Paulina
Wierzbicka
a,
Hassan
Abdoul-Carime
b and
Janina
Kopyra
*a
aFaculty of Sciences, Siedlce University, 3 Maja 54, Siedlce 08-110, Poland. E-mail: janina.kopyra@uws.edu.pl
bUniversité de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, UMR5306, Villeurbanne F-69622, France
First published on 16th February 2024
5-Fluorouracil is now routinely used in chemo- and radiotherapy. Incorporated within DNA, the molecule is bound to the sugar backbone, forming the 5-fluorouridine sub-unit investigated in the present work. For the clinical usage of the latter, no information exists on the mechanisms that control the radiosensitizing effect at the molecular level. As low energy (< 12 eV) electrons are abundantly produced along the radiation tracks during cancer treatment using beams of high energy particles, we study how these ballistic secondary electrons damage the sensitizing molecule. The salient result from our study shows that the N-glycosidic bonds are principally affected with a cross-section of approximately two orders of magnitude higher than the canonical thymidine, reflecting to some degree the surviving factor of radiation-treated carcinoma cells with and without 5-fluorouracil incorporation. This result may help in the comprehension of the radiosensitizing effect of the fluoro-substituted thymidine in DNA.
Fig. 1 Structure of 5-fluorouridine (5FUrd) (a). The molecule consists of (b) dehydrogenated 5-fluorouracil bound to (c) dehydrogenated ribose (or DNA sugar) via the N-glycosidic bond. |
During radiation therapy, high energy particle beams produce along their tracks various secondary species (e.g., ions and radicals); among them, a large amount of ballistic electrons are produced.7 It is known from simulations and measurements that when considering only a single ionization event per primary particle, the secondary electrons vs energy has a maximum around 9–10 eV.8,9 Subsequent secondary ionization processes can further shift the energy distribution to lower energies. It is now established that these slow particles are capable of damaging DNA in terms of single and double bond breakages10 and more locally they induce the rupture of the N-glycosidic bonds between the nucleobase and the (deoxy)ribose.11 Moreover, substituting the canonical thymine by bromo-containing nucleobases within oligonucleotides sensitizes the modified-DNA strands to the ballistic electrons.12 The fragmentation of halogenated nucleobases by low energy electrons (LEEs) has been explored in the gas phase experiments.13–15 For 5-fluorouracil, it has been observed that electrons induce the fragmentation of the nucleobase into two predominant dissociation channels producing the dehydrogenated nucleobase anion and the OCN− anion species, via resonant processes. The question is whether the fragmentation process reflects these observations when 5FU is bound to the deoxyribose moiety. Indeed, it has been reported that the fragmentation of thymine produces a large variety of anion fragments (i.e., 9 fragment species),16 while once bound to the ribose moiety, the fragmentation of thymidine (Thd) by electrons in the same energy range generates only three fragments including the dehydrogenation of the nucleoside and the cleavage of the N-glycosidic bond with an excess electron residing in the thymine or sugar counterparts.17–19 Therefore, it is desirable to investigate the collision of 5FUrd for comparison with not only 5FU13–15 but also with Thd17–19 to deepen the understanding of the fragmentation mechanism and potentially the beneficial use of this molecule for the treatment of radiation therapy.
The present study aims to investigate the interaction of low energy (< 12 eV) electrons with 5-fluorouridine. We show the ability of such slow particles to fragment the molecule at energies as low as near 0 eV. Various fragmentation channels are observed; however, the three predominant pathways lead to the dehydrogenation of the halogenated nucleoside, the cleavage of the N-glycosidic bond, and the fragmentation of the sugar moiety. For the fragment anions generated through these pathways, we provide the values of the branching ratios and the cross-sections.
