CE analysis and molecular characterisation of depurinated DNA samples

A DNA sample was partially degraded by scalar heat-acid treatments to study the extent of apurinic-apyrimidinic (A-P) lesions produced along the molecule. A CE-UV method allowed us to measure the rate of depurination at pH 5.0 and 70°C which was calculated to be 5.41×10(-6) s(-1) for adenine and 6.27×10(-6) s(-1) for guanine. CE identified depurination on treated samples when it occurred with a loss of >4% of the basic moieties. The molecular features of the A-P enriched samples were investigated by using molecular assays (agarose gel electrophoresis, UV spectrophotometry and quantitative PCR) and the consistency of the results of the STR typing were compared with the degree of depurination of the PCR template. The treated DNA samples showed molecular features such as fragmentation, altered OD(260) /OD(280) ratios and decreased ability of the quantitative PCR to synthesise the human target, related to the severity of depurination. A satisfactory correlation between the degree of damage and the amount of residual PCR-sensitive target sequences was also demonstrated (r(2) =0.9717). The conventional and mini-STR typing of the samples showed that the genetic outcome was influenced by a depurination damage that exceeded 4% when locus drop-outs and artefactual PCR results were evident. As the success of STR typing depends on the integrity of the DNA recovered from the samples, the CE-UV, physical and molecular assays described here are proposed as a set of useful methods in the analysis of certain forensic and clinical samples, for a critical evaluation of the outcome of the genetic testing.     

Electrochemical behaviors of native and thermally denatured fish DNA in the presence of cytosine derivatives and porphyrin by cyclic voltammetry using boron-doped diamond electrode

The electrochemical behaviors of native and thermally denatured fish DNA was investigated using boron-doped diamond (BDD) film electrode by cyclic voltammetry. The BDD electrode afforded us to measure weak current less than muA for the DNA solution in 100 microl. The mixture of acetic acid and sodium acetate solution (0.2 M) was used as a supporting electrolyte. Two oxidation peaks were observed at about +1.1 V and +1.3 V at pH 4.6 for thermally denatured fish DNA. This is due to the oxidation of guanine and adenine in the denatured fish DNA, respectively. In contrast, the native fish DNA showed ill-defined peaks at +1.1 V. Furthermore, the electrochemical behaviors of thermally denatured fish DNA were studied in the presence of cytosine, cytidine, cytidine-5-monophosphate, tetrakis(1-methypyridinium-4-yl)porphyrin (H(2)(TMPyP)(4+)) and Ru(II)(TMPyP)(4+). The oxidation peak intensity at +1.1 V gradually decreased with the increase of the concentrations of the above compounds. Based on the above studies, electrochemical behaviors of the thermally denatured fish DNA at BDD electrode is discussed.     

Effects of cytosine methylation on pyrimidine dimer formation in DNA

The relative induction of cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4)pyrimidone photoproducts ([6-4]PD) was quantified in the duplex homopolymers polydeoxyadenosine:polydeoxythymidine, polydeoxyguanosine:polydeoxycytidine and polydeoxyguanosine:polydeoxy-5-methylcytidine irradiated with UVC or UVB radiation. Cytosine methylation significantly increased the yield of cytosine (6-4)PD after irradiation with UVC light and of cytosine CPD and (6-4)PD after irradiation with UVB light. The data suggest that CPD and (6-4)PD are preferentially induced at 5-methylcytosine bases in DNA of cells exposed to sunlight and comprise a major component of the mutation spectrum leading to the initiation of sunlight-induced skin cancer.     

Toward the understanding of DNA fluorescence: the singlet excimer of cytosine

By using the multiconfigurational second-order perturbation method CASPT2, including corrections for the basis set superposition error, the lowest-singlet excited state of the face-to-face pi-stacked cytosine homodimer is revealed to be bound by about half an eV, being the source of an emissive feature consistent with the observed redshifted fluorescence.     

