Identification of 4-(3-Pyridyl)-4-oxobutyl-2'-deoxycytidine Adducts Formed in the Reaction of DNA with 4-(Acetoxymethylnitrosamino)-1-(3-pyridyl)-1-butanone: A Chemically Activated Form of Tobacco-Specific Carcinogens.

Metabolic activation of the carcinogenic tobacco-specific nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK, 1) and N'-nitrosonornicotine (NNN, 2) results in the formation of 4-(3-pyridyl)-4-oxobutyl (POB)-DNA adducts, several of which have been previously identified both in vitro and in tissues of laboratory animals treated with NNK or NNN. However, 2'-deoxycytidine adducts formed in this process have been incompletely examined in previous studies. Therefore, in this study we prepared characterized standards for the identification of previously unknown 2'-deoxycytidine and 2'-deoxyuridine adducts that could be produced in these reactions. The formation of these products in reactions of 4-(acetoxymethylnitrosamino)-1-(3-pyridyl)-1-butanone (NNKOAc, 3), a model 4-(3-pyridyl)-4-oxobutylating agent, with DNA was investigated. The major 2'-deoxycytidine adduct, identified as its stable cytosine analogue O2-[4-(3-pyridyl)-4-oxobut-1-yl]-cytosine (12), was O2-[4-(3-pyridyl)-4-oxobut-1-yl]-2'-deoxycytidine (13), whereas lesser amounts of 3-[4-(3-pyridyl)-4-oxobut-1-yl]-2'-deoxycytidine (14) and N4-[4-(3-pyridyl)-4-oxobut-1-yl]-2'-deoxycytidine (15) were also observed. The potential conversion of relatively unstable 2'-deoxycytidine adducts to stable 2'-deoxyuridine adducts by treatment of the adducted DNA with bisulfite was also investigated, but the harsh conditions associated with this approach prevented quantitation. The results of this study provide new validated standards for the study of 4-(3-pyridyl)-4-oxobutylation of DNA, a critical reaction in the carcinogenesis by 1 and 2, and demonstrate the presence of previously unidentified 2'-deoxycytidine adducts in this DNA.

Introduction

The tobacco-specific nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK, 1, Scheme ) and N′-nitrosonornicotine (NNN, 2) are among the most important carcinogenic compounds in tobacco products.[1] Both are powerful cancer-causing agents in animal models, NNK targeting mainly the lung in rats, mice, hamsters, and ferrets, whereas NNN causing tumors of the oral cavity and esophagus in rats and respiratory tract tumors in mice, hamsters, and mink.[2] NNK and NNN are considered “carcinogenic to humans” by the International Agency for Research on Cancer.[1] NNK and NNN are typical nitrosamine carcinogens, requiring metabolic activation, generally by cytochrome P450 enzymes, to exert their carcinogenic properties.[2] Methyl hydroxylation of NNK and 2′-hydroxylation of NNN are catalyzed by cytochrome P450s, such as human P450s 2A6, 2A13, and others (Scheme ).[3,4] (There are also other hydroxylation reactions that are not shown here.)[2] The resulting α-hydroxynitrosamines, 4 and 5, are unstable, with lifetimes in the range of seconds, spontaneously decomposing to diazohydroxide 6, which reacts with DNA, producing 4-(3-pyridyl)-4-oxobutyl (POB)-DNA adducts (7).[5] These adducts can be hydrolyzed with acid to release 4-hydroxy-1-(3-pyridyl)-1-butanone (HPB, 8), which has been used to quantify 4-(3-pyridyl)-4-oxobutylation of DNA as well as is an indicator of human exposure to tobacco-specific compounds.[6,7]

Scheme 1

Metabolic Activation of NNK and NNN by P450s and Hydrolysis of NNKOAc by Esterase Yield Reactive Intermediates That Form POB-DNA Adducts

POB-DNA adducts can release HPB upon acid hydrolysis.

Previous studies have characterized and quantified POB-DNA adducts in DNA reacted with the model compound 4-(acetoxymethylnitrosamino)-1-(3-pyridyl)-1-butanone (NNKOAc) (3, Scheme ).[8−10] NNKOAc hydrolysis can be catalyzed by esterase to produce intermediate 4, leading to the identified DNA adducts O2-POB-dThd (9), O6-POB-dGuo (10), 7-POB-Gua (11), and O2-POB-Cyt (12) (Chart ), as well as POB-phosphate adducts.[11] The same adducts have been detected in the tissues of rats treated with NNK or NNN.[12−18] Adduct 12 is produced by neutral thermal hydrolysis (NTH) of its relatively unstable precursor O2-POB-dCyd (13) and is a relatively minor product among these four commonly analyzed DNA adducts; in fact, it was not always observed, possibly due to the instability of 13.[17] These studies also indicated by measurement of released HPB (8) that the identified DNA adducts in rats treated with NNK comprised approximately 45–95% of the total POB-DNA adducts.

Chart 1

Structures of DNA Adducts Discussed in the Text

Therefore, one objective of our research has been to characterize more completely DNA adduct formation from NNK and NNN. In the study reported here, we focused on dCyd adducts. We hypothesized that there may be additional POB-dCyd adducts formed from NNK or NNN but that have not been previously detected due to lack of appropriate standards and/or inherent instability. Thus, the 3-position and exocyclic N4-amino group of dCyd are also potentially reactive sites for 4-(3-pyridyl)-4-oxobutylation, which could result in adducts such as 14 and 15. Additionally, 3-substituted dCyd adducts can undergo facile hydrolysis of the N4-imino group to produce deoxyuridine (dUrd) adducts (e.g., 16).[19−22] Furthermore, we hypothesized that treatment of the adducted DNA with bisulfite could convert the relatively unstable O2-POB-dCyd adduct, 13, to a stable dUrd adduct, 17, as O2-POB-dThd (9), a close structural analogue of 17, is stable. While the bisulfite treatment approach proved to be untenable due to its relatively harsh conditions, the newly synthesized dUrd standards, 16 and 17, were useful in our analysis. Thus, in this study, we focused on the POB-dCyd and -dUrd adducts and report an improved synthesis of adduct 12, the preparation of standards for the identification of dCyd adducts 14 and 15 and dUrd adducts 16 and 17, and analysis of these adducts in DNA reacted with NNKOAc (3).

