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Review
. 2013 Apr 10;113(4):2395-436.
doi: 10.1021/cr300391r. Epub 2013 Feb 26.

Mass spectrometry of structurally modified DNA

Natalia Tretyakova  1 , Peter W Villalta, Srikanth Kotapati
Affiliations
Review

Mass spectrometry of structurally modified DNA

Natalia Tretyakova et al. Chem Rev. .
No abstract available

PubMed Disclaimer

Figures

Figure 1
Figure 1
Central role of DNA adducts in chemical carcinogenesis.
Figure 2
Figure 2
Observed (top) and theoretical (bottom) accurate mass spectra of O6-pyridyloxobutyl-2-deoxyguanosine [O6-POB-dG+H]+. The top spectrum was obtained with an LTQ Orbitrap Velos (Thermo Scientific) operated at a resolution of 60,000. Shown on the bottom is the predicted spectrum generated with Xcalibur Qualbrowser software (Thermo Scientific).
Figure 3
Figure 3
Comparison of “beam-type CAD” (triple quadrupole) and “ion-trap-type CAD” MS/MS spectra of N2-ethyl-2′-deoxyguanosine obtained at increasing collision energy.
Figure 4
Figure 4
MS/MS spectra of unmodified dG and representative dG adducts: N2-ethyl-2′-deoxyguanosine (N2-ethyl-dG), O6-methyl-2-deoxyguanosine (O6-methyl-dG), O6-pyridyloxobutyl-2-deoxyguanosine (O6-POB-dG), and exocyclic crotonaldehyde adduct (CPr-dG).
Figure 5
Figure 5
Chromatograms obtained upon UPLC-MS3 analysis of renal cortex DNA from human subject with a carcinoma of the upper urinary tract along with MS3 fragmentation spectra of dA-AL-II and dA-AL-I. Reprinted with permission from Reference 166. Copyright 2012 American Chemical Society.
Figure 6
Figure 6
Chromatograms obtained upon LC-NSI-HRMS/MS analysis of human leukocyte DNA (129 μg, 12.9 μg on column) containing 59.4 fmol N7-ethyl-Gua /μmol Gua. The relatively higher amount of analyte in this sample allowed for the confirmation of its identity by additional monitoring of the accurate mass of the molecular ion of N7-ethyl-Gua and the internal standard. Panel A shows the result from monitoring of the accurate mass of 7-ethyl-Gua (m/z 180.08799). Panel B shows the result from the monitoring of the accurate mass of [15N5]7-ethyl-Gua (m/z 185.07317). Panel C shows the results from the transition at m/z 180 [M + H]+ → m/z 152.05669 [Gua + H]+ for 7-ethyl-Gua, and panel D shows the corresponding transition m/z 185 [M + H]+ → m/z 157.04187 [Gua + H]+ for the internal standard. Results are shown with a 5 ppm mass tolerance. Reprinted with permission from Reference 66. Copyright 2011 American Chemical Society.
Figure 7
Figure 7
Relationship between detected and added 7-ethyl-Gua. Various amounts of 7-ethyl-Gua were added to calf thymus DNA (0.3 mg, 30 μg on column) and analyzed by the method described in the text; R2 = 0.99. 7-Ethyl-Gua present in the calf thymus DNA was subtracted from each value. Reprinted with permission from Reference 66. Copyright 2011 American Chemical Society.
Figure 8
Figure 8
Diagram of valve positions employed in column switching HPLC-ESI-MS/MS. The sample is loaded onto the trapping column in position A and washed to remove contaminants. In position B, the second pump backflushes the analyte from the trapping column onto the analytical column and into the mass spectrometer.
Figure 9
Figure 9
(A) Simplified illustration showing concentration and flow rate effects on the ESI process. For larger flow rates, which produce larger droplets, analyte surface activity, concentration, and competition from other species can affect overall ionization efficiency, the extent of ionization “suppression”, and quantitation. At sufficiently low flow rates and analyte concentrations, each droplet contains on average less than one analyte molecule, ionization efficiency is 100%, and suppression/matrix effects are eliminated. Reprinted with permission from Reference 59. Copyright 2004 American Chemical Society. (B) Normal flow rate electrospray (top) vs a lower flow rate electrospray (bottom) that produces smaller droplets. By allowing closer proximity to the MS inlet, the lower flow rate electrospray affords more efficient ion introduction. Reprinted with permission from Reference 59. Copyright 2004 American Chemical Society.
Figure 10
Figure 10
Column switching capLC-ESI+-MS/MS analysis of 1,N6-HMHP-dA in liver DNA from a control mouse (A) and a mouse exposed to 200 ppm BD for 2 weeks (B). Dose-dependent formation of 1,N6-HMHP-dA in liver of laboratory mice exposed to increasing concentration of BD by inhalation (C). Reprinted with permission from Reference 26. Copyright 2010 American Chemical Society.
Figure 11
Figure 11
Examples of representative MS/MS spectra of oligonucleotides obtained using an Orbitrap Velos mass spectrometer.
