Hydroxyl radical is a significant player in oxidative DNA damage in vivo

Graphical Abstract

Short Statement

Recent publications have suggested that oxidative DNA damage mediated by hydroxyl radical (^•OH) is unimportant in vivo, and that carbonate anion radical (CO₃^•−) plays the key role. We examine these claims and summarize the evidence that ^•OH does play a key role as an important member of the reactive oxygen species (ROS) in vivo.

1. Introduction to reactive oxygen species and DNA damage

A wide range of reactive oxygen species (ROS) is formed in vivo in the human body and in other living organisms (reviewed in [1]). The term “reactive” covers a broad spectrum: some ROS, such as superoxide anion radical (O₂^•−), nitric oxide (NO^•) and hydrogen peroxide (H₂O₂) are very selective in their reactions. Others, such as hypochlorous acid (HOCl), carbonate anion radical (CO₃^•−) and the two singlet states of oxygen (¹O₂), are fiercer and can attack several biomolecules. By contrast, the hydroxyl radical (^•OH) reacts at or near a diffusion-controlled rate with almost every organic biomolecule found in living organisms [1, 2]. Several ROS, generally the ones of lower reactivity such as H₂O₂ and NO^•, play important physiological roles in vivo, but the ones of higher reactivity can cause oxidative damage to biomolecules, resulting in impairment of cellular functions (reviewed in [1, 3]). In particular, oxidative damage to DNA plays an important role in the origin and progression of a number of human diseases, most prominently cancer but also others, such as neurodegenerative diseases and atherosclerosis [1, 4–6]. The ability of several ROS to attack DNA and generate mutagenic end-products plays a key role in cancer development in humans. Much attention has been paid to the mutagenic lesion 8-hydroxy-2′-deoxyguanosine (8OHdG) in this context [1, 7], but many other mutagenic and/or cytotoxic lesions are formed when ^•OH attacks DNA [1, 5, 8–15]. However, recent articles [16–18] have suggested that ^•OH is not involved in DNA damage caused by oxidative stress and argue a key role instead for CO₃^•¯, which attacks guanine residues in DNA to form 8OHdG. We would like to bring two matters to the attention of the journal readership,

1. that there is much more to biologically-significant oxidative DNA damage than only 8OHdG formation, and

2. that ^•OH does play a significant role in causing oxidative DNA damage in vivo.

2. How does hydroxyl radical arise in vivo?

Hydroxyl radical is generated in vivo by several mechanisms, including:

1. through the reaction of certain transition metal ions (especially Fe²⁺ and Cu⁺ (reaction 1, Fenton reaction) with H₂O₂ (reviewed in [1, 3]).

   (1)

   The question of the availability, catalytic activity and chemical nature of transition metal ions in vivo has been repeatedly discussed [1, 3, 19–21], but there is no clear consensus as yet, although the recent discovery of ferroptosis, a form of iron ion-induced cell death, has rekindled interest in this topic [3, 22]. For example, Fe²⁺ ions bound to phosphate, polyphosphate, citrate, ATP etc. have shown variable activities in ^•OH generation in vitro [1, 21–28], but these simple studies in solution rarely reflect the complex cellular and extracellular environment in vivo (which is enormously rich in proteins, lipids, nucleic acids and hundreds of different metabolites). We return to this question in Section 4 below.
2. in certain circumstances, by homolysis of H₂O₂ (reaction 2, reviewed in [1]).

   $${\text{H}}_2{\text{O}}_2\to 2{}^{•}\text{OH}$$ (2)
3. The fission of H₂O upon exposure to ionizing radiation (to which we have a constant background exposure [1, 9, 31]). Water cation radical (H₂O^•+) is the primary species formed in the physical stage (~10⁻¹⁵s) due to the interaction of ionizing radiation with water (reviewed in [31]). Subsequently, there is ultrafast proton transfer from H₂O^•+ in the physicochemical stage (10⁻¹⁵ – 10⁻¹² s) to a surrounding water molecule (reaction 3).

   $${\text{H}}_2{\text{O}}^{•+}+{\text{H}}_2\text{O}\to {}^{•}\text{OH}+{\text{H}}_3{\text{O}}^{•+}$$ (3)
   In addition, ^•OH is formed by homolysis (reaction 4) of the excited water molecule ((H₂O)*) [1, 9, 31].

   $${\left({\text{H}}_2\text{O}\right)}^{\ast }\to {}^{•}\text{OH}+{\text{H}}^{•}$$ (4)

   Indeed, the damage that ^•OH causes to DNA helps to explain why exposure to ionizing radiation can lead to cancer development [1, 4, 5, 9].