Results

Starting with commercially available 4-amino-2-chloropyrimidine (18), an efficient synthesis of O2-POB-Cyt (12) was achieved through a reaction with HPB (8), in 44% yield, much higher than that previously reported (Scheme ).[10]

Scheme 2

Synthesis of O2-POB-Cyt (12)

Syntheses of adducts 14–17 were based on the literature procedures for related compounds.[23] Some general procedures are worth noting. All 2′-deoxyribonucleoside intermediates were prepared with the 2′-deoxyribose hydroxyl groups protected as t-butyldimethylsilyl (TBS) derivatives to direct reactivity toward the O2, 3, or N4 position of the base. In an effort to make these reactions as selective as possible, a dithiane-protected HPB intermediate, 26 (Scheme ), or the tosylated version, 22 (Scheme ), was used under basic alkylation conditions in the syntheses. Despite these efforts to increase the yields, the maximum yields of the purified adducts did not exceed about 2%. Deprotection of the TBS intermediates was achieved through a mixture of tetrahydrofuran (THF) and aqueous trifluoroacetic acid (TFA). In the synthesis of 3-POB-dCyd (14) (Scheme ), the Boc group was removed under the same conditions but with a higher concentration of TFA. The dithiane was removed with a mixture of N-chlorosuccinimide (NCS) and AgNO3.

Scheme 5

Preparation of O2-POB-dUrd (17)

NCS, N-chlorosuccinimide.

Scheme 3

Preparation of 3-POB-dCyd (14)

TBSCl, t-butyldimethylsilyl chloride; DMAP, 4-dimethylaminopyridine.

The synthesis of 3-POB-dCyd (14) is summarized in Scheme . This product could only be confirmed by mass spectrometry because it was unstable to HPLC collection, deaminating to 3-POB-dUrd (16) on the column. Therefore, our studies with this adduct were performed using a crude mixture resulting from the final deprotection of 23. However, the protected precursor, 23, was fully characterized, confirming its structure and connectivity. Because the structural similarities between the 3- and N4-POB-dCyd adducts make it difficult to discern the two, two-dimensional (2D) NMR was utilized to determine multiple-bond connectivities. For compound 23, the fully protected precursor to 3-POB-dCyd (14), the first methylene of the pyridyloxobutyl side chain showed equal interactions with C2 and C4 of the pyrimidine ring. In contrast, a 2D-HMBC of N4-POB-dCyd (15) confirmed that alkylation occurred at the N4 position; a strong signal was observed between the first methylene group of the pyridyloxobutyl chain and C4 and C5 of the pyrimidine ring.

The synthesis of N4-POB-dCyd (15) is summarized in Scheme . The protected dCyd, 20, was reacted with the HPB derivative, 22, to yield 24, which was deprotected to give N4-POB-dCyd (15).

Scheme 4

Preparation of N4-POB-dCyd (15)

NCS, N-chlorosuccinimide.

The synthesis of O2-POB-dUrd (17) (Scheme ) utilized cyclic precursor 25, activating the O2 position to alkylation with protected alcohol 26 under basic conditions. When compared to the 13C shifts of 3-POB-dUrd (16), it was clear that 17 had an O-connectivity, as the carbon of the pyridyloxobutyl chain attached to the 2-oxygen atom of the dUrd ring was far downfield at 68 ppm compared with the N-connectivity of 16 at 40.2 ppm.

The preparation of 3-POB-dUrd (16) (Scheme ) followed the same basic strategy used for 3-POB-dCyd (14), except that 16 was stable and readily isolable, in contrast to 14.

Scheme 6

Preparation of 3-POB-dUrd (16)

TBSCl, t-butyldimethylsilyl chloride; TBAF, tetrabutylammonium fluoride.

Compounds 12 and 14–17 were subjected to acid, base, and neutral thermal stability tests. O2-POB-Cyt (12) was unstable to basic conditions; 3-POB-dCyd (14) partially degraded when heated or subjected to HPLC analysis; and O2-POB-dUrd (17) was unstable to pH extremes. Otherwise, these compounds were reasonably stable under acidic, basic, and NTH conditions.

O2-POB-Cyt (12) was the major dCyd-related adduct observed in the reaction of calf thymus DNA with NNKOAc (3) (Table and Figure ). The levels of 3-POB-dCyd (14) and N4-POB-dCyd (15) were lower. When the reaction mixture was subjected to NTH at 100 °C for 1 h, the amount of 12 increased, consistent with previous results.[10,12] After NTH, 3-POB-dCyd (14) was no longer detected but N4-POB-dCyd (15) was still observed. No POB-dUrd adducts were detected.

Table 1

Levels of POB-DNA Adducts of dCyd and Cyt in Reactions of Calf Thymus DNA with NNKOAc (3)a

	levels (fmol/mg DNA)
adduct	EH	NTH + EH
O2-POB-Cyt (12)	26 300	64 200
3-POB-dCyd (14)	1820	ND
N4-POB-dCyd (15)	1990	3050

LC–ESI-MS/MS monitoring was carried out at m/z 375.1 → 259.1, m/z 375.1 → 148.1, and m/z 259.1 → 148.1 for adducts 12, 14, and 15 and m/z 376.1 → 260.1, m/z 376.1 → 148.1, and m/z 260.1 → 148.1 for dUrd adducts 16 and 17. Adduct levels are expressed in fmol adduct/mg DNA and represent the average of two trials. EH, enzyme hydrolysis; NTH + EH, enzyme hydrolysis followed by 1 h NTH at 100 °C; ND, not detected.

Figure 1

LC–MS/MS analysis of POB-DNA adducts for m/z 259.1 → 148.1. (A) Calf thymus DNA exposed to NNKOAc and subjected to enzymatic hydrolysis; (B) synthetic N4-POB-dCyd (15); (C) synthetic 3-POB-dCyd (14); (D) synthetic O2-POB-Cyt (12). Approximately 50% of the signal from adducts 14 and 15 exhibit in-source fragmentation and loss of the 2′-deoxyribose moiety.

With respect to the proposed bisulfite treatment of DNA, O2-POB-Cyt (12) was not stable to the basic DNA denaturation conditions and 3-POB-dCyd (14) converted to 3-POB-dUrd (16). The results of the experiment in which DNA was denatured with base and then treated with bisulfite are illustrated in Figure . 3-POB-dUrd (16) was detected, and 4-POB-dCyd (15) was also observed, but there was no evidence for O2-POB-dUrd (17). Quantitation was not feasible due to extensive degradation of the internal standard, [pyridine-D4]O2-POB-dThd, under the reaction conditions.

Figure 2

LC–MS/MS analysis of bisulfite-treated POB-DNA. (A) DNA exposed to NNKOAc and subjected to base denaturation, bisulfite treatment, and enzymatic hydrolysis; (B) synthetic 3-POB-dUrd (16); (C) synthetic O2-POB-dUrd (17). N4-POB-dCyd (15) was also observed but is not shown.

