Analysis of DNA Adducts in DNA Hydrolysates by Capillary Zone Electrophoresis and Capillary Zone Electrophoresis−Electrospray Mass Spectrometry

Deforce, Dieter; Ryniers, and Filip P. K.; Eeckhout, Elfriede G. Van den; and, Filip Lemière; Esmans, Eddy L.

doi:10.1021/ac9600013

Cited by 91 publications

(86 citation statements)

References 32 publications

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“…-modified guanosine monophosphate and adenosine monophosphate [72], anti-7,8,9,10-tetrahydrobenzo[a]pyrene-7,8-diol-9,10-epoxidemodified nucleotides [79], phenyl glycidyl ether-modified nucleotides, and phenyl glycidyl ether 5' phosphate-modified nucleotides [78], NAD 1 and FAD 1 dinucleotides [74], modified nucleosides including benzo[g]chrysene and 5,6-dimethylchrysene-modified deoxypurines [84], and styrene oxide-modified adenosine adducts [85]. By using sample stacking technique, CE-MS reached the detection limit of 6.3610…”

Section: Dna Adducts Damaged Dna and 8-hydroxydeoxyguanosinementioning

confidence: 99%

Recent developments in the determination of urinary cancer biomarkers by capillary electrophoresis

Liu

et al. 2004

Electrophoresis

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Investigation of effective biomarkers for cancers is currently a popular area of study in clinical and cancer researches, because it can potentially lead to pre-cancer screening or pre-cancer diagnosis and may provide useful information on cancer type and the disease's stage of progression. More and more biochemical or chemical fluid components of the human body such as urine, blood, and cerebrospinal fluid have been considered to contain biomarkers, which are useful in cancer researches, pre-cancer diagnosis, and cancer follow-ups during or after cancer treatment. Several modern analytical techniques, such as gas chromatography (GC), high-performance liquid chromatography (HPLC), capillary electrophoresis (CE), and other separation techniques as well as hyphenated techniques, have been extensively used in study of cancer biomarkers. Among these techniques, CE is considered to be a highly efficient and practical analytical technique because of the small sample volume requirement and its wide separation versatility, ranging from small inorganic molecules to large biomolecules. This review discusses the latest developments involving biomarkers and their analysis by CE, including a discussion of instrumental conditions, method developments, and data analysis.

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Section: Dna Adducts Damaged Dna and 8-hydroxydeoxyguanosinementioning

confidence: 99%

Recent developments in the determination of urinary cancer biomarkers by capillary electrophoresis

Liu

et al. 2004

Electrophoresis

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“…Over the years, mass spectrometry has been employed directly or coupled with high-performance separation techniques to characterize a variety of covalent adducts produced by alkylation of nucleic acids in vivo and in vitro [11][12][13][14][15][16][17][18][19]. The combination of direct infusion electrospray ionization (ESI) [20] and Fourier transform mass spectrometry (FTMS) [21] constitutes an ideal platform for the analysis of this type of samples, which affords the benefits of high mass accuracy and resolving power [22].…”

mentioning

confidence: 99%

Toward building a database of bifunctional probes for the MS3D investigation of nucleic acids structures

Zhang

Kellersberger

et al. 2006

J. Am. Soc. Mass Spectrom.

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This report illustrates the approaches employed to investigate critical aspects of the activity of crosslinking reagents toward nucleic acid substrates, which should be evaluated to identify candidate probes for mass spectrometric 3D (MS3D) investigations of biomolecules and macromolecular complexes. Representative members of different classes of bifunctional reagents were taken into consideration, including bikethoxal and phenyl-diglyoxal [bis-(1,2-dicarbonyls)], cisplatin (coordinative binding agents), chlorambucil and nitrogen mustard [bis-(2-chloroethyl)amines], and sym-triazine trichloride (triazines). Nanospray-Fourier transform mass spectrometry (FTMS) was applied without desalting or separation procedures to characterize the covalent products obtained by probing dinucleotide and trinucleotide substrates under a variety of experimental conditions in vitro. The carefully controlled composition of these substrates enabled us to obtain valid comparisons of probe activity toward individual nucleotides and evaluate possible base-specific effects, including the stability of the different adducts in solution under the selected reaction conditions. The gas-phase behavior of the observed products was investigated using sustained off-resonance irradiation collision-induced dissociation (SORI-CID) to obtain valuable information for guiding the design of sequencing experiments and helping the data interpretation. Structured RNA substrates, such as HIV-1 stemloop 1, were finally employed to investigate the structural determinant of adduct formation and highlight the different nature of the spatial information provided by the various candidate probes. (J Am Soc Mass Spectrom 2006, 17, 1570 -1581) © 2006 American Society for Mass Spectrometry M ass spectrometric 3D (MS3D) approaches seek to obtain information about the three-dimensional structure of biomolecules using chemical crosslinking and footprinting reagents followed by MS analysis [1][2][3][4]. The very wide range of applicability offered by these techniques is rapidly advancing MS3D to the forefront of the new technologies developed for the structural elucidation of biomolecules that exceed the size accessible by NMR, or afford inadequate crystallization. Fulfilling this potential, however, will require expanding the repertoire of available probes and developing new computational tools for the interpretation and utilization of this type of information in biomolecular modeling. For this purpose, a bioinformatics infrastructure has been recently created to support the efforts of investigators engaged in the development of enabling technologies for MS3D (http://ms3d.org) [5].The MS3D investigation of nucleic acids and proteinnucleic acid complexes can count on mono-and bifunctional alkylating reagents to reveal the location of base pairs, tertiary interactions, and inter-molecular contacts [4,6,7]. The ability of such reagents to support the elucidation of complex RNA structures was recently tested by completing the determination of two ribosome-frameshifting pseu...

