Natural Occurrence of Enantiomeric and meso-Astaxanthin. 5. Ex wild salmon (Salmo salar and Oncorhynchus)

The configurational isomers of astaxanthin (3,3′-dihydroxy-β,β-carotene-4,4′-dione) from the flesh of salmon (Salmo salar and Oncorhynchus) caught at different places in Europe and Canada were isolated and analyzed as (?)-camphanic acid diesters by means of HPLC. The biological variation in the composition of the configurational isomers in seven fish was surprisingly similar: 78 to 85% of (3S, 3′S)-astaxanthin, 12 to 17% (3R, 3′R)-astaxanthin and 2 to 6% meso-astaxanthin.     

液相色谱-串联质谱分析组织中基因组脱氧核糖核酸羟甲基胞嘧啶水平

5-羟甲基胞嘧啶通过阻止脱氧核糖核酸(DNA)甲基化转移酶1(DMNT1)甲基化胞嘧啶来影响DNA甲基化的程度。本文建立了液相色谱-串联质谱(LC-MS/MS)测定组织中全基因组5-羟甲基胞嘧啶水平的方法。采用苯酚-氯仿提取组织DNA,提取的DNA用88%甲酸在140 ℃下裂解,DNA裂解液加入同位素胞嘧啶作内标,经N2吹干后,加乙腈-水(9:1, v/v)溶解,用LC-MS/MS检测5-羟甲基胞嘧啶的含量,并计算全基因组中5-羟甲基胞嘧啶的水平。结果表明,5-羟甲基胞嘧啶的线性范围为0.1～30 ng/mL,相关系数为0.9969,检出限(信噪比为3计)和定量限(信噪比为10计)分别为0.057 ng/mL和0.090 ng/mL;日内相对标准偏差和日间相对标准偏差分别为5.13%和6.24%;加标回收率为90.24%～97.53%。用该方法检测了大鼠大脑组织DNA羟甲基化水平,平均结果为0.66%。该方法简便,重现性好,灵敏度较高,能满足全基因组5-羟甲基胞嘧啶定量检测的要求。     

UV degradation of deoxyribonucleic acid

The effects of UV synchrotron radiation on deoxyribonucleic acid (DNA) cast films have been systematically investigated by vacuum ultraviolet and infrared spectrophotometry as a function of irradiation time. Cast DNA films exposed at 140 nm (8.85 eV) for different irradiation times, revealed consistent changes in their VUV spectra which indicate a decrease of thymine groups and an increase of π → π* transition spectral signature associated with the CO group of the open sugar chain. This result was corroborated by a decrease in CO stretching vibration at 1061 cm⁻¹ observed in the infrared spectra. Both these results are consistent with the creation of single strand breaks in the deoxyribose component of DNA molecule and a decrease in the phosphate groups. It was also shown that UV radiation is effective in damaging the thymine groups involved in Hoogsteen base pairing with adenine. The analysis of the infrared data suggests that the usual spectroscopic fingerprints of DNA denaturation are not necessarily a reliable measure of DNA damage.     

Repair processes on deoxyribonucleic acid

Many cells have the ability to recognize and eliminate damage to their DNA, particularly thymine dimers formed by UV light. The elimination of this damage may be achieved by enzymatic, light-dependent cleavage of the dimers into the monomers (photoreactivation) or more frequently by dark repair, in which the damaged part is completely removed from the, DNA. In this repair process, the DNA is incised by an endonuclease in the immediate vicinity of the thymine dimers. Oligonucleotides containing the thymine dimer are removed hydrolytically from the DNA by the 5→3′ exonuclease activity of DNA polymerase I (Kornberg enzyme). The resulting gaps are immediately closed by a de novo synthesis with the aid of the same DNA polymerase I, the complementary strand serving as a template (excision repair). The final step is the formation of the phosphodiester bond between the newly synthesized DNA fragment and the old DNA strand by a DNA ligase. Xeroderma pigmentosum patients lack the endonuclease as a result of a genetic defect; they therefore cannot eliminate thymine dimers from their DNA, and are extremely sensitive to sunlight. All information so far suggests that genetic recombination and DNA repair are performed by the same enzyme system.     

Interaction of asterriquinone with deoxyribonucleic acid in vitro

The interaction of asterriquinone (ARQ), a novel antitumor agent isolated from Aspergillus fungi, with deoxyribonucleic acid (DNA), has been studied. The binding of ARQ in vitro with DNA (calf thymus) was ascertained by its behavior in gel filtration using a Sephadex G-25 column at pH 5.4. Some ARQ analogs having no, or less, antitumor activity did not exhibit any evidence of interaction with DNA under the same condition. From the results obtained in this work, the pKa value of ARQs seemed to be critical between 6 and 7 for their binding to DNA and for exhibition of antitumor activity. Also, ARQ showed serious membrane deformations and an inhibitory effect on the membranous adenosine triphosphatase of Ehrlich carcinoma cells.     