Discussion

The results of this study provide a more complete picture of dCyd adduct formation in the reaction of NNKOAc with DNA. Our results indicate that O2-POB-dCyd (13), isolated and analyzed as O2-POB-Cyt (12), is the major dCyd adduct formed in these reactions. Considerably lower amounts of 3-POB-dCyd (14) and N4-POB-dCyd (15) were observed, and we were unable to provide conclusive evidence for substantial amounts of dUrd adduct formation in these reactions. In previous studies of cytidine alkylation, reactivity at the O2-position versus the 3- or N4-position was dependent on the alkylating agent;[24] thus, the predominance of O2-POB-dCyd (13) may result mainly from the properties of the POB intermediate, 6. Overall, these results do not indicate that dCyd adduct formation is a quantitatively significant pathway of DNA 4-(3-pyridyl)-4-oxobutylation compared with the previously established reactions, which produce the major products observed in vitro and in vivo, such as 7-POB-Gua (11) and O2-POB-dThd (9).

Although our results do not contribute significantly to the identification of any major and previously unknown DNA adduct formed in 4-(3-pyridyl)-4-oxobutylation reactions using NNKOAc, we were able to achieve and/or improve the preparation of five relevant DNA adducts: O2-POB-Cyt (12), 3-POB-dCyd (14), N4-POB-dCyd (15), O2-POB-dUrd (17), and 3-POB-dUrd (16), four of which are novel. O2-POB-Cyt (12) has been previously synthesized by NTH of O2-POB-dCyd (13), which results from the alkylation of dCyd with NNKOAc (3) in very low yields.[10] Here, by utilizing commercially available 4-amino-2-chloropyrimidine (18) and reacting it with HPB (8), a 44% yield was achieved in a one-step synthesis. The synthesis of 3-POB-dCyd (14) posed a stability problem. The deprotected adduct, 14, readily deaminated to 3-POB-dUrd (16) during the HPLC purification process, partially confirming our hypothesis that the POB-dUrd adducts were more stable and therefore potentially more easily detected than the POB-dCyd adducts. O2-POB-dUrd (17) was synthesized in a selective manner using a cyclic dUrd precursor, 25, and reacting with the protected dithiane, 26 (Scheme ), to yield the O2 adduct exclusively. These new standards will be useful in future investigations of DNA adduct formation in laboratory animals and humans exposed to NNK and NNN.

The bisulfite treatment approach initially appeared attractive for the conversion of potentially unstable O2-POB-dCyd adducts (13) to stable O2-POB-dUrd adducts (17), particularly in view of the established stability of O2-POB-dThd (9), a major DNA adduct of NNK and NNN in the tissues of rats treated with these carcinogens. Bisulfite sequencing is a well-studied reaction that is utilized extensively in the methylation analysis of dCyd. Bisulfite treatment only deaminates unmethylated dCyd, converting it into dUrd. This modified DNA is then subjected to PCR, where methylated dCyd is amplified as dCyd but dUrd is amplified as dThd. This allows one to determine the location of methylated dCyd in a strand of DNA. This is a very efficient reaction that takes very little DNA, as low as nanogram amounts, but bisulfite conditions are also very harsh and can degrade as much as 95% of a DNA sample.[25,26] We were unable to identify bisulfite treatment conditions that did not degrade DNA or our internal standard during the proposed conversion of O2-POB-dCyd (13) to O2-POB-dUrd (17) and thus had to abandon this approach, although we did observe 3-POB-dUrd (16) in these reactions (Figure ).

In summary, we report a more complete analysis of adduct formation with dCyd during 4-(3-pyridyl)-4-oxobutylation of DNA by intermediates formed in the metabolic activation of the tobacco-specific carcinogens NNK and NNN. Using newly prepared synthetic standards encompassing potential reactions with dCyd and possible conversion of these to dUrd adducts, we demonstrate that 3-POB-dCyd (14) and N4-POB-dCyd (15) are relatively minor products of these reactions compared with the previously identified O2-POB-Cyt (12), a thermal hydrolysis product of O2-POB-dCyd (13).

Experimental Procedures

Chemicals and Reagents

HPB (8),[27] NNKOAc (3),[28] 2′-deoxy-3′,5′-bis-O-(t-butyldimethylsilyl)cytidine (20),[29] 3-[2-(3-pyridyl)-1,3-dithian-2-yl]propan-1-ol (26),[30,31] and 2′-deoxy-3′,5′-bis-O-[t-butyldimethylsilyl]-uridine (29)[32] were synthesized as reported previously. Phosphodiesterase II, micrococcal nuclease, and calf thymus DNA were purchased from Worthington. Unless otherwise noted, all other chemicals were purchased from Sigma-Aldrich. Accurate masses were obtained on an Orbitrap Fusion Tribrid instrument (Thermo Scientific). UV spectra were recorded for a 15 mM NH4OAc/MeCN mixture on an Agilent 1100 Series LC-UV. NMR studies were performed on a 500 MHz Bruker spectrometer equipped with a Bruker Avance IIIHD console using a 5 mm probe or a 700 MHz Bruker UltraShield using a 1.7 mm CryoProbe. Submilligram yields were calculated by quantitative NMR.[33]

General Methods

Removal of the Dithiane Protecting Group

This was adapted from a published procedure.[23] The reactants were dissolved in MeCN (65 mM) and stirred at room temperature. Separately, N-chlorosuccinimide (NCS, 1 equiv) and AgNO3 (1 equiv) were weighed and dissolved in 4:1 MeCN/H2O (200 mM), which was added to the reaction mixture. This was stirred at room temperature for 30 min, followed by the addition of 0.1 mL each of saturated NaCl, Na2SO3, and Na2CO3, and the mixture was allowed to stir at room temperature for an additional 20 min. MeCN was removed in vacuo, and the remaining aqueous solution was filtered through a preconditioned (washed with 1 mL MeOH, followed by 2 × 1 mL distilled H2O washes) 30 mg Strata-X 33 μm cartridge (Phenomenex) and washed twice with 1 mL H2O, and the analytes were eluted in 1.5 mL MeOH.

Removal of TBS and Boc Protecting Groups

For TBS removal, the reactants were dissolved in 2:1:1 THF/TFA/H2O (100 mM) for 60 min at room temperature. For removal of Boc, a mixture of 8:20:1 THF/TFA/H2O was used. Saturated NaHCO3 (5 volume equiv) was added and stirred for an additional 20 min. THF was removed in vacuo, and the remaining aqueous layer was loaded on a preconditioned (washed with 6 mL MeOH, followed by 2 × 6 mL H2O washes) 200 mg Strata-X 33 μm cartridge (Phenomenex) and washed twice with 6 mL H2O, and the analytes were eluted in 6 mL MeOH.

