Ester and related derivatives of ring N-pentafluorobenzylated 5-hydroxymethyluracil. Hydrolytic stability, mass spectral properties, and trace detection by gas chromatography-electron-capture detection, gas chromatography-electron-capture negative ion mass spectrometry, and moving-belt liquid chromatography-electron-capture negative ion mass spectrometry

Measurement of the incorporation and repair of exogenous 5-hydroxymethyl-2'-deoxyuridine in human cells in culture using gas chromatography-negative chemical ionization-mass spectrometry

The DNA of all organisms is constantly damaged by oxidation. Among the array of damage products is 5-hydroxymethyluracil, derived from oxidation of the thymine methyl group. Previous studies have established that HmU can be a sensitive and valuable marker of DNA damage. More recently, the corresponding deoxynucleoside, 5-hydroxymethyl-2'-deoxyuridine (HmdU), has proven to be valuable for the introduction of controlled amounts of a single type of damage lesion into the DNA of replicating cells, which is subsequently repaired by the base excision repair pathway. Complicating the study of HmU formation and repair, however, is the known chemical reactivity of the hydroxymethyl group of HmU under conditions used to hydrolyze DNA. In the work reported here, this chemical property has been exploited by creating conditions that convert HmU to the corresponding methoxymethyluracil (MmU) derivative that can be further derivatized to the 3,5-bis-(trifluoromethyl)benzyl analogue. This derivatized compound can be detected by gas chromatography-negative chemical ionization-mass spectrometry (GC-NCI-MS) with good sensitivity. Using isotopically enriched exogenous HmdU and human osteosarcoma cells (U2OS) in culture, we demonstrate that this method allows for the measurement of HmU in DNA formed from the incorporation of exogenous HmdU. We further demonstrate that the addition of isotopically enriched uridine to the culture medium allows for the simultaneous measurement of DNA replication and repair kinetics. This sensitive and facile method should prove valuable for studies on DNA oxidation damage and repair in living cells.

Measurement of urinary excretion of 5-hydroxymethyluracil in human by GC/NICI/MS:

5-Hydroxymethyluracil (5-HMU) is derived from radiation in addition to endogenous oxidative DNA damage and it is one of the most abundant DNA adducts. Human 5-HMU-DNA-glycosylase has been shown to repair this lesion. Whether urinary levels of 5-HMU is a valid biomarker for oxidative DNA damage in vivo has been investigated. However, controversial results on its relation to cigarette smoking were reported. To facilitate analysis of urinary 5-HMU in epidemiological studies, a highly sensitive and specific assay based on stable isotope dilution gas chromatography/negative ion chemical ionization/mass spectrometry was developed. The limit of detection for N1,N3-bis(pentafluorobenzyl)-HMU is 10 fg (20 amol) (S/N=4) injected on column and the limit of quantification in urine was 0.7 nM of 5-HMU. Using as little as 10 microL of human urine samples, levels of urinary 5-HMU in 21 healthy volunteers were accurately quantified. No correlation was observed between urinary 5-HMU levels and cigarette smoking. However, there was a statistically significant association between urinary levels of 5-HMU and thiobarbituric acid-reactive substances (r=0.71, p=0.0003). In addition, urinary 5-HMU levels also correlated with urinary levels of 1,N6-ethenoadenine (r=0.54, p=0.01). These findings suggest that this assay should be valuable in assessing the role of urinary 5-HMU as a biomarker of oxidative DNA damage and repair.

Electron-capture mass spectrometry: recent advances

Electron-capture (EC) is a sensitive and selective ionization technique for mass spectrometry (MS). In the most familiar form of EC, a susceptible analyte (electrophore) is detected after eluting from a gas chromatography (GC) column, where a low attomole detection limit for standards is routine. High-performance liquid chromatography can facilitate sample cleanup prior to detection by GC-EC-MS, but carryover and shifts in retention time for the "invisible" analyte can be difficulties. Solid-phase extraction avoids these difficulties, but the degree of cleanup and recovery can be problems. Alternative electrophoric derivatizing reagents are available to help deal with interferences, and new reagents such as "AMACE1" are emerging. Releasable forms of electrophores can be used as tags for labeling macromolecules, motivated by the desire to multiplex ligand-type assays. The conventional, gas-phase ion source for EC is not well-understood, especially the role of wall reactions. Using an electron monochromator to tune the electron energy adds to the selectivity and information provided by EC-MS. High-resolution and tandem EC-MS measurements are emerging. Electron-capture dissociation is a new technique to sequence small- to medium-sized peptides, having the advantage of providing more extensive sequence information relative to other MS techniques. Particle-beam EC-MS tends to be less sensitive than GC-EC-MS, but not always. Recently it was demonstrated that EC-MS can be accomplished on an ordinary laser desorption time-of-flight mass spectrometer, and also by using atmospheric pressure chemical ionization. Two applications are discussed here in detail: bile acids and oxidized phenylalanine. EC-MS is well-established as a useful technique for trace analysis in special cases, and the scope of its usefulness is broadening (qualitative analysis and detection of more polar and larger molecules), based on advances in both the chemical and instrumental aspects of this technique.