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“…In earlier studies by Deforce et al [22] where nucleotides has been treated in vitro, phosphate-alkylated dAMP has been shown together with base-alkylated dAMP, where the differentiation is based on the formation of the non-alkylated base fragment ([B Ϫ 2H] 2Ϫ in negative ionization mode of ESI) and the phosphatealkylated 2Ј-deoxyribofuranosyl moiety for the phosphate-alkylated dAMP. However, in some publications where DNA, treated in vitro in combination with enzymatic degradation into nucleotides and nucleosides, has been analyzed, it is often stated that phosphate alkylations were not formed due to the lack of phosphatealkylated nucleotides.…”

Section: Detection Of Ethyl Ptes In Enu-treated Dnamentioning

confidence: 99%

Analysis of DNA-phosphate adducts in vitro using miniaturized LC-ESI-MS/MS and column switching: Phosphotriesters and alkyl cobalamins

Haglund

Dongen

Lemière

et al. 2004

J Am Soc Mass Spectrom

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Belgium DNA-phosphate adducts are known to be formed by a variety of alkylating agents. Due to little or no repair of DNA-phosphate adducts, these adducts may offer increased possibilities of both identifying and quantifying DNA adducts. The formation of DNA-phosphate adducts leads to a complete esterification of the phosphate group giving rise to a phosphotriester configuration. This work consists of the characterization of ethyl phosphotriesters (Ethyl PTE) using miniaturized LC-ESI-MS/MS and column switching in enzymatic hydrolysate of DNA treated in vitro with the model compound N-ethyl-N-nitrosourea (ENU). In vitro ENU-treated DNA was enzymatically degraded using nuclease P1, phosphodiesterase, and alkaline phosphatase. The use of column switch allowed for large-volume injections, where unmodified nucleosides were discarded in the loading step. The analytes were forward flushed to the analytical column in the eluting step and separated using a linear gradient. Ten different ethyl PTEs (dGpEtdG, dApEtdA, dCpEtdC, TpEtT, dGpEtdA, dGpEtdC, dGpEtT, dApEtdC, dApEtT, and dCpEtT) were characterized by their masses and CAD product ion spectra. Measurements of accurate masses were carried out yielding experimental masses within 5 ppm of the calculated masses for 9 of the 10 ethyl PTEs. For comparison, the enzymatic hydrolysate of ENU-treated DNA was subjected to transalkylation of the DNA-phosphate adducts by cob(I)alamin. Formed ethyl-cobalamins were analyzed according to earlier developed methods. The limit of detection of an alkyl-cobalamin standard and an alkyl PTE standard was 2 fmol and 5 fmol, respectively. (J Am Soc Mass Spectrom 2004, 15, 593-606)

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Analysis of DNA Adducts in DNA Hydrolysates by Capillary Zone Electrophoresis and Capillary Zone Electrophoresis−Electrospray Mass Spectrometry

Cited by 91 publications

References 32 publications

Recent developments in the determination of urinary cancer biomarkers by capillary electrophoresis

Recent developments in the determination of urinary cancer biomarkers by capillary electrophoresis

Toward building a database of bifunctional probes for the MS3D investigation of nucleic acids structures

Analysis of DNA-phosphate adducts in vitro using miniaturized LC-ESI-MS/MS and column switching: Phosphotriesters and alkyl cobalamins

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