Purification of Analytical Standards

Purification was carried out using a Luna 5 μm C18, 100 Å, 250 × 10 mm2 preparatory column (Phenomenex) with a linear gradient and a 3 mL/min flow rate. The initial composition of the eluents was 85% A, and it decreased to 76.5% A over 12 min, where A was H2O and B was MeCN. Analytes were collected between 9 and 11 min, concentrated, and reinjected onto a Luna 5 μm C18, 100 Å, 250 × 4.6 mm2 analytical column (Phenomenex). A linear gradient and a 1 mL/min flow rate were used, with an initial composition of 95% A, which was decreased to 50% A over 40 min.

O2-[4-(3-Pyridyl)-4-oxobut-1-yl]cytosine (O2-POB-Cyt, 12)

In a 5 mL round-bottom flask, HPB (2, 105.8 mg, 0.51 mmol) was dissolved in 1.0 mL of THF. NaH (60% immersion in oil, 20.8 mg, 0.52 mmol) was slowly added. The reactants were stirred at room temperature for 20 min. 4-Amino-2-chloropyrimidine (18, 25.1 mg, 0.19 mmol) was dissolved in 0.5 mL of THF and slowly added to the flask. The flask was fitted with a jacketed condenser, and the mixture was heated under reflux at 70 °C overnight. The reaction mixture was then dissolved in 2 mL H2O and extracted three times with CHCl3, and the CHCl3 extracts were dried over Na2SO4, filtered, and concentrated to dryness. A Florisil plug was eluted with EtOAc to remove unreacted HPB; then, the product was purified by HPLC as described, with a yield of 21.6 mg (0.084 mmol, 44%). The spectral data matched those reported previously.[10]

3-[4-(3-Pyridyl)-4-oxobut-1-yl]-2′-deoxycytidine (3-POB-dCyd, 14)

Compound 23 was deprotected using the procedures outlined above. These reactions were monitored by HPLC–MS/MS. Purification was attempted by HPLC; however, the major product isolated was the deaminated 3-POB-dU analogue, 16, and could not be fully characterized by NMR. HRMS calcd for C18H22N4O5•H+, 375.1663; found, 375.1672. UV: 229, 268.

N4-[4-(3-Pyridyl)-4-oxobut-1-yl]-2′-deoxycytidine (N4-POB-dCyd, 15)

3′,5′-bis-O-t-Butyldimethylsilyl-2′-deoxycytidine[29] (14.1 mg, 0.030 mmol) was dissolved in 0.1 mL dimethylformamide (DMF). NaH was added (60% in oil, 3.3 mg, 0.08 mmol), and the reaction mixture was kept at room temperature for 20 min. A solution of 3-[2-(pyridin-3-yl)-1,3-dithian-2-yl]propyl 4-methylbenzenesulfonate (22) (10.5 mg, 0.026 mmol) in 0.14 mL of DMF was added. The reaction mixture was capped, sealed with parafilm, and stirred overnight at 37 °C. DMF was removed in vacuo, and the residue was taken up in H2O and extracted three times with CH2Cl2. The combined organic layers were washed with brine, dried over Na2SO4, filtered, and concentrated in vacuo. This crude product was then desilylated using the general protocol outlined above. The products were concentrated in vacuo, and the dithiane was removed using the general protocol to give crude 15, which was purified as described in the general methods. Isolated, 208 μg (0.55 μmol, 1.8% overall). 1H NMR (500 MHz, methanol-d4): δ 9.12 (s, 1H, H2-pyridyl), 8.74 (d, J = 4.3 Hz, 1H, H6-pyridyl), 8.39 (d, J = 7.4, 1H, H4-pyridyl), 7.88 (d, J = 7.5 Hz, 1H, H6-pyrimidyl), 7.58 (dd, J = 7.6, 5.4 Hz, 1H, H5-pyridyl), 6.25 (t, J = 6.7 Hz, 1H, H1′), 5.83 (d, J = 7.6 Hz, 1H, H5-pyrimidyl), 4.38–4.35 (m, 1H, H3′), 3.93 (q, J = 3.6 Hz, 1H, H4′), 3.80 (dd, J = 11.7, 3.1 Hz, 1H, H5′), 3.73 (dd, J = 12.5, 3.5 Hz, 1H, H5″), 3.50 (t, J = 7.1 Hz, 2H, NCH2), 3.17 (t, J = 7.3 Hz, 2H, CH2CH2CO), 2.36–2.32 (m, 1H, H2′), 2.15–2.11 (m, 1H, H2″), 2.03–2.01 (m, 2H, CH2CH2CO). 13C NMR (175 MHz methanol-d4): δ 198.8 (CH2CO), 164.0 (C4-pyrimidyl), 157.5 (C2-pyrimidyl), 151.8 (C6-pyridyl), 148.1 (C2-pyridyl), 139.2 (C6-pyrimidyl), 136.0 (C4-pyridyl), 136.0 (C3-pyridyl), 123.4 (C5-pyridyl), 95.1 (C5-pyrimidyl), 87.4 (C4′), 85.6 (C1′), 70.4 (C3′), 61.3 (C5′), 40.7 (C2′), 39.4 (NCH2), 35.7 (CH2CO), 22.8(CH2CH2CO). HRMS calcd for C18H22N4O5•H+, 375.1663; found, 375.1660. UV: 227, 270.

O2-[4-(3-Pyridyl)-4-oxobut-1-yl]-2′-deoxyuridine (O2-POB-dUrd, 17)