Modeling deoxyribonucleic acid and ribonucleic acid damage in the gas phase

This short review outlines the tandem mass spectrometric methods for the generation and analysis of transient nucleobase radicals relevant to deoxyribonucleic acid and ribonucleic acid damage. Radical hydrogen atom adducts to uracil, adenine, cytosine and N-methylcytosine were generated by femtosecond electron transfer to the corresponding gas-phase cations in fast beams at 8 keV kinetic energy. Radical unimolecular dissociations were monitored by product analysis following collisional ionization to cations or anions using neutralization-reionization mass spectrometry. The radical energetics and dissociation kinetics were further analyzed by mapping the potential energy surfaces by high-level ab initio calculations in combination with Rice-Remsberger-Kassel-Marcus calculations of unimolecular rate constants. This first- principles-based approach allows one to model radical dissociations occurring from doublet ground electronic states of radical intermediates, assign reaction mechanisms and derive quantitative branching ratios for dissociation channels that are in agreement with experiments. Theoretical analysis also provides distinction between radical dissociations occurring on the ground and excited electronic state potential energy surfaces. Specific characterization of excited state dissociations of nucleobase and other polyatomic radicals remains a challenging topic for both experimentalists and computational chemists.     

The enzymatic degradation of ultraviolet-irradiated deoxyribonucleic acid

Abstract— Double-stranded DNA, after u.v. irradiation, was degraded by the action of deoxy-ribonuclease and snake venom phosphodiesterase. In addition to mononucleotides a number of nuclease-resistant oligonucleotides, containing photochemically altered bases, could be detected and separated by column chromatography. The phosphorus contents indicated the existence of some photoproducts other than dimers of pyrimidines, especially within the trinucleotide fraction. Comparison of the DNase action on irradiated and on unirradiated DNA suggests that DNase is hindered from splitting the chain next to a photoproduct, tetra-nucleotides being the smallest and octanucleotides the most frequent degradation products bearing an altered base.     

Effects of direct radiation on deoxyribonucleic acid

It is argued that effects of ionizing radiation on DNA in cell nuclei may frequently be direct in the sense that many electron-gain and electron-loss centres become localised within the DNA molecules. The water of solvation that would also be present in the cell is presumed to pass on holes and electrons prior to the formation of OH· radicals and solvated electrons since these are not detected by ESR of in vitro model systems. Furthermore, a case is made that this direct damage may be particularly significant in that the cationic and anionic centres (G⁺ and T^- according to ESR results) are thought to be formed close enough together to lead, ultimately, to double strand breaks. Evidence that both G⁺ and T^- can lead to strand breaks is discussed. The presence of histone proteins modifies the yields of G⁺ and T^- to a significant extent. The effects of various additives are discussed. Oxygen has been shown by ESR spectroscopy to scavenge electrons in competition with DNA and also to react to form RO₂· radicals that are located on the DNA. It has been shown that this is accompanied by a significant enhancement of strand breaks. Nitroimidazoles act as efficient electron scavengers, their anions being clearly detected by ESR studies. The yield of T^- is consequently reduced and that of the protonated form, TH·, falls to zero. However, the initial yields of G⁺ are not greatly affected. This results in a reduction in the yield of single strand breaks and a proportionately greater decrease in the yield of double-strand breaks due to scavenging of only one of the radical centres. The origin of this is discussed in terms of a proposal for the mechanism of double-strand-break formation. Thus, at the molecular level these drugs protect the DNA against strand sission, in marked contrast with their radiosensitisation in vivo, particularly of hypoxic cells. Other additives studied include hydrogen peroxide and iodoacetamide. The studies on hydrogen peroxide have allowed us to assess the role of OH· radicals under the conditions used for ESR studies. Iodoacetamide gives ·CH₂CONH₂ radicals which are detected by ESR and, on annealing, these apparently attack the DNA to give species thought to be sugar radicals. This is associated with a significant increase in the yields of strand breaks. The ESR features assigned to sugar radicals have been shown to decay at temperatures below which the DNA radicals G⁺ and T^- are normally lost. This provides a good explanation of our failure to detect sugar radical intermediates by ESR spectroscopy on annealing samples in the absence of additives.     

Hydrogen-bonding interactions in peptide nucleic acid and deoxyribonucleic acid: a comparative study

Peptide nucleic acid (PNA) is a synthetic analogue of deoxyribonucleic acid (DNA) capable of tightly binding to itself and DNA with high specificity. Using hybrid density functional methods, hydrogen-bond (H-bond) strengths have been evaluated for isolated Watson-Crick base pairs, PNA base pairs, and charged as well as neutral DNA base pairs. Heterogeneous base pairs of PNA with charged and neutral DNA have also been investigated. The competing effects of short-range H-bonding and long-range Coulombic repulsions in charged DNA base pairs have been analyzed. Polarizable continuum models have been employed to evaluate solvation effects on the binding energies.     

Light and host-guest inclusion mediated salmon sperm DNA/surfactant interactions

DNA/cationic surfactant interaction is relevant from the viewpoint of gene therapy, where the complexation and resulting compaction are essential to protect DNA from nuclease, and to allow entry of DNA into cells. In this work, light input and host-guest inclusion controlled DNA complexation by a novel cationic surfactant 1-[6-(4-phenylazo-phenoxy)-hexyl]-3-methylimidazolium bromide (AzoC6Mim) is reported. The surfactant is covalently attached with an azobenzene group, which undergoes reversible photoisomerizations by changing light input. Under visible light, trans-AzoC6Mim can bind to salmon sperm DNA through electrostatic attraction and hydrophobic interaction, resulting into DNA compaction. Under UV light, although cis-AzoC6Mim still binds to DNA chain, DNA/surfactant complex is decompacted owing to the decrease of surfactant hydrophobicity. On the other hand, azobenzene group can form an inclusion complex with α-CD through host-guest interaction, which removes AzoC6Mim from DNA chain and decompacts the DNA/surfactant complex.