Determination of cis-thymine glycol in DNA by gas chromatography-mass spectrometry with selected ion recording and multiple reaction monitoring

A novel method for the determination of cis-thymine glycol in DNA has been developed, using gas chromatography-mass spectrometry with selected ion recording or multiple reaction monitoring. The procedure involves acidic hydrolysis of DNA in the presence of the internal standard cis-[2H3]thymine glycol, followed by derivatisation with N-methyl-N-(tert.-butyldimethylsilyl)trifluoroacetamide. The method was validated on DNA that had been oxidatively modified in vitro by radiation treatment, and was then applied to determine cis-thymine glycol in human placental DNA. Background levels of 5.45+/-2.98 ng cis-thymine glycol/mg DNA were observed in the human samples.

32P-postlabelling and mass spectrometric methods for analysis of bulky, polyaromatic carcinogen-DNA adducts in humans

There has been significant recent progress toward the development of human carcinogen-DNA adduct biomonitoring methods. 32P-Postlabelling is a technique which has found wide application in human studies. 32P-Postlabelling involves enzymatic preparation and labelling of DNA samples, followed by chromatographic separation of carcinogen-nucleotide adducts from unadducted nucleotides. Thin-layer ion-exchange and high-performance liquid chromatography (HPLC) have been utilized. This paper critically reviews 32P-postlabelling methods for analysis of bulky, polyaromatic carcinogen-DNA adducts and details a strategy to optimize this technique for monitoring human samples. Development of a human carcinogen biomonitoring method requires that the biomarker meet certain criteria: that the biomarker be responsive to exposures known to increase human cancer risk, to reductions in those exposures, and to the influence of metabolic differences. In addition, reliable samples must be available by non-invasive means. The ability of 32P-postlabelling to meet these criteria is traced in the literature and discussed. Identification of specific carcinogen-DNA adducts is a difficult task due to the low (femtomole) levels in human target tissues. Because co-chromatography in thin-layer chromatography (TLC) is generally not considered to be proof of chemical identity, both synchronous fluorescence and HPLC in conjunction with 32P-postlabelling and TLC are used to confirm the identity of specific carcinogen-DNA adducts in human samples. Mass spectrometry is a highly specific method, the sensitivity of which has been improved to the point which may allow its use to confirm the identity of carcinogen-DNA adducts isolated by 32P-postlabelling and other methods. The literature relating to the use of mass spectral techniques in carcinogen-DNA adduct analysis is reviewed.

Preparation and mass spectral characterization of pentafluorobenzyl derivatives of alkyl and hydroxyalkyl-nucleobase DNA adducts

Pentafluorobenzyl (PFBz) derivatives of the following nucleobases were prepared: cytosine, 5-methylcytosine, O2-methylcytosine, O2-ethylthymine, O4-ethylthymine, 5-hydroxymethyluracil, N6-methyladenine, O6-methylguanine, O6-hydroxyethylguanine and O6-hydroxyethylpurine. 13C nuclear magnetic resonance was diagnostic for O- versus N-attachment of the PFBz moiety: the resonance of the methylene carbon appeared in the range 29.15-42.13 ppm for NCH2C6F5, and 58.45-69.01 for OCH2C6F5. Considerable structural information was provided by mass spectrometry with ionization by electron impact. All of the derivatives were detected with high sensitivity and specificity by gas chromatography with detection by electron capture negative ion mass spectrometry, reflecting not only their chemical and physical stability, but also their strong tendency to form a structurally diagnostic anion, [M - PFBz]-, in high yield under these ionization conditions. PFBz derivatives are therefore attractive forms of alkyl-substituted nucleobases for analysis by mass spectrometry.