That ^•OH is generated in vivo (including by Fenton chemistry) has been demonstrated by a multiplicity of methods, including aromatic hydroxylation and ESR spin trapping [1, 32–42]. Owing to its high electrophilicity and high reactivity [1, 2, 9], ^•OH reacts at or near a diffusion-controlled rate (rate constant >10⁹ M⁻¹s⁻¹) with almost all organic biomolecules. As a result, when ^•OH is generated in vivo, it will attack whichever of these organic molecules are adjacent to it [1, 2, 9].

3. The role of bicarbonate in vivo

As mentioned, recent articles [16–18] have argued that CO₃^•¯ and not ^•OH plays the major role in causing oxidative DNA damage in vivo. It is well known that bicarbonate anion (HCO₃¯) is important in maintaining physiological pH and is indeed present intracellularly at high mM (10–40 mM) concentration [16–18 and references therein]. In vitro studies have suggested that in the presence of HCO₃¯ the reaction of Fe²⁺ and H₂O₂ does not generate ^•OH but instead CO₃^•¯ [16–18, 43]. An alternative explanation is that ^•OH is generated but immediately reacts with HCO₃¯ to give CO₃^•¯. However, the rate constant for the formation of CO₃^•¯ via H-atom abstraction from HCO₃¯ by ^•OH (reaction 5) under physiological conditions has been measured by pulse radiolysis and is found to be quite low, 8.5 × 10⁶ M⁻¹s⁻¹ [44].

$${{\text{HCO}}_3}^{-}+{}^{•}\text{OH}\to {{\text{CO}}_3}^{•-}+{\text{H}}_2\text{O}$$ (5)

Molecules such as 2′-deoxyribose phosphate, the purine and pyrimidine bases of DNA and RNA, reduced glutathione (GSH) and proteins, present in vivo also at substantial concentrations, react much faster with ^•OH, at diffusion-controlled rates (>10⁹ M⁻¹s⁻¹) and so may be preferred targets, depending on the location and environment in which the ^•OH is generated [1, 2, 6, 8, 9], as we discuss in Section 4. However, CO₃^•¯ (and possibly some ^•OH) can also be generated in pathways involving NO^•, CO₂ and peroxynitrite (reviewed in [1, 45, 46]). The rate constant of the reaction of CO₂ with peroxynitrite involved in this process, ranges from 3 × 10⁴ M⁻¹ s⁻¹ to 5.8 × 10⁴ M⁻¹ s⁻¹ [1, 45, 46].

4. The relative reactivities of ^•OH and CO₃^•¯ with DNA

Two approaches can throw light on this question, an examination of thermodynamic parameters and direct experimental studies. The absolute reduction potentials (E°) and midpoint potentials (E₇) of ^•OH, CO₃^•¯, and the DNA components are presented in Table 1 below [8, 47–50].

Table 1.

The absolute reduction potentials (E°) and the midpoint potential (E₇) of ^•OH, CO₃^•¯ and of base cation radicals. The E₇ value of 2′-deoxyribose (dR) is also listed.

Bases and radical	E vs. SHE (V)
	Couple (E°)	E° in DMF	Couple (E7)	E7 by pulse radiolysis in water
G (Guanine base)	(G•+/G)	1.49	(G(N1–H)•)/H+, G)	1.29
A (Adenine base)	(A•+/A)	1.96	(A(N6–H)•)/H+, A)	1.42
C (Cytosine base)	(C•+/C)	2.14	(C(N4–H)•)/H+, C)	1.6
T (Thymine base)	(T•+/T)	2.11	(T(N3–H)•)/H+, T)	1.7
•OH			•OH, H+/H2O	2.3
CO3•¯			CO3•¯/CO32¯	1.59
•CH2CH3			•CH2CH3, H+/CH3CH3	1.9
dR•			dR• / H+, dR	>1.8

From Table 1 and assuming the E₇ of ^•CH₂CH₃ [48] and of dR [49] as a guide for that of the sugar moiety in DNA, we conclude that CO₃^•¯ is very unlikely to cause oxidative damage to dR and pyrimidines and should be capable of oxidizing only guanine , and perhaps adenine to a much lesser extent. Following the ionization potentials of the bases and according to Table 1 above, guanine should be the major or only site of oxidative damage by CO₃^•¯ in DNA. Indeed, a combination of laser flash photolysis and product analysis studies has confirmed that CO₃^•¯ oxidizes guanine in DNA, to form 8OHdG [45, 51]. We can find no literature evidence of adenine oxidation by CO₃^•¯. Also, if CO₃^•¯ were the main player in oxidative DNA damage, as argued in [16–18] and due to the repulsive forces of the highly negative charged polymer (DNA) and CO₃^•¯, we should not expect CO₃^•¯ mediated sugar-phosphate damage leading to strand break formation and indeed this is scarcely observed [51, 52].