Figure 12
Figure 12
Exonuclease ladder sequencing of a synthetic DNA 18-mer containing site specific O6-Me-dG. Reprinted with permission from Reference 253. Copyright 2010 American Chemical Society.
Figure 13
Figure 13
ILD-MS based mapping of diastereomeric N2-BPDE –dG adducts along DNA sequence: HPLC-ESI-MS/MS traces of N2-BPDE –dG adducts originating from 15N3-labeled guanine (m/z 573.1) and elsewhere in the sequence (m/z 570.1) (A). N2-BPDE –dG distribution along p53 gene-derived DNA duplex as determined by ILD-MS (B). Reprinted with permission from Reference 201. Copyright 2004 American Chemical Society.
Figure 14
Figure 14
HPLC-ESI-MS detection of primers extension products following in vitro replication of DNA template containing 1,N6-HMHP-dA. MS analysis reveals multiple mutated products and -1 deletions.
Figure 15
Figure 15
Persistence of bifunctional DEB-DNA adducts in mouse and rat liver DNA. (A) Female B6C3F1 mice were exposed to 625 ppm BD for 2 weeks, and tissues were collected 2, 72, or 240 h post exposure. (B) Female F344 rats were exposed to 1250 ppm BD for 2 weeks, and tissues were collected 2, 24, 72, or 144 h post exposure. Bis-N7G-BD, N7G-N1A-BD, and 1,N6-HMHP-dA, were quantified by isotope dilution HPLC-ESI-MS/MS analysis of DNA hydrolysates.
Scheme 1
Scheme 1
DNA sites frequently modified by carcinogens and their metabolites.
Scheme 2
Scheme 2
Tandem mass spectrometry scanning modes.
Scheme 3
Scheme 3
Sample processing scheme for HPLC-ESI-MS/MS analysis of DNA adducts.
Scheme 4
Scheme 4
Nomenclature of common ion series observed upon MS/MS sequencing of DNA.
Scheme 5
Scheme 5
Exonuclease ladder sequencing of DNA. In separate experiments, DNA is partially digested with phosphodiesterases I and II to generate two series of DNA fragments, which are analyzed by MALDI-TOF MS. Mass differences between adjacent signals in MALDI-TOF spectra can be used to identify DNA sequence and to detect the presence of endogenous or chemical modifications.
Scheme 6
Scheme 6
Strategy for quantitation of dG adducts at specific sites within DNA by stable isotope labeling of DNA – mass spectrometry (ILD-MS) approach.
Scheme 7
Scheme 7
MS/MS identification of in vitro replication products of adduct-containing DNA following site-specific cleavage with UDG/piperidine.
Chart 1
Chart 1. Structures of representative DNA adducts
a1,N6-etheno-2′-deoxyadenosine (εAdo); 3,N4-etheno-2′-deoxycytosine (εdCyd); O6-methyl-2′-deoxyguanosine (O6-Me-dG); N7-ethylguanine (N7-Me-G); 8-oxo-7,8-dihydro-2′deoxyguanosine (8-oxo-dG); 8-oxo-7,8-dihydro-2′deoxyadenosine (8-oxo-dA); N7-ethylguanine (N7-Ethyl-G); 1, 1,N6-(1-hydroxymethyl-2-hydroxypropan-1,3-diyl)-2′-deoxyadenosine (1,N6 -αHMHP-dA); 1,N6-(2-hydroxy-3-hydroxymethyl-propan-1,3-diyl)-2′-deoxyadenosine (1,N6 -γHMHP-dA)
Chart 2
Chart 2. Structures of DNA adducts used for discussion of molecular formula determination.a
aguanine (G); 2′-deoxyguanosine (dG); O6-[4-(3-pyridyl)-4-oxobut-1-yl]guanine (O6-POB-G); O6-[4-(3-pyridyl)-4-oxobut-1-yl]-2′-deoxyguanosine (O6-POB-dG); 7,8,9-trihydroxy-10-(N2-deoxyguanosyl)-7,8,9,10-tretrahydrobenzo[a]pyrene (N2-BPDE-dG)
Chart 3
Chart 3. Structures of DNA adducts used for discussion of nucleobase fragmentation.a
a2′-deoxyguanosine (dG); N2- ethyl-2′deoxyguanosine (N2-Ethyl-dG); N2-[4-(3-pyridyl)-4-oxobut-1-yl]-2′-deoxyguanosine (N2-POB-dG); O6-methyl-2′-deoxyguanosine (O6-Methyl-dG); O6-[4-(3-pyridyl)-4-oxobut-1-yl]-2′-deoxyguanosine (O6-POB-dG); (CPr-dG); N7-ethylguanine (7-Ethyl-G); 8-Hydroxy-2′-deoxyguanosine (8OH-dG)
Chart 4
Chart 4. Structures of DNA adducts highlighted in Section 5.5.a
aN7-(2′-hydroxyethyl)guanine (N7-HEG); 5-hydroxymethyl-2′-deoxyuridine (HmdU); 3,N4-ethenocytosine (εCyt); 7-(1′,2′-dihydroxyheptyl)-3H-imidozo(2,1-i)purine (DHH- εAde); 1,N6-ethenoadenine (εAde); N2,3-ethenoguanine (N2,3-εGua); 1,N2-ethenoguanine (1,N2- εGua); 4-hydroxyestrogen-1-N3-adenine (4-OH-E-1-N3Ade); 1,N6-etheno-2′-deoxyadenosine (εdAdo); 3,N4-etheno-2′-deoxycytidine (εdCyt); 1,N2- etheno-2′-deoxyguanosine (1,N2- εdGuo); O2-ethylthymidine (O2-edT); O4-ethylthymidine (O4-edT); 1-(guan-7-yl)-4-(aden-1-yl)-2,3-butanediol (N7G-N1A-BD); 1,4-bis-(guan-7-yl)-2,3-butanediol (bis-N7G-BD); N2-hydroxymethyl-2′-deoxyguanosine (N2-HOMe-dG); N7-ethylguanine (N7-Ethyl-G); N-(deoxyguanosin-8-yl)-PhIP (C8-dG-PhIP); 10-(deoxyguanosin-N2-yl)-7,8,9-trihydroxy-7,8,9,10-tetrahydrobenzo[a]pyrene (dG-N2-B[a]P); 7-(deoxyadenosin-N6-yl)aristolactam I (dA-AL-I); 7-deoxyguanosin-N2-yl aristolactam I (dG-AL-I)
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