Assessment of DNA oxidative damage by quantification of thymidine glycol residues using gas chromatography/electron capture negative ionization mass spectrometry.

A technique to assess DNA oxidative damage by quantification of thymidine glycol residues is described. 2-Methylglycerate was released from thymidine glycol in DNA by alkaline cleavage/borodeuteride reduction, then derivatized to form a combined pentafluorobenzyl-tertbutyldimethylsilyl (PFB-TBDMS) derivative and analyzed by gas chromatography/electron capture negative ionization mass spectrometry. [2H4]Thymine glycol was used as an internal standard. The derivatization chemistry was assessed by using [14C-methyl]glycerate. Successful esterification was achieved with 75-80% yield using tetrabutylammonium sulfate-assisted anhydrous pentafluorobenzylation. The PFB-TBDMS derivative exhibits excellent chromatographic and detection properties with a detection limit of 41 amol injected on column. Freshly dissolved calf thymus DNA was used to test the method performance. The background level of thymidine glycol detected in this DNA was 11.7 +/- 0.3 x 10(-6) mol thymidine glycol per 1 mol thymidine. The thymidine glycol background in undamaged DNA establishes a lower limit of oxidative damage below which biological oxidation events would not be measured by this method. The method was linear for 4-20 micrograms DNA added per tube. The minimum measurable amount of thymidine glycol in DNA sample was 36 fmol. An increased level of thymidine glycol was measured in salmon sperm DNA which had autoxidized during storage in a refrigerated aqueous solution, 71.2 +/- 14.3 x 10(-6) mol thymidine glycol per 1 mol thymidine.

Metabolism of L-tryptophan to kynurenate and quinolinate in the central nervous system: effects of 6-chlorotryptophan and 4-chloro-3-hydroxyanthranilate.

The metabolism of L-tryptophan to the neuroactive kynurenine pathway metabolites, L-kynurenine, kynurenate and quinolinate, and the effects of two inhibitors of quinolinate synthesis (6-chlorotryptophan and 4-chloro-3-hydroxyanthranilate) were investigated by mass spectrometric assays in cultured cells and in vivo. Cell lines obtained from astrocytoma, neuroblastoma, macrophage/monocytes, lung, and liver metabolized L-[13C6]-tryptophan to L-[13C6]kynurenine and [13C6]kynurenate, particularly after indoleamine-2,3-dioxygenase induction by interferon-gamma. Kynurenine aminotransferase activity was measurable in all cell types examined but was unaffected by interferon-gamma. These results suggest that many cell types can be sources of kynurenate following immune activation. In vivo synthesis of L-[13C6]kynurenine and [13C6]kynurenate from L-[13C6]tryptophan was studied in the CSF of macaques infected with poliovirus, as a model of inflammatory neurologic disease. The effects of 6-chlorotryptophan and 4-chloro-3-hydroxyanthranilate on the synthesis of kynurenate were different. 6-Chlorotryptophan attenuated formation of L-[13C6]kynurenine and [13C6]kynurenate and was converted to 4-chlorokynurenine and 7-chlorokynurenate. It may be an effective prodrug for the delivery of 7-chlorokynurenate, which is a potent antagonist of NMDA receptors. In contrast, 4-chloro-3-hydroxyanthranilate did not reduce accumulation of L-[13C6]kynurenine and [13C6]kynurenate. 6-Chlorotryptophan and 4-chloro-3-hydroxyanthranilate are useful tools to manipulate concentrations of quinolinate and kynurenate in the animal models of neurologic disease to evaluate physiological roles of these neuroactive metabolites.

Pentafluorobenzylation method for quantification of acidic tryptophan metabolites using electron capture negative ion mass spectrometry.

An improved pentafluorobenzylation method was developed for derivatization of L-tryptophan and its acidic metabolites (L-kynurenine, kynurenic acid, anthranilic acid, xanthurenic acid, 3-hydroxyanthranilic acid, picolinic acid, quinolinic acid) present at trace levels in aqueous samples. This method employs lyophilization of aqueous samples in the presence of excess tetrabutylammonium hydrogen sulfate, followed by base-catalyzed anhydrous pentafluorobenzylation. A comparison with other published methods shows the advantage of this modification for the derivatization of kynurenine metabolites. The derivatives were analyzed by gas chromatography/electron capture negative ion mass spectrometry (GC/ECNI-MS) or liquid chromatography/particle beam/ECNI-MS (LC/ECNI-MS). The detection limits for injected standards are in the femtogram range by GC/ECNI-MS and in the low picogram range by LC/ECNI-MS. GC/ECNIMS is 3.6 (xanthurenic acid) to 66 (quinolinic acid) times more sensitive than LC/ECNI-MS. The simultaneous determination of two neuroactive metabolites, quinolinic and kynurenic acids, in culture medium is presented. The minimum measurable concentrations of these metabolites in 100 microL of culture medium are 0.11 nM for quinolinic acid and 0.21 nM for kynurenic acid.

Quantification of L-tryptophan and L-kynurenine by liquid chromatography/electron capture negative ion chemical ionization mass spectrometry.