Negative ions produced in the reaction area due to collision of electrons with intact molecules were extracted from the interaction zone by a small draw-out-field (< 1 V cm−1) towards the QMA and detected using a single pulse counting technique. Prior to the measurements, the electron energy scale was calibrated by using the SF6 gas flowing through the oven, yielding the well-known SF6−s-wave resonance near zero eV. However, the measurements were performed without the presence of the calibration gas, avoiding potentially unwanted reactions, such as dissociative electron transfer, with the investigated molecules producing an additional signal near 0 eV.22
Fig. 2 Yield function of the (a) dehydrogenated parent anion [5FUrd-H]−, (b) dehydrogenated 5-fluorouracil anion [5FU-H]− produced from the N-glycosidic bond cleavage, and (c) [HCO2]− anion. |
m/z | Anion fragment assessment | Peak position |
---|---|---|
261 | [5FUrd-H]− | 0.01 (14.8) |
1.4 (2.3) | ||
169 | [(5FU-H)C2O]− (F-nucleobase + C2O) | 0.07 (1.8) |
1.5 (57.0) | ||
155 | [(5FU-H)C2H2]− (F-nucleobase + C2H2) | 0.07 (6.5) |
129 | [5FU-H]− | 0.06 (37.4) |
1.2 (40.7) | ||
114 | [C5H6O3]− ⇒ sugar or [C4H2O4]− ⇒ sugar or [FC4O2NH]− ⇒ nucleobase | 0.05 (3.4) |
101 | [C4H5O3]− ⇒ sugar | 0.05 (5.8) |
71 | [C3H3O2]− ⇒ sugar or [C2O2NH]− ⇒ nucleobase | 0.05 (1.7) |
59 | [C2H3O2]− ⇒ sugar | 0.06 (1.6) |
45 | [HCO2]− ⇒ sugar | 0.07 (27.0) |
16 | O− | 7.4 |
9.5 |
The anion yield functions shown in Fig. 2–5 exhibit structures indicating that the fragmentation of 5FUrd is controlled by a resonant process, i.e., dissociative electron attachment (DEA).27 Briefly, the incoming electron is captured in some virtual molecular orbitals (MOs) of the neutral molecule to form a transitory negative ion (TNI). This TNI undergoes dissociation into an anion fragment and a neutral counterpart if the dissociation time is shorter than the electron auto-detachment time (i.e., survival probability). The peak position observed in the anion signal (Table 1) is obtained as a convolution of the electron capture in the resonance state cross-section and the survival probability.25 Four states with a dissociative character (i.e., σ* or π* decaying into σ*) are reported: ∼0.05 eV and ∼1.4 eV for all negative fragments except for the O− anion, which exhibit peak positions at 7.4 eV and 9.5 eV. The very low-energy resonances, typically below ∼4.5 eV (i.e., first electronically excited state), usually arise from the shape resonance or the occupation of virtually unoccupied MOs by the excess electron.28 At higher energies, the core-excited resonance prevails (i.e., excitation of a valence electron to a MO concomitantly to the trapping of the excess electron by the positive core).26 The production of all fragments is likely to arise from the shape resonance, except for the O− anion, which is controlled by the core-excited resonance. The resonance at 7.4 eV has been calculated not only for glucose that partially implicates the σ* character of the C–O bonding of the molecule,29 but also for the canonical nucleobase uracil.30 The resonances below 2 eV, calculated for many nucleobases,31–33 have been suggested to arise from the excess electron captured into a π* orbital for forming the TNI. In particular, for thymidine, the TNI may further decay, via a fast transfer of the additional electron to the ribose (and ultimately to the phosphate) moiety for fragmentation, producing both the dehydrogenated nucleobase and the dehydrogenated ribose anion.14,15,34
The three dominant anion fragments, that is (5FUrd-H)−, (5FU-H)− and HCO2−, deserve particular discussion. For the dehydrogenated 5-flourouridine anion, the loss of a hydrogen atom may arise either from the nucleobase side through N–H or C–H bond cleavage or from the ribose side through C–H or O–H bond rupture. From the electron impact on thymidine,17,18 thymine14,35 and partially deuterated thymine,36 it has been concluded that at electron energies below 2 eV, hydrogen is abstracted from the nitrogen site. Therefore, in the present experiment, the loss of hydrogen must also arise from the nitrogen site of the 5FUrd. The production of the (5FU-H)− anion arises from the rupture of the N-glycosidic bond, as has been reported for thymidine,17,18 2′-deoxy-5-bromouridine,23 and 2′-deoxy-5-fluorocytidine.26 For thymidine, the cleavage of the N–H bond is energetically accessible due to the high electron affinity of the thymine moiety (∼3.6–3.8 eV37) with respect to the typical C–N bond dissociation energy (3.0–3.6 eV).38 The HCO2− anion can be assessed as a carboxylate and/or hydrocarboxyl anion, i.e. HCOO− or HOCO−, respectively. Such an anion must arise from fragmentation of the ribose counterpart via at least a C–O and a C–C bond rupture. The HCOO radical, for which the electron affinity is higher, that is, 3.5 eV,39 than that of the HOCO radical (1.51 eV (cis) and 1.37 eV (trans)),40 is likely to drive the fragmentation process that must operate via complex atom rearrangements. Further fragments are also observed and we tentatively assess the nature of these anions (Table 1), suggesting that they arise mainly from the fragmentation of the sugar moiety. For these fragments listed in Table 1, we refrain from further speculation on the potential mechanisms by which they are produced.