This procedure was adapted from the preparation of the thymidine analogue.[23] A solution of 3-[2-(3-pyridyl)-1,3-dithian-2-yl]propan-1-ol (26) in DMF (48.2 mg, 0.16 mmol, 30 mM) was flushed with N2. To it, 20.5 mg of NaH (60% in oil, 0.51 mmol) was added, and the reaction mixture was stirred at room temperature for 30 min. Then, 2,5′-anhydro-2′-deoxyuridine (25, 20.8 mg, 0.10 mmol) was added, the reaction mixture was flushed again with N2, capped, sealed with parafilm, and stirred at 37 °C for 72 h. DMF was then removed under vacuum, and excess starting materials were removed by passage through a silica plug eluted with 4:1 CHCl3/MeOH. This mixture was then treated using the general protocol for removal of the dithiane group, and the product was purified by HPLC as in the general methods, 224 μg, 0.60 μmol, 0.6%. 1H NMR (700 MHz, methanol-d4): δ 9.16 (d, J = 1.9 Hz, 1H, H2-pyridyl), 8.75 (dd, J = 4.9, 1.5 Hz, 1H, H6-pyridyl), 8.44 (dt, J = 1.9, 7.8 Hz, 1H, H4-pyridyl), 8.22 (d, J = 7.8 Hz, 1H, H6-pyrimidyl), 7.60 (dd, J = 8.1, 5.0 Hz, 1H, H5-pyridyl), 6.25 (t, J = 6.6 Hz, 1H, H1′), 6.04 (d, J = 7.8 Hz, 1H, H5-pyrimidyl), 4.58 (8, J = 5.3 Hz, 2H, CH2CH2CO), 4.41 (dt, J = 6.5, 3.4 Hz, 1H, H3′), 3.99 (q, J = 3.5 Hz, 1H, H4′), 3.82 (dd, J = 12.1, 3.2 Hz, 1H, H5′), 3.75 (dd, J = 12.1, 3.7 Hz, 1H, H5″), 3.32–3.30 (m, 2H, OCH2), 2.41 (ddd, J = 13.7, 6.2, 3.9 Hz, 1H, H2′), 2.30–2.26 (m, 3H, H2′, and CH2CH2CO). 13C NMR (175 MHz methanol-d4): δ 198.0 (CH2CO), 173.7 (C4-pyrimidyl), 156.0 (C2-pyrimidyl), 152.0 (C6-pyridyl), 148.2 (C2-pyridyl), 139.5 (C6-pyrimidyl), 136.0 (C4-pyridyl), 132.3 (C3-pyridyl), 123.8 (C5-pyridyl), 106.6 (C5-pyrimidyl), 88.0 (C4′), 86.7 (C1′), 70.2 (C3′), 68.2 (NCH2), 61.0 (C5′), 40.5 (C2′), 34.3 (CH2CO), 22.0(CH2CH2CO). HRMS calcd for C18H22N3O6•H+, 376.1503; found, 376.1503. UV: 227, 257.

3-[4-(3-Pyridyl)-4-oxobut-1-yl]-2′-deoxyuridine (3-POB-dUrd, 16)

Compound 31 was deprotected using the general procedure outlined above and purified by HPLC as in the general methods, with a yield of 130 μg (0.346 μmol, 5%). 1H NMR (700 MHz, methanol-d4): δ 9.10 (d, J = 2.1 Hz, 1H, H2-pyridyl), 8.74 (dd, J = 4.9, 1.2 Hz, 1H, H6-pyridyl), 8.37 (dt, J = 8.0, 1.9 Hz, 1H, H4-pyridyl), 8.00 (d, J = 8.2 Hz, 1H, H6-pyrimidyl), 7.59 (dd, J = 7.9, 4.9 Hz, 1H, H5-pyridyl), 6.24 (t, J = 6.6 Hz, 1H, H1′), 5.75 (d, J = 8.1 Hz, 1H, H5-pyrimidyl), 4.39 (dt, J = 6.3, 3.2 Hz, 1H, H3′), 4.07 (t, J = 6.6 Hz, 2H, NCH2), 3.94 (dd, J = 7.1, 3.5 Hz, 1H, H4′), 3.80 (dd, J = 12.1, 3.3 Hz, 1H, H5′), 3.73 (dd, J = 12.0, 3.8 Hz, 1H, H5″), 3.15 (t, J = 6.7 Hz, 2H, CH2CH2CO), 2.31–2.28 (m, 1H, H2′), 2.23–2.19 (m, 3H, H2″), 2.13–2.10 (m, CH2CH2CO). 13C NMR (125 MHz methanol-d4): δ 199.0 (CH2CO), 164.0 (C4-pyrimidyl), 153.3 (C6-pyridyl), 151.0 (C2-pyrimidyl), 149.3 (C2-pyridyl), 140.6 (C6-pyrimidyl), 136.8 (C4-pyridyl), 133.0 (C3-pyridyl), 125.1 (C5-pyridyl), 100.1 (C5-pyrimidyl), 88.6 (C4′), 87.7 (C1′), 70.5 (C3′), 61.1 (C5′), 40.4 (NCH2), 40.0 (C2′), 36.0 (CH2CO), 21.3 (CH2CH2CO). HRMS calcd for C18H22N3O6•H+, 376.1503; found, 376.1499. UV: 227, 265.

2′-Deoxy-4-[(1,1-dimethylethoxy)carbonyl]-3′,5′-bis-O-(t-butyldimethylsilyl)cytidine (21)

A solution of 2′-deoxy-[3′,5′-bis-O-(t-butyldimethylsilyl)]cytidine[29] (20, 87.6 mg, 0.192 mmol), DMAP (23.8 mg, 0.192 mmol), and triethylamine (27 μL, 0.192 mmol) in 1.5 mL of CH2Cl2 was stirred at room temperature. Boc anhydride (63 μL, 0.275 mmol) was added, the reaction mixture was stirred for 5 h at room temperature and concentrated in vacuo, and the product was purified on silica gel with elution by 1:1 hexane/ethyl acetate, with a yield of 58.6 mg (0.105 mmol, 55%). 1H NMR (500 MHz; CDCl3): δ 8.30 (d, J = 6.9 Hz, 1H, H6-pyrimidyl), 7.50 (br.s., 1H, NH), 7.13 (d, J = 6.9 Hz, 1H, H5-pyrimidyl), 6.24 (t, J = 5.7 Hz, 1H, H5′), 4.38 (q, J = 5.3 Hz, 1H, H3′), 3.95–3.93 (m, 2H, H4′ and H5′), 3.80–3.75 (m, 1H, H5″), 2.54–2.46 (m, 1H, H2′), 2.14–2.07 (m, 1H, H2″), 1.51 (s, 9H, OC(CH3)3), 0.90 (d, J = 26.9 Hz, 18H, [SiC(CH3)3]2), 0.14–0.02 (m, 12H, [Si(CH3)2]2).