In agreement with the E° values in Table 1, direct experimental results show that when ^•OH reacts with DNA it forms a multiplicity of damage products (Figure 1) from all four purine and pyrimidine bases and from the dR moiety [1, 8–14, 53, 54]. No other known ROS forms such a wide range of products: some (such as H₂O₂ and O₂^•¯) do not react directly with DNA at all whereas others (e.g. CO₃^•¯, ¹O₂) target guanine selectively [1, 8, 16]. Hence, the demonstration that this wide range of products (shown in Figure 1) is formed in vivo is excellent evidence that ^•OH has been generated and has attacked DNA, whatever studies on simplified systems in vitro that do not reflect the complex cellular environment in vivo may suggest. To take one example, when human respiratory tract epithelial cells were exposed to 100 μM H₂O₂, there was rapid induction of DNA strand breakage and chemical modifications to all 4 DNA bases, diagnostic of attack by ^•OH [53]. How can this diagnostic damage pattern of ^•OH attack be explained, since H₂O₂ does not react with DNA? We have already mentioned our poor knowledge of the availability and distribution of transition metal ions in vivo, but evidence suggests that DNA in vivo has transition metal ions such as Fe²⁺ and Cu⁺ bound to it, given its very strong negative charge due to the phosphate groups (reviewed in [1]). Indeed, Fe²⁺ bound to phosphate is generally agreed (even by Prof. Burrows [17]) to generate ^•OH from H₂O₂, and the reasons for this have been recently elucidated [55]. The phosphate levels in the nucleus are very high due to the phosphate residues in DNA and so ^•OH formation will be favoured. H₂O₂ crosses plasma and intracellular membranes reasonably freely [1] and, if it reaches the nucleus, H₂O₂ can react with such metal ions to generate ^•OH directly upon the DNA, causing immediate oxidative damage, often called “site-specific” damage [1, 2]. This “site-specific” damage by localized ^•OH generation also occurs with biomolecules other than DNA, such as proteins, again generating multiple products diagnostic of ^•OH attack [1, 56, 57]. It cannot be prevented by external molecules that scavenge ^•OH, such as HCO₃¯, glucose or GSH [1]. Furthermore, the formation of a thymine-tyrosine crosslink has been observed upon treatment of mammalian cells with Fe(II), and involvement of ^•OH has been suggested in this crosslink formation [58]. The free radical mechanistic pathways of ^•OH - mediated formation of multiple guanine and other DNA base damage products that are produced via oxidative damage, have been well documented in the literature [1, 6, 8, 12, 59].

Figure 1. Products resulting from attack of hydroxyl radicals on DNA.

By contrast, carbonate anion radical modifies only guanine residues

The exact molecular ratios of different DNA base and sugar damage products generated by site-specific ^•OH formation or other modes of ^•OH attack upon DNA depend on several factors, including where upon the DNA the metal ions are bound [9–12]. This pattern of multiple DNA base damage products is indeed observed in vivo: low levels of multiple base DNA damage products are present in DNA from all human and other animal tissues examined and the levels increase when oxidative stress is imposed by a variety of mechanisms [1, 6, 8–14, 59–64], e.g. in diabetes [65]. For example, 8,5′-cyclopurine-2′-deoxynucleosides in DNA are generated exclusively by ^•OH attack upon 2′-deoxyribose units generating C5′ radicals, followed by cyclization with the C8 position of the purine base [59, 66, 67]. This vast literature unequivocally demonstrates the formation of ^•OH-induced DNA base and 2′-deoxyribose products in vivo. In addition, oxidative stress can liberate catalytically-active transition metal ions (especially iron ions) from a range of cellular proteins (such as iron-sulphur proteins, and ferritin) [1, 19, 29, 68, 69], and some of these may bind to DNA, making it a further in vivo target of oxidative damage by site-specific ^•OH generation [1].

5. There is much more to biologically-significant oxidative DNA damage than 8OHdG formation

Apart from 8OHdG, the importance of many other DNA lesions, some of which are shown in Fig. 1, in cancer development in vivo has been highlighted, and the existence of DNA repair enzymes needed for their removal and whose genetic deletions increase cancer development in animals is further evidence that these mutagenic and/or cytotoxic lesions are formed in vivo and are important in the development of cancer and other diseases [1, 8, 70, 71].

6. Conclusion

There is unequivocal evidence of the ^•OH-specific pattern of oxidative DNA damage in vivo and in isolated cells subjected to oxidative stress. This, combined with the ability to trap ^•OH by specific methods in living systems, provides substantial evidence that ^•OH plays an important role in oxidative DNA damage, and other aspects of oxidative damage, including protein and lipid damage, in vivo [1]. This is in part due to formation of 8OHdG, which can also be generated by attack of ¹O₂ and of CO₃^•¯ on DNA, but also due to many other mutagenic and/or cytotoxic lesions, formed from purines, pyrimidines and 2′-deoxyribose by ^•OH attack (Fig. 1). Carbonate anion radical might also play an important role in vivo [16–18]. Certain other ROS, such as HOCl, can also attack DNA. Hypochlorous acid forms chlorinated base products, which have indeed been detected in vivo [72, 73].