Fig. 2–5 also show that, near 0 eV, molecular fragmentation leads to different competitive channels. By integrating the yield of each fragment near 0 eV, it is possible to estimate the branching ratios for each dissociative channel. The estimates are provided in Table 1 (in parentheses). For instance, three dominant (5FUrd-H)−, (5FU-H)−, and HCO2− anionic fragments represent a total of 79.2% of the all fragmentation channels at this energy (i.e., 14.8%, 37.4% and 27%, respectively). Molecular dissociation can be quantified by the evaluation of the DEA cross-section for each fragmentation channel. In the first approximation, the number of measured ions by our experiment, irrespective to their nature, Nions, can be estimated as: Nions = ε·Ne·(Nmol/V)σ·L, where ε is the detection efficiency (assuming the same for all ions), Ne represents the number of electrons (or current), Nmol/V is the density of the target molecule (proportional to the injected gas pressure), σ is the ion production cross-section and L is the collision length. Thus, the relative fragmentation cross-section can also be estimated by comparing the integrated yield of the negative ion with that of the calibration gas, SF6−, σion/σSF6. We have evaluated the relative cross-sections for the production of the (5FUrd-H)−, (5FU-H)−, and HCO2− fragment anions to be 0.0027, 0.075 and 0.055, respectively, within 30% accuracy from the reproducibility of our measurements. Knowing the cross-section for the formation of the SF6− anion at 420 K (c.a., ∼ 9 × 10−14 cm2),41,42 the DEA cross-sections for the production of these anions can be derived to be 2.4 × 10−15 cm2, 6.8 × 10−15 cm2 and 5.0 × 10−15 cm2, respectively. For comparison, the cross-section for the N-glycosidic bond dissociation of thymidine producing the dehydrogenated thymine anion has been estimated to be 4 × 10−17 cm2 (430 K).14 Here, the cross-section for the (5FU-H)− anion production estimated at 433 K (c.a., 1.1 × 10−15 cm2 within 50% accuracy) is about 170 times higher than that for thymidine. It should be noted that since the local temperature in the vicinity of the ionizing track may locally increase dramatically above 400 K,43 the present measurements may be relevant to the evaluation of the local damage of the nucleoside. Finally, the fragmentation cross-section is temperature dependent and may possibly drop by two orders of magnitude at biologically relevant temperatures.44
The generated mobile hydrogen radical concomitantly to the formation of the (5FUrd-H)− anion may further react with the neighboring molecules, while the damage at the sugar moiety may result in a scission of the DNA strand.45 It is established that the formation of the reactive sugar radical favors the DNA strand break.46,47
The present work also shows that the cross-section for the cleavage of the N-glycosidic bond in 5FUrd, induced by LEEs, is found to be approximately two orders of magnitude higher than that in thymidine, providing valuable information for radiosensitization observation of a halogen surrogate of the canonical thymine. Indeed, this value of ratio is high, but not surprising, and it reflects to some degree the surviving fraction measured for radiation treated carcinoma cells with and without 5FU substitution,48 assuming the different experimental conditions and the systems studied, that is, the cell vs. model subunit of DNA. For example, it has been shown that 60Co radiation treatment of HT29 carcinoma cells containing 5-fluorouracil with a dose of above 5 Gy led to a drop in the cell survival factor by two orders of magnitude or more.48 Finally, in a more realistic environment, i.e., in the presence of surrounding water, it is likely that the main dissociation channels, which include the glycosidic bond cleavage reported from the present gas phase experiments, also arise, as it has been reported that the quasi-free electrons induce N-glycosidic bond dissociation of ribothymidine in the 18–22 MeV pulse radiolysis experiment,11 and the local temperature in the vicinity of the ionizing track may increase above 400 K.43
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