3-[2-(Pyridin-3-yl)-1,3-dithian-2-yl]propyl 4-methylbenzenesulfonate (22)

The alcohol 3-[2-(3-pyridyl)-1,3-dithian-2-yl]propan-1-ol (26, 0.535 g, 2.1 mmol) in 6 mL of CH2Cl2 was added to a round-bottom flask and cooled to 0 °C. Triethylamine (0.636 g, 6.3 mmol) was added. p-Toluenesulfonyl chloride (0.504 g, 2.6 mmol) was dissolved in 4 mL of CH2Cl2, and the solution was added dropwise to the reaction mixture. The mixture was stirred overnight while warming to room temperature and then washed with 20 mL of distilled H2O. The organic layer was removed, and the aqueous layer was extracted twice with CH2Cl2. The organic layers were combined and washed with brine, dried over MgSO4, filtered, and evaporated to dryness. The product was purified by flash chromatography on silica with elution by EtOAc, with a yield of 0.429 g (1.05 mmol, 50%). 1H NMR (500 MHz; CDCl3): δ 9.10 (d, J = 2.0 Hz, 1H, H2-pyridyl), 8.55 (dd, J = 4.7, 0.9 Hz, 1H, H6-pyridyl), 8.22 (dt, J = 8.1, 1.8 Hz, 1H, H4-pyridyl), 7.75 (d, J = 8.2 Hz, 2H, (=CH)2), 7.39–7.32 (m, 3H H5-pyridyl, (=CH)2), 3.95 (t, J = 6.1 Hz, 2H, CH2O), 2.73–2.61 (m, 4H, (SCH2)2), 2.46 (s, 3H, CH3), 2.04–1.91 (m, 4H, CCH2, (CH2)2CH2), 1.69–1.63 (m, 2H, CH2CH2CH2O). 13C NMR (125 MHz, CDCl3, HSQC data): δ 149.8 (C2-pyridyl), 148.0 (C6-pyridyl), 137.1 (C4-pyridyl), 129.6 (2C, (=CH)2), 127.6 (2C, (=CH)2), 123.4 (C5-pyridyl), 69.6 (CH2CH2O), 40.8 (CCH2CH2), 27.1 (2C, SCH2)2CH2), 24.6 (SCH2)2CH2), 23.6 (CCH2CH2CH2O), 21.7 (CH3). Quaternary carbon was not observed.

3-[3-[2-(3-Pyridyl)-1,3-dithian-2-yl]propyl]-2′-deoxy-N4-[(1,1-dimethylethoxy)carbonyl]-3′,5′-bis-O-(t-butyl-dimethylsilyl)cytidine (23)

To a solution of 21 (58.6 mg, 0.11 mmol) in 0.35 mL of DMF was added NaH (60% in oil, 8.8 mg, 0.22 mmol), and the mixture was allowed to stir 20 min at 37 °C. A solution of 22 (37.7 mg, 0.09 mmol) in 0.2 mL of DMF was then added; the reaction flask was capped and allowed to stir at 37 °C overnight. DMF was then removed in vacuo, and the reaction mixture was redissolved in H2O and extracted three times with CH2Cl2, and the organic layers were combined and washed with brine, dried over Na2SO4, filtered, and concentrated in vacuo. Excess starting materials were removed by chromatography on silica, with elution by 1:1 hexane/ethyl acetate, giving crude 23. 1H NMR (500 MHz; CDCl3): δ 8.80 (s, 1H, H2-pyridyl), 8.58 (d, J = 0.4 Hz, 1H, H6-pyridyl), 7.93 (d, J = 8.3 Hz, 1H, H4-pyridyl), 7.60 (d, J = 8.3 Hz, 1H, H6-pyrimidyl), 7.39–7.37 (m, 1H, H5-pyridyl), 6.25 (t, J = 6.0 Hz, 1H, H1′), 6.09 (d, J = 8.2 Hz, 1H, H5-pyrimidyl), 4.42–4.40 (m, 1H, H3′), 3.98–3.87 (m, 4H, H4′, H5′, NCH2CH2), 3.77–3.75 (m, 1H, H5″), 2.78–2.58 (m, 4H, C(SCH2)2CH2), 2.33–2.28 (m, 1H, H2′), 2.15–2.09 (m, 2H, NCH2CH2CH2C), 2.05–1.96 (m, 3H, H2″ and C(SCH2)2CH2), 1.72–1.65 (m, 2H, NCH2CH2), 1.57–1.37 (m, 9H, COC(CH3)3), 0.97–0.82 (m, 18H, (SiC(CH3)3)2), 0.14–0.01 (m, 12H, (Si(CH3)2)2). 13C NMR (125 MHz, CDCl3) 155.2 (C4-pyrimidyl), 149.4 (C2-pyrimidyl), 148.7 (C6-pyridyl), 147.6 (C2-pyridyl), 141.0 (2C, C3-pyridyl, and NCOC(CH3)3), 135.6 (C4-pyridyl), 134.7 (C6-pyrimidyl), 123.4 (C5-pyridyl), 97.33 (C5-pyrimidyl), 87.2 (C4′), 85.4 (C1′), 80.0 (NCOC(CH3)3), 70.6 (C3′), 62.2 (C5′), 55.7 (C(SCH2)2), 42.0 (NCH2CH2CH2C), 41.6 (2C, C2′, NCH2CH2CH2C), 28.5 (3C, COC(CH3)3), 27.4 (2C, C(SCH2)2CH2), 25.9 (6C, Si(C(CH3)3)2), 24.7 (C(SCH2)2CH2), 21.8 (NCH2CH2CH2C), 18.0 (2C, (SiC(CH3)3)2), −5.0 (4C, (Si(CH3)2)2).

2,5′-Anhydro-2′-deoxyuridine (25)

This was prepared following a procedure designed for the thymidine analogue.[23] Briefly, 5′-O-p-tosyl-2′-deoxyuridine[34] (55.4 mg, 0.145 mmol) was weighed into a 100 mL round-bottom flask and dissolved in 60 mL of MeCN (2 mM). 1,8-Diazabicycloundec-7-ene (31.2 mg, 0.205 mmol) was dissolved in 3 mL of MeCN and then added dropwise to the reaction mixture over 15 min. The reaction flask was then fitted with a reflux condenser, and the mixture was heated under reflux at 88 °C for 2 h. The mixture was then concentrated in vacuo to dryness, and the product was semipurified by flash chromatography on silica with elution by 4:1 CHCl3/MeOH, with a yield of 44.3 mg (0.12 mmol, 80%, some pTsOH co-elution). 1H NMR (500 MHz; D2O): δ 7.82 (d, J = 7.6 Hz, 1H, H6), 6.14 (d, J = 7.4 Hz, 1H, H5), 6.06 (dd, J = 8.0, 1.9 Hz, 1H, H1′), 4.74–4.72 (m, 1H, H3′), 4.60 (dd, J = 13.0, 1.6 Hz, 1H, H5′), 4.52 (s, 1H, H4′), 4.24 (dd, J = 13.0, 1.2 Hz, 1H, H5″), 2.62 (ddd, J = 15.8, 6.9, 1.9 Hz, 1H, H2′), 2.45 (ddt, J = 15.8, 8.0, 1.0 Hz, 1H, H2″). 13C NMR (125 MHz): δ 165.9 (C4), 157.7 (C2), 144.9 (C6), 108.3 (C5), 94.6 (C1′), 86.1 (C4′), 75.4 (C5′), 71.7 (C3′), 41.7 (C2′).