Formation of hydrogen-bridged cytosine dimers on Cu(110)

Cytosine was adsorbed onto a Cu(110) surface under UHV conditions. Annealing to 370 K resulted in the formation of a (6 x 6)gg low energy electron diffraction (LEED) pattern, even at submonolayer coverages. Examination of this structure with scanning tunneling microscopy (STM) revealed islands of zigzag chains at low coverages and large ordered domains at monolayer saturation. Further annealing to 480 K initiated a phase transition to a (6 x 2)gg structure observed both by LEED and STM. High resolution electron energy loss spectroscopy spectra for both overlayer structures exhibited mainly in-plane modes suggesting upright/tilted species on the surface. Based on the experimental data and supported by density functional theory calculations, a model is proposed for the (6 x 2)gg structure, which involves the formation of deprotonated hydrogen bridge-bonded cytosine dimers, adsorbed through the oxygen atoms.     

Synthesis of modified uracil and cytosine nucleobases using a microwave-assisted method

Modified nucleobases and nucleic acids have found many biological and pharmaceutical applications. Here we report a microwave-directed synthesis of a variety of modified uracil and cytosine nucleobases with high yields under solvent-free conditions. The reaction yields were further improved by addition of Lewis acid. The crystal structures of 5-isopropyl-6-methyluracil and 6-phenyluracil were also determined.     

Determination of herbicide residues in soil in the presence of persistent organochlorine insecticides

Summary A rapid and reproducible gas-chromatographic method has been developed for determination of residues in soil of some widely used herbicides such as trifluralin, metribuzin, alachlor, acetochlor, metolachlor, pendimethalin, simazine, atrazine, prometryne, in the presence of persistent organochlorine insecticides (p,p-DDT, o,p-DDT, p,p-DDE, alpha-HCH, gamma-HCH, heptachlor). Determination of some herbicides by GC/ECD is difficult since their relative retention times on packed columns usually used for pesticide analysis are equal or close to those of some persistent organochlorine insecticides which can still be found almost everywhere, especially in cultivated soils. A 1.8 m column of 3% OV-225 + 5% SE-52 in a ratio of 1.4:0.9 gave good separation of all herbicides and insecticides mentioned. The influence of 6 solvents and solvent systems applied most frequently for soil extraction of pesticide residues on recovery of the compounds under study was examined. Acetonitrile was the most suitable extractant as it rendered highest residue recoveries and minimal amount of co-extractives. Residues of simazine, atrazine, and prometryne were determined in the same extracts by the use of NP-detector and a column of 5% Carbowax 20M. Recoveries of the compounds under study were in the interval of 86–103% without cleanup and 78–94% when cleanup was carriet out. The method can be used in pesticide monitoring of soil as it offers an opportunity for rapid determination of soil applied herbicides and persistent organochlorine insecticides which are some of the most common pollutants in cultivated soils.     

Noncovalent interactions between modified cytosine and guanine DNA base pair mimics investigated by terahertz spectroscopy and solid-state density functional theory

Modified cytosine and guanine nucleobases cocrystallize in a hydrogen bonding configuration similar to that observed in native DNA. The noncovalent interactions binding these base pairs in the crystalline solid were investigated using terahertz (THz) spectroscopy and solid-state density functional theory (DFT). While stronger hydrogen bonding interactions are responsible for the general molecular orientations in the crystalline state, it is the weaker dipole-dipole and dispersion forces that determine the overall packing arrangement. The inclusion of dispersion interactions in the DFT calculations was found to be necessary to accurately simulate the unit cell structure and THz vibrational spectrum. Using properly modeled intermolecular potentials, the lattice vibrational motions of the cytosine and guanine derivatives were calculated. The vibrational characters of the modes exhibited by the DNA base pair mimic in the THz region were primarily rotational motions and are indicative of the energies and the nature of vibrations that would likely be observed between similar base pairs in DNA molecules.     

