Radical and Radical Ion Reactivity in Nucleic Acid Chemistry (Wiley Series of Reactive Intermediates in Chemistry and Biology)

Comprehensive coverage of radical reactive intermediates in nucleic acid chemistry and biochemistryThe Wiley Series on Reactive Intermediates in Chemistry and Biology investigates reactive intermediates from the broadest possible range of disciplines. The contributions in each volume offer readers fresh insights into the latest findings, emerging applications, and ongoing research in the field from a diverse perspective.The chemistry and biochemistry of reactive intermediates is central to organic chemistry and biochemistry, and underlies a significant portion of modern synthetic chemistry. Radical and Radical Ion Reactivity in Nucleic Acid Chemistry provides the only comprehensive review of the chemistry and biochemistry of nucleic acid radical intermediates.With contributions by world leaders in the field, the text covers a broad range of topics, including: A discussion of the relevant theory Ionization of DNA Nucleic acid sugar radicals Halopyrimidines Oxidative, reductive, and low energy electron transfer Electron affinity sensitizers Photochemical generative of reactive oxygen species Reactive nitrogen species Enediyne rearrangements Phenoxyl radicals A unique compilation on the cutting edge of our understanding, Radical and Radical Ion Reactivity in Nucleic Acid Chemistry provides an unparalleled resource to student and professional researchers in such fields as organic chemistry, biochemistry, molecular biology, and physical chemistry, as well as the industries associated with these disciplines.