In a number of infectious and inflammatory diseases, stimulation of the immune system can lead to increased accumulation of tryptophan metabolites via induction of kynurenine pathway enzymes in extrahepatic tissues. We developed a liquid chromatographic/mass spectrometric (LC/MS) method suitable for tracing the disposition of 13C isotopomers of L-tryptophan and L-kynurenine in various cultured cell, tissue slice, and whole animal model systems used to investigate tryptophan flux through the kynurenine pathway. The method employs extractive derivatization of the analytes and their 2H internal standards with pentafluorobenzyl bromide in order to enhance the negative ion chemical ionization (NICI) mass spectrometric response. Normal-phase liquid chromatographic separation of derivatized analytes was optimized using a silica column with organic solvents, followed by particle beam transfer and NICI-MS. Standard curves were linear over the range 1-250 ng per sample. Particle beam and mass spectrometric operating parameters were optimized with direct flow injections of 1-(methylamino) anthraquinone, which is an ideal test compound for the evaluation of LC/NICI-MS. The developed method was used to quantify the conversion of (13C6)L-tryptophan to (13C6)L-kynurenine by human monocytes (THP-1) stimulated with interferon-gamma, lung and brain tissue slices obtained from gerbils immune-stimulated with pokeweed mitogen. The effect of whole body immune stimulation on the plasma levels of endogenous L-kynurenine in mice stimulated with interferon-gamma was also quantified.

Melting of oligodeoxynucleotides with various structures.

Effects of DNA fragments end structures on their melting profiles were studied experimentally and theoretically. We examined melting of hairpins and dumbbells obtained from 62-bp-long linear DNA duplex which is a perfect palindromic sequence. To fit theoretical melting profile to experimental ones additional theoretical parameters were incorporated into the standard statistical mechanical helix-coil transition theory. From comparison theoretical and experimental melting profiles theoretical parameters connected with end-structure effects were evaluated. Analysis revealed the stabilization effect of the hairpin loops and helix ends with respect to DNA duplex melting. Both type of ends make melting these oligodeoxynucleotides more cooperative than predicted by the standard helix-coil transition theory. At low ionic strength ([Na+] less than 0.04 M) this effect becomes so pronounced that melting of the DNA duplexes 30-40 bp-long conforms to the two state model. From the analysis experimental data obtained for dumbbell structures loop-weighting factor for single-stranded loop consisting of 132 nucleotides was determined. This parameter decreases 10 times with the ionic strength decreasing by an order of magnitude from 0.2 to 0.02 M Na+.

Content of phenylalanine, tyrosine and their metabolites in CSF in phenylketonuria.

By using ion-exchange chromatography and gas chromatography coupled with mass spectrometry, the content of phenylalanine, tyrosine and their metabolites typical of phenylketonuria (PKU) was determined in the cerebrospinal fluid (CSF) of 8 untreated children with classical PKU and 9 controls. At the same time, plasma and urine were analysed. In PKU the content of phenylalanine is increased on average 23 times in plasma and CSF. The content of phenylalanine and tyrosine in CSF is about 4 times less as compared with plasma. The phenylalanine-to-tyrosine ratio is approximately the same for these fluids both in control and in PKU. This indicates that the transport of phenylalanine and tyrosine through the blood-brain barrier is not disturbed in PKU. Phenylpyruvate and 4-hydroxyphenylpyruvate are either not detected or present in very low concentrations in the CSF of children with PKU; their derivatives, phenyllactate and 4-hydroxyphenyllactate, are present in relatively higher concentrations. This indicates increased metabolic conversion in brain tissues.

[Melting of short DNA fragments. Relation between the nucleation constant of a spiral region and the ionic strength]. / Plavlenie korotkikh fragmentov DNK. Opredelenie zavisimosti konstanty nukleatsii spiral'nogo uchastka ot ionnoi sily.

Melting of two DNA duplexes of known nucleotide sequences containing 14 and 36 base pairs has been investigated within the range of ionic strength from 0.2 to 0.02 M [Na+]. The values of melting enthalpy of base pair delta H were measured for the duplex of 14 base pairs in the solutions of varying ionic strength. The values of delta H were obtained from slopes of linear plots of reciprocal melting temperature versus logarithm of oligonucleotide chains concentration. In the aforementioned range the decrease of the ionic strength causes a 5% decrease of delta H. By fitting the theoretical profiles to the experimental ones the ionic strength dependence of the nucleation constant beta was measured for DNA fragments of various lengths. With the decrease of the ionic strength the value of beta drops 2 times for the short duplex and 8 times for the long one.

The kinetics of DNA helix-coil subtransitions.

The kinetic analysis of individual helix-coil subtransitions were performed by comparing melting and renaturation profiles obtained at different temperature change rates. The duration of the three transition stages and its dependence on temperature and ionic strength were determined for a T7 phage DNA fragment. The obtained temperature dependence of the melting time for a stretch flanked by melted regions is in quantitative agreement with that predicted by the theory of slow processes (V.V. Anshelevich, A.V. Vologodskii, A.V. Lukashin, M.D. Frank-Kamenetskii, Biopolymers 23, 39 (1984)). The reasons are discussed for the increasing relaxation time of this stretch in the middle of its transition with decreasing ionic strength. The zipping kinetics of a melted region under essentially nonequilibrium conditions was examined for T7 fragment and pAO3 DNAs. The obtained temperature dependence of the zipping time is in quantitative agreement with calculations based on the theory of slow processes. The renaturation times of stretches flanked by helical regions proved fairly small even at a low ionic strength. These times are several orders of magnitude smaller than the renaturation times of the same stretches with one helical boundary. A formal application of the theory of slow processes failed to account for the small renaturation times of stretches that are zipped from both ends. This is probably due to the non-allowance for the changing entropy of the loop linking two helix-coil boundaries migrating towards each other. Slow processes have been revealed in the intramolecular melting of Col E1 DNA at a high ionic strength. The reason for the long relaxation time of one subtransition is the large size of the loop that separates the melting stretch from the helical part of the molecule. This result can be accounted for by the theory of slow processes.