas and results mentioned above. Here we describe the synthetic procedures and applications of the new C3‐symmetric CSPs (CSP 2–CSP 4).     

Removal of Serum Lipids and Lipid‐Derived Metabolites to Investigate Breast Cancer Cell Biology

The use of cultured cells has been instrumental in studying biochemical, molecular, and cellular processes. The composition of serum that cells are maintained in can have a profound impact on important cellular checkpoints. Cell growth and apoptosis are analyzed in an estrogen receptor positive breast cancer cell line in the presence of serum that have been treated to remove steroids or lipids, as well‐described in the literature. It is shown that maintaining cells in the presence of charcoal‐dextran‐treated serum causes reduced growth rate, which can be reversed by the addition of estradiol. Silica‐treated‐serum also slows down cell growth and induces apoptosis. In order to investigate the role of lipids in these phenotypes, the levels of a wide range of lipids in different sera are investigated. It is shown that silica‐treatment significantly depletes phosphatidylcholines and cholesterol. It is also shown that lipogenesis is stimulated when cells are cultured with silica‐treated‐serum and this is reversed by the addition of exogenous lipids, which also restores growth rate and apoptosis. The results show that cultured cells are sensitive to different serum, most likely due to the differences in levels of structural and signaling metabolites present in their growth environment.     

Synthesis and Application of C2 and C3 Symmetric (R)‐Phenylglycinol‐Derived Chiral Stationary Phases

A C3 symmetric (R)‐phenylglycinol N‐1,3,5‐benzenetricarboxylic acid‐derived chiral stationary phase (CSP) and three C2 symmetric (R)‐phenylglycinol CSPs were newly synthesized using o‐, m‐, and p‐phthaloyl dichlorides. © 2016 Wiley Periodicals, Inc. These CSPs were used to compare the resolution of 25 chiral samples using a previously reported 3,5‐dinitrobenzoyl (R)‐phenylglycinol‐derived CSP. Even though all CSPs have the same chiral moiety, the C3 symmetric CSP showed the best resolution. Chirality 28:186–191, 2016.© 2016 Wiley Periodicals, Inc.     

Antioxidant and anti‐inflammatory effects of the monocarbonyl curcumin analogs B2BRBC and C66 in monocrotaline‐induced right ventricular hypertrophy

For 22 days after monocrotaline injection two groups of rats received either of the monocarbonyl curcumin analogs (2E,6E)‐2,6‐bis(2‐bromobenzylidene)cycloxehanone (B2BrBC) and (2E,6E)‐2,6‐bis([2‐tri?uoromethyl]benzylidene)cyclohexanone (C66), and their right ventricle parameters were compared to those from the control and the monocrotaline injected animals. B2BrBC and C66 treatments did not prevent the monocrotaline‐induced right ventricular hypertrophy but attenuated the changes in antioxidant enzyme activities and reduced inflammation. The level of thiol‐based nonenzymatic antioxidants did not change in the function of monocrotaline or curcumin analogs treatment. However, due to its stronger antioxidant properties, only B2BrBC treatment was effective in the reduction of monocrotaline‐associated lipid peroxidation. The obtained results suggest that increasing the levels of antioxidant enzymes may not be sufficient to reduce oxidative stress and chronic inflammation optimally and our current study supports the potential of compounds with more than one beneficial biological activity as a promising treatment against the progression of cardiac hypertrophy.     

One‐pot synthesis of (R)‐1‐(pyridin‐4‐yl)ethyl acetate using tandem catalyst prepared by co‐immobilization of palladium and lipase on mesoporous foam: Optimization and kinetic modeling

The synthesis of (R )‐1‐(pyridin‐4‐yl)ethyl acetate was achieved over tandem palladium‐lipase catalyst with 100% selectivity using 4‐acetyl pyridine as a reactant. The 2% w /w palladium and lipase catalyst was successfully co‐immobilized in the microenvironment of the mesocellular foam and characterized by various techniques. The palladium metal from catalyst hydrogenated 4‐acetyl pyridine to form 1‐(pyridin‐4‐yl)ethanol. The generated intermediate product then underwent kinetic resolution over lipase and selectively gave (R )‐1‐(pyridin‐4‐ yl)ethyl acetate. The catalytic conditions were then studied for optimal performance of both steps. The reaction conditions were optimized to 50 °C and toluene as a solvent. Both chemical and enzymatic kinetic models of the reaction were developed for a given set of reaction conditions and kinetic parameters were predicted. At optimal conditions, the obtained selectivity of intermediate (1‐(pyridin‐4‐yl)ethanol) was 51.38%. The final product yield of ((R )‐1‐(pyridin‐4‐yl)ethyl acetate) was 48.62%.     