Excerpt

<h2>CHAPTER 1</h2> <p><b>THEORETICAL MODELING OF RADIATION-INDUCED DNA DAMAGE</b></p> <p>Anil Kumar and Michael D. Sevilla <i>Department of Chemistry, Oakland University, Rochester, MI 48309, USA</i></p> <br> <p><b>1.1. INTRODUCTION</b></p> <p>Ionizing radiation causes a variety of damages to DNA in living systems. Thus, the understanding of radiation-induced chemical processes leading to specific damage in DNA is of substantial biological importance. Radiation ionizes each component of DNA (i.e., base, sugar, phosphate) and the surrounding water molecules in a random fashion and produces a cascade of secondary electrons, most of which are below 15 eV and are designated as low-energy electrons (LEE). LEE are produced in a large quantity (4 × 10⁴ per MeV energy deposited) along the tracks of the ionizing radiation and have been shown to result indirect DNA damage in model systems in the seminal work of Sanche and co-workers, who found that LEEs create single- and double-strand breaks (SSBs and DSBs)in DNA through dissociative electron attachment (DEA). These findings having been substantiated by the work of others. Only a small fraction of LEE result in DNA damage, because most electrons are thermalized and either recombine with positive charge ("hole") or are captured by the pyrimidines [thymine (T) and cytosine (C)], resulting in radical anion formation. During ionization events, all the bases are randomly ionized and "holes" (radical cations) are formed, which travel within DNA toward the base having lowest ionization potential, the order being guanine (G) < adenine (A) < cytosine (C) ≠ thymine (T) Therefore, in a randomly ionized DNA double strand, the hole tunnels or hops from one base to the next, finally localizing on guanine to form the guanine radical cation (G^•+). Ionization radiation also induces holes on the sugar–phosphate backbone site that lead to two competitive reactions: (i) deprotonation of the sugar cation radical at a carbon site resulting in the formation of neutral sugar radicals at carbon C'₁ to C'₅ sites and (ii) transfer of hole to a nearby base in DNA.</p> <p>Since most sugar radicals lead to DNA strand breaks, sugar radical formation in DNA becomes of crucial importance to the biological consequences of radiation. Recently, it has been found that irradiation of DNA by a high LET (linear energy transfer) radiation, a high-energy argon ion beam, produced a far higher yield of sugar radicals than was found by a low LET radiation, γ-irradiation. The authors report that the excess sugar radicals were created within the track core. The energy density in the track core is high and results in ionizations and excitations in close proximity. For this reason, it was hypothesized that excited states of radical cations might result in the neutral sugar radicals in the core of the ion track. To test this hypothesis, recent experiments in our laboratory were performed on the photoexcitation of guanine and adenine radical cations (G^•+, A^•+) in DNA model systems. It was found that excited DNA base cation radicals formed high yield of sugar radicals which confirmed the proposed hypothesis.</p> <p>While strand breaks are biologically significant, it is combinations of DNA damages known as multiple damage sites (MDS) that are the most lethal type of DNA damage. Such combinations of single- and double-strand breaks and base Damages with 10 base pairs are known to lead to irreparable damage because of the loss of local structural information. High-LET radiations (α particles, atom ion beams, neutrons) are found to be about 10 times more damaging than the low-LET radiations such as β particles, X rays, and γ rays in the production of such damage.</p> <p>From the above discussion, it is evident that ionization and excitation are the initial events in DNA damage. As the damage unfolds from these initial events, the processes may become complex in nature; however, the simplicity of the initial events allow for a clear understanding of these initial processes. Thus ionization, excitation, and electron addition to DNA bases have been extensively treated by theoretical calculations using a variety of methods with density functional theory (DFT) perhaps the most useful to large systems. The advent of substantial computing power and the availability of inexpensive computational resources allows the application of more sophisticated level of theoretical calculation such as TD-DFT, Møller–Plesset perturbation theory (MP2), CCSD(T), and CASPT2 that can shed light on the underlying chemical processes controlling the DNA damage. A close agreement between theory and experiment is eexpected, given an appropriate use of theory. In this review we present recent investigations that emplloy theory to aid understanding of DNA base and sugar radical formation, via ionization, excitation, and elecccctron attachment to DNA. Specific topics include (1) ionization energies and electron affinities of bases and base pairs, (2) excited states of radical DNA base cations and their roles in leading to sugar radicals, (3) the role of excited states of DNA base anion radicals in the formation of LEE (low-energy electron)-induced DNA single-strand breaks, (4) the nature of hole delocalization in adenine stacks systems including the usual stability of the dimer radical cation (A₂)^•+ and its importance to the unusual long-range hole transfer within A stacks in DNA, and (5) the prototropic equilibria found for the guanosine radical cation, which also modulates hole transfer in DNA.</p> <br> <p><b>1.2. DIRECT EFFECT OF IONIZING RADIATION IN RADICAL ION FORMATION</b></p> <p>As described in the Introduction, the direct interaction of ionizing radiation with DNA initially creates "hole" (cation radical) in DNA and ejects an electron that is usually captured as an anion radical in DNA. Electron spin resonance (ESR) spectroscopy studies show that for γ-irradiated salmon testes DNA at 77 K, the relative amounts of the observed initial ion radicals are: 35% guanine radical cation (G^•+) with a small amount (< 5%) of adenine radical cation (A^•+) with nearly equal amounts of thymine and cytosineradical anions (T^•-, C^•-) summing to ~45%. The remaining fraction of 10–15% is made up of neutral radicals primarily on the sugar–phosphate backbone. The minimum energy required to form a radical cation is estimated from the ionization potential (IP), while the energy of formation for the anion radical is estimated from the electron affinity (EA) of the corresponding DNA base, sugar, and phosphate. The determination of these fundamental properties are of substantial importance, and much effort has been expended in this area.</p> <p>Theoretical calculations of molecular structures of bases in their neutral and ionized radical states, their spin density distributions, and their IPs and EAs provide valuable information that aid interpretations of experiment. In Figure 1.1, the molecular structures of guanine (G), adenine (A), thymine (T), cytosine (C), uracil (U) (present in RNA), and sugar moiety are shown.</p> <br> <p><b>1.2.1. Ionization Potential of DNA Bases and Base Pairs</b></p> <p>The vertical ionization potential (IPvert) of DNA bases G, C, A, and T in the gas phase has been measured experimentally using photoelectron spectroscopy by Hush and Cheung while the corresponding adiabatic ionization potential (IP_adia) values were measured by Orlov et al. using photoionization mass spectrometry in the gas phase. Recently, Kim and co-workers reported the ionization potential of thymine (T) using the high-resolution vacuum ultraviolet mass-analyzed threshold ionization (VUV-MATI) spectroscopy. The ionization potential of a neutral molecule M is the energy required to remove an electron from the molecule. In Figure 1.2, theoretical estimates of the IP_vert, IP_adia are shown. If the energies are zero point energy (ZPE)-corrected, the ionization potentials are referred to as ZPE-corrected (IP_zero). Another quantity, the nuclear relaxation energy (NRE), calculated as the difference between IP_vert and IP_adia, is of interest because it provides an additional energetic barrier to "hole" transfer within DNA. Figure 1.3 shows the experimental IPs of A, T, G, and C along with their NRE energies. Using different theoretical methods, the gas-phase ionization potential of DNA bases were also calculated. A comparison of the theoretically calculated IP values of G, A, C and T along with their corresponding experimental values are presented in Table 1.1. In Table 1.1, we see that both theory and experiment predict the same order of ionization potential of DNA bases as G < A <C < T.</p> <p>The adiabatic ionization potentials of adenine and cytosine have been studied using CCSD(T)/6-311++G(3<i>df</i>, 2p) level of theory, and the corresponding values are in an excellent agreement with those calculated using experiment, see Table 1.1. Recently, Cauet et al. used the MP2 method to calculate the vertical and adiabatic ionization potentials of DNA bases. In their study, they added another polarization function (α_<i>d</i>) for C, N, and O atoms to the standard 6-31G(<i>d</i>) basis set, resulting in the so-called 6-31G(2<i>d</i>(0.8, 0.1), <i>p</i>) basis set. Use of this basis set gave good values of IPs which are in close agreement to the experimental values, except for IP_vert of adenine. Generally, it is found that unrestricted MP2 (UMP2) method for open-