3-[3-[2-(3-Pyridyl)-1,3-dithian-2-yl]propyl]-2′-[3′,5′-O-di(t-butyl-dimethylsilyl)]deoxyuridine (30)

The procedure was adapted.[23] 2′-Deoxy-3′,5′-bis-O-[(1,1-dimethylethyl)dimethylsilyl]uridine (29, 142.1 mg, 0.27 mmol) and triphenylphosphine (127.2 mg, 0.49 mmol) were dissolved in 2 mL of anhydrous THF. 3-[2-(3-Pyridyl)-1,3-dithian-2-yl]propan-1-ol (26, 69.3 mg, 0.27 mmol) was dissolved in 0.5 mL of anhydrous THF and added dropwise to the reaction mixture, which was then flushed with N2, capped, and stirred at room temperature for 30 min. DEAD (47.4 mg, 0.27 mmol), dissolved in 0.5 mL of anhydrous THF, was added dropwise to the reaction mixture, which was again flushed with N2, capped, and stirred overnight at room temperature. The reaction mixture was then concentrated in vacuo and purified by column chromatography on silica gel with elution by 7:3 hexane/ethyl acetate. This resulted in 15.4 mg of 30 (0.022 mmol, 7%). 1H NMR (500 MHz; MeOD): δ 9.03 (s, 1H, H2-pyridyl), 8.46 (d, J = 4.7 Hz, 1H, H6-pyridyl), 8.34 (dd, J = 8.2, 1.0 Hz, 1H, H4-pyridyl), 7.88 (d, J = 8.1 Hz, 1H, H6-pyrimidyl), 7.48 (dd, J = 8.1, 4.9 Hz, 1H, H5-pyridyl), 6.19 (t, J = 6.3 Hz, 1H, H1′), 5.70 (d, J = 8.1 Hz, 1H, H5-pyrimidyl), 4.50–4.47 (m, 1H, H3′), 3.96–3.93 (m, 1H, H4′), 3.91 (dd, J = 11.4, 3.0 Hz, 1H, H5′), 3.85–3.80 (m, 3H, H5″ and NCH2CH2), 2.77 (dt, J = 14.5, 3.7 Hz, 2H, C(SCH2)2CH2), 2.67–2.60 (m, 2H, C(SCH2′)2CH2)), 2.34–2.29 (m, 1H, H2′), 2.17 (t, J = 6.7 Hz, 1H, H2″), 2.10–2.07 (m, 2H, CH2CH2CH2C), 2.00–1.90 (m, 2H, C(SCH2)2CH2), 1.64–1.58 (m, 2H, NCH2CH2), 0.95 (d, J = 5.6 Hz, 18H, (SiC(CH3)3)2), 0.14 (bs, 12H, (Si(CH3)2)2). 13C NMR (126 MHz; MeOD): δ 163.4 (C4-pyrimidyl), 150.6 (C2-pyrimidyl), 149.4 (C2-pyridyl), 147.2 (C6-pyridyl), 138.9 (C6-pyrimidyl), 138.5 (C3-pyridyl), 137.6 (C4-pyridyl), 123.6 (C5-pyridyl), 100.4 (C5-pyrimidyl), 87.8 (C4′), 86.1 (C1′), 71.5 (C3′), 62.3 (C(SCH2)2), 61.2 (C5′), 41.4 (CH2CH2C), 40.8 (C2′), 40.1 (NCH2CH2), 27.0 (2C, C(SCH2)2CH2), 25.0 (3C, SiC(CH3)3), 24.8 (3C, SiC(CH3)3), 24.6 (C(SCH2)2CH2), 22.0 (NCH2CH2), 17.8 (SiC(CH3)3), 17.4 (SiC(CH3)3), −5.88 to −6.77 (4C, (Si(CH3)2)2).

3-[4-(3-Pyridyl)-4-oxobut-1-yl]-2′-(3′,5′-bis-O-[t-butyldimethylsilyl])deoxyuridine (31)

Compound 30 was deprotected using the general procedure outlined above, with a yield of 3.9 mg (0.0065 mmol, 30%). 1H NMR (500 MHz; MeOD): δ 9.09 (d, J = 1.5 Hz, 1H, H2-pyridyl), 8.73 (dd, J = 4.8, 0.8 Hz, 1H, H6-pyridyl), 8.36 (d, J = 8.0 Hz, 1H, H4-pyridyl), 7.91 (d, J = 8.1 Hz, 1H, H6-pyrimidyl), 7.58 (dd, J = 8.0, 5.0 Hz, 1H, H5-pyridyl), 6.18 (t, J = 6.3 Hz, 1H, H1′), 5.70 (d, J = 8.1 Hz, 1H, H5-pyrimidyl), 4.48 (q, J = 4.7 Hz, 1H, H3′), 4.06 (td, J = 6.6, 1.6 Hz, 2H, NCH2CH2CH2), 3.95 (q, J = 2.9 Hz, 1H, H4′), 3.91 (dd, J = 11.4, 3.3 Hz, 1H, H5′), 3.83 (dd, J = 11.4, 2.4 Hz, 1H, H5″), 3.15 (t, J = 6.6 Hz, 2H, CH2CH2CO), 2.30–2.25 (m, 1H, H2′), 2.20–2.15 (m, 1H, H2″), 2.12 (dd, J = 13.4, 6.7 Hz, 2H, CH2CH2CO), 0.95 (d, J = 11.0 Hz, 18H, (C(CH3)3)2), 0.15–0.13 (m, 12H, (Si(CH3)2)2). 13C NMR (125 MHz, MeOD): δ 152.6 (C6-pyridyl), 148.6 (C2-pyridyl), 138.6 (C6-pyrimidyl), 136.1 (C4-pyridyl), 123.8 (C5-pyridyl), 100.2 (C5-pyrimidyl), 87.9 (C4′), 85.7 (C1′), 71.3 (C3′), 62.1 (C5′), 40.6 (C2′), 39.8 (NCH2CH2), 35.5 (CH2CH2C), 24.6 (6C, (SiC(CH3)3)2), 21.1 (NCH2CH2), −5.9 (4C, (Si(CH3)2)2).

Analytical Standards’ Stability

Solutions of the analytical standards were treated with base, acid, and heat to gauge stability. Standards of 12 and 14–17 (50 fmol/μL) were treated with HCl and NaOH separately at a final concentration of 0.1 M. These solutions were incubated at room temperature for 1 h before neutralizing to pH 7. Separate aliquots were incubated for 1 h at 100 °C to determine the thermal stability.