Photoisomerization of arylstilbazolium ligands in the presence of DNA

The ability of the DNA duplex to behave as an efficient organized medium for trans-cis photoisomerization has been explored. The presence of DNA affected isomerization in a variety of ways depending on the aryl moiety properties of the ligand and its DNA-binding mode. Contrary to intercalating ligands, 9-[2-(N-methylpyridinium-4-yl)vinyl]phenanthrene (2) and 9-[2-(N-methylpyridinium-4-yl)vinyl]anthracene (3), which gave only cis and trans isomers, the additional products--cyclobutane photodimers--were detected for 2-[2-(N-methylpyridinium-4-yl)vinyl]naphthalene (1), which binds cooperatively to the minor groove of DNA. Photostationary states (pss) for all ligands were seriously affected by the presence of DNA. A trans isomer-rich pss and restriction of trans --> cis process, observed for ligands 1 and 2, were explained in terms of a different binding affinity of DNA toward particular isomers. On the contrary, 9-anthryl derivative 3 isomerized against the isomer-binding preferences, showing cis isomer-rich pss and enhanced quantum yield of isomerization. The unique behavior of ligand 3-DNA complex was attributed to different isomerization mechanism that consists in quantum chain isomerization from an excited singlet state possessing a charge transfer character. This is the first example of ligand, which undergoes DNA-mediated cis-trans isomerization in the opposite direction than expected from DNA-binding preferences. The analysis of pss data based on two alternative pathways of photoisomerization showed that investigated ligands follow the model that allows isomerization of both free and DNA-bound ligands.     

Determination of 5-methyl-cytosine and cytosine in tumor DNA of cancer patients

The determination of the relative methylation in DNA tumor samples, in order to evaluate the activity of some anti-cancer drugs, has become a very important issue in the clinical field. Capillary electrophoresis (CE) applications in this area have been done previously but no good separation for model samples or tumor samples has been reported. In this work, the CE conditions have been optimized in order to obtain baseline separation and efficient peaks for cytosine and 5-methylcytosine in both, standard mixtures and actual tumor samples; other bases (adenine, uracil, guanine, and thymine) have also been integrated in the optimization studies. More efficient peaks and shorter analysis time compared with the already reported conditions have been obtained employing a fused-silica capillary (75 microm inner diameter) of 44.5 cm effective length, 20 mM carbonate buffer (pH 9.6) plus 80 mM sodium dodecyl sulfate, a separation voltage of 20 kV, and detection at 223 nm.     

Site-specific transition of cytosine to uracil via reversible DNA photoligation

We report that deamination coupled with 5-carboxyvinyldeoxyuridine-mediated photobranching causes the heat-induced transition of cytosine to uracil with high efficiency without any side reaction.     

Exchange reactions of alkyl residues in the presence of orthophosphoric and benzenephosphonic monoesters

Experimental data obtained from the study of the behaviour of monoalkyl phosphates ROP(O)(OH)O^? or monoalkyl phosphonates C₆H₅P(O)(OR)O^? in aquo-alcoholic (H₂O + R′OH) solutions suggest: (1) in the case of monoalkyl phosphonates the exchange of R and R′ must proceed by a direct alcoholysis; (2) in the case of monoalkyl phosphates, where the scission of the ester at about pH 4,5 proceeds via the intermediate formation of metaphosphate ion PO₃^?, R′OPO₃H^? can also be formed by the addition of R′OH to PO₃^? (competitive to the addition of water) besides direct alcoholysis of ROPO₃H^?.     

Bisulfite-free mapping of DNA cytosine modifications: challenges and perspectives

The mapping of DNA cytosine modifications is crucial for understanding the dynamic landscape of epigenetic regulation. While bisulfite sequencing has been the gold standard for decades, it suffers from limitations such as DNA degradation and low library quality due to harsh chemical treatment. In recent years, bisulfite-free methods have emerged as promising alternatives for detecting and quantifying DNA cytosine modifications. These methods employ enzymatic and chemical strategies to investigat...     

Coke making of residues of refining and petrochemical industries in the presence of hydrogen

A new version of a regulation of output and product quality in coke making of various residues in oil refining and petrochemical industries was suggested. Regularities of a hydrogen effect on the carbonization yield and an amount of sulfur in it were found.     

Asymmetric hydrogenation of carbonyl group in the presence of modified ruthenium catalyst

Conclusions The hydrogenation of acetoacetic ester in the presence of ruthenium, deposited on silica gel, modified with D-tartaric acid at pH 4.2–5.9, yields the (–)--hydroxybutyrate, which possesses optical activity. The highest asymmetric yield is observed when the modifying solution has a pH of 5.5.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1803–1804, August, 1971.     

Hydrogenation of unsaturated compounds in the presence of palladium-containing modified carbon nanofibers

Palladium-containing carboxylated carbon nanofibers were studied as catalysts for hydrogenation of double bond >C=C< in olefins, unsaturated alcohols, and acids, as well as for hydrogenation of nitroarenes. The developed catalyst is 7 times more efficient than the industrial analog (Pd/C).