Scale‐up and intensification of (S)‐1‐(2‐chlorophenyl)ethanol bioproduction: Economic evaluation of whole cell‐catalyzed reduction of o‐Chloroacetophenone

Escherichia coli cells co‐expressing genes coding for Candida tenuis xylose reductase and Candida boidinii formate dehydrogenase were used for the bioreduction of o‐chloroacetophenone with in situ coenzyme recycling. The product, (S)‐1‐(2‐chlorophenyl)ethanol, is a key chiral intermediate in the synthesis of polo‐like kinase 1 inhibitors, a new class of chemotherapeutic drugs. Production of the alcohol in multi‐gram scale requires intensification and scale‐up of the biocatalyst production, biotransformation, and downstream processing. Cell cultivation in a 6.9‐L bioreactor led to a more than tenfold increase in cell concentration compared to shaken flask cultivation. The resultant cells were used in conversions of 300 mM substrate to (S)‐1‐(2‐chlorophenyl)ethanol (e.e. >99.9%) in high yield (96%). Results obtained in a reaction volume of 500 mL were identical to biotransformations carried out in 1 mL (analytical) and 15 mL (preparative) scale. Optimization of product isolation based on hexane extraction yielded 86% isolated product. Biotransformation and extraction were accomplished in a stirred tank reactor equipped with pH and temperature control. The developed process lowered production costs by 80% and enabled (S)‐1‐(2‐chlorophenyl)ethanol production within previously defined economic boundaries. A simple and efficient way to synthesize (S)‐1‐(2‐chlorophenyl)ethanol in an isolated amount of 20 g product per reaction batch was demonstrated. Biotechnol. Bioeng. 2013; 110: 2311–2315. © 2013 Wiley Periodicals, Inc.     

Differential response of male and female emerald ash borers (Col., Buprestidae) to (Z)‐3‐hexenol and manuka oil

We conducted two trapping experiments in green ash plantations in Ontario, Canada to compare the response of the emerald ash borer (EAB), Agrilus planipennis, to (Z)‐3‐hexenol (Z3‐6:OH) and manuka oil. In the first experiment, Z3‐6:OH (7.6 mg/day) in purple prism traps hung 1.5 m above ground caught significantly more EAB than the unbaited controls, with male catches significantly greater than female catches at two locations. Manuka oil (50 mg/day) attracted equal numbers of males and females but they were significantly greater than the controls at only one location. Adding (Z)‐3‐hexenal or (Z)‐3‐hexenyl acetate in binary or ternary combinations with Z3‐6:OH did not enhance trap catch. In the second experiment, Z3‐6:OH released at two rates (7.6 or 80 mg/day) in light green prism traps placed in the ash canopy also caught significantly more males than females and more males than the unbaited controls or manuka oil‐baited traps. Manuka oil had no significant effect on catches relative to the controls. Combining Z3‐6:OH with manuka oil did not enhance catches of EAB. We conclude that there was a strong male‐biased EAB response to Z3‐6:OH lures, whereas manuka oil, when effective, attracted both sexes equally. Z3‐6:OH in light green prism traps in the canopy is an effective lure for EAB, particularly for males.     

Enantioselective analysis of ibuprofen enantiomers in mice plasma and tissues by high‐performance liquid chromatography with fluorescence detection: Application to a pharmacokinetic study

A direct fluorometric high‐performance liquid chromatography (HPLC) method was developed and validated for the analysis of ibuprofen enantiomers in mouse plasma (100 μl) and tissues (brain, liver, kidneys) using liquid–liquid extraction and 4‐tertbutylphenoxyacetic acid as an internal standard. Separation of enantiomers was accomplished in a Chiracel OJ‐H chiral column based on cellulose tris(4‐methylbenzoate) coated on 5 μm silica‐gel, 250 x 4.6 mm at 22 °C with a mobile phase composed of n‐hexane, 2‐propanol, and trifluoroacetic acid that were delivered in gradient elution at a flow rate of 1 ml min⁻¹. A fluorometric detector was set at: λ_excit. = 220 nm and λ_emis. = 290 nm. Method validation included the evaluation of the selectivity, linearity, lower limit of quantification (LLOQ), within‐run and between‐run precision and accuracy. The LLOQ for the two enantiomers was 0.125 μg ml⁻¹ in plasma, 0.09 μg g⁻¹ in brain, and 0.25 μg g⁻¹ in for liver and kidney homogenates. The calibration curves showed good linearity in the ranges of each enantiomers: from 0.125 to 35 μg ml⁻¹ for plasma, 0.09–1.44 μg g⁻¹ for brain, and 0.25–20 μg g⁻¹ for liver and kidney homogenates. The method was successfully applied to a pharmacokinetic study of ibuprofen enantiomers in mice treated i.v. with 10 mg kg⁻¹ of racemate.