Reaction of NNKOAc with DNA

This was carried out essentially as described previously.[10] Briefly, calf thymus DNA (5.5 mg) was dissolved in 2.5 mL of 0.1 M phosphate buffer, pH 7.0. To this, porcine liver esterase (3.8 mg, 70 U) and NNKOAc (9.2 mg, 35 μmol in 25 μL of methanol) were added, and the reaction was gently agitated at 37 °C for 2 h. The mixture was diluted with 3 mL of H2O and washed twice with 6 mL of CHCl3/isoamyl alcohol (24:1), followed by 6 mL of ethyl acetate. The DNA was precipitated from the aqueous portion by the addition of ethanol, washed with 70% of aqueous ethanol followed by ethanol, and then briefly dried in a stream of N2. A small aliquot was set aside for analysis of the nucleotide content, and the rest was carried forward.

Base Denaturation of Pyridyloxobutylated DNA

Prior to reaction with bisulfite, DNA must be denatured. Aliquots of DNA that had been reacted with NNKOAc (0.9 mg each) and analytical standards 15 (small aliquot), 12, and 16 (30 pmol each, including 2 pmol internal standard [pyridine-D4]O2-POB-dThd) were dissolved in 0.5 mL of distilled H2O, and 5 μL of 10 N NaOH was added to achieve a final concentration of 0.1 N NaOH; the solution was kept at 37 °C for 20 min. A small sample (which included 1 pmol internal standard [pyridine-D4]O2-POB-dThd) was neutralized by the addition of 5 N HCl and set aside for analysis. To the remaining reactions, 1.0 mL of distilled H2O was added and taken immediately forward.

Reactions of Pyridyloxobutylated DNA with Bisulfite

A saturated solution of bisulfite was prepared by adding 6 g of Na2S2O5 to a solution of aqueous 100 mM hydroquinone and 0.4 M NaOH for a total volume of 10.0 mL. Saturated bisulfite solution (1 mL) was added to each DNA aliquot, analytical standard, and one H2O blank (for a total volume of 2.5 mL), and the reaction mixture was stirred at 50 °C overnight, shielded from light. DNA reactions were then desalted on prepacked PD-10 Desalting Columns (GE Healthcare) and eluted into 3.5 mL of distilled H2O. Analytical standards were desalted on a 200 mg Strata-X cartridge using a scaled-up version of the procedure described earlier (4 mL per wash), and analytes were eluted in 4 mL of MeOH. MeOH eluates were evaporated in vacuo, and the reaction mixtures were redissolved in 0.5 mL of distilled H2O. For desulfonation, 53 μL of 10 N NaOH was added to the DNA reaction mixtures and 9 μL was added to the analytical standards, and the reaction mixtures were gently agitated at 37 °C for 20 min. The reaction mixtures were then neutralized by the addition of 5 N HCl, and DNA was precipitated from ethanol and then washed with 70% aqueous ethanol followed by ethanol and then briefly dried in a stream of N2. Analytical standards were purified on 30 mg Strata-X cartridges, as described above. MeOH eluates were concentrated in vacuo and reconstituted in 30 μL of 2% MeCN in 15 mM NH4OAc for analysis.

Enzymatic DNA Hydrolysis

This was performed essentially as described.[35] Briefly, 1 mg of treated DNA aliquots was dissolved in 1.0 mL of 5 mM CaCl2, 10 mM succinic acid buffer, pH 6.5. Internal standard [pyridine-D4]O2-POB-dThd (1 pmol), phosphodiesterase II (250 mU), and micrococcal nuclease (30 U) were added, and the mixture was gently agitated at 37 °C for at least 5 h. Alkaline phosphatase (75 U) was then added, and agitation was continued at 37 °C overnight. The samples were then loaded onto Centrifree 30 kDa MWCO centrifugal filters (Millipore) and centrifuged at 4 °C for 20 min at 4000 rpm. A 10 μL aliquot of each filtrate was removed for dGuo analysis and quantitation by HPLC, and the remaining filtrate was purified by solid-phase extraction on a Strata-x 33 μm polymeric reversed-phase cartridge (30 mg; Phenomenex, Torrance, CA). The cartridge was preconditioned with one 1.0 mL MeOH wash, followed by two 1.0 mL H2O washes. The reaction mixtures were loaded and washed with 1 mL of H2O and 1 mL of 10% (v/v) MeOH sequentially, and the analytes were eluted into 1.0 mL of MeOH. The MeOH eluates were then concentrated in vacuo and reconstituted in 30 μL of 2% MeCN in 15 mM NH4OAc. Adduct formation was normalized to the dGuo content of each sample.[35] Quantitation of dGuo was performed on an Agilent 1100 series HPLC, with a UV diode array detector set at 254 nm. LC was performed on a 0.5 × 250 mm2 Luna C18(2) 5 μm, 100 Å column (Phenomenex), with a linear gradient at 10 μL/min from 5 to 20% MeOH in H2O over 22 min, with subsequent washout and re-equilibration.

DNA Adduct Analysis by LC–MS/MS

The DNA hydrolysates and analytical standard reactions were analyzed for standards 12, 14–17, and internal standard [pyridine-D4]O2-POB-dThd by liquid chromatography–positive electrospray ionization–tandem mass spectrometry (LC–ESI+-MS/MS). LC was carried out on a 0.5 × 150 mm2 Zorbax SB-C18 5 μm column (Agilent, Santa Clara, CA) with a gradient and a flow rate of 15 μL/min. After maintaining the initial conditions at 2% B for 3 min, the composition was increased to 39.1% B from 3 to 20 min, followed by washout and re-equilibration, where solvent A was 15 mM NH4OAc and solvent B was MeCN. MS was performed on a TSQ Quantum Discovery MAX triple quadrupole mass analyzer (Thermo Scientific, Waltham, MA). Selected reaction monitoring mass transitions were m/z 375.1 → 259.1, 375.1 → 148.1, and 259.1 → 148.1 for dC-POB adducts. Transitions monitored for dU-POB adducts were m/z 376.1 → 260.1, 376.1 → 148.1, and 260.1 → 148.1. For internal standard [pyridine-D4]O2-POB-dThd, the transition m/z 394.1 → 152.1 was monitored, as well as m/z 390.1 → 148.1, corresponding to the nondeuterated O2-POB-dThd (9). The collision energy was 23 eV and scan width was 0.4 amu. Calibration curves that covered the range observed in the in vitro DNA samples for 12, 15, and 16 were used for quantitation. As we were unable to purify 3-POB-dCyd (14) fully, the calibration curve for N4-POB-dCyd (15) was applied to quantify the formation of 14 in vitro, making the assumption that the LC–MS/MS response for 14 was similar to that for 15. The calibration curves for all adducts were linear (R2 > 0.998) between 2.5 and 250 fmol on the column, which covered the range observed in the samples. The limit of detection was found to be 1.0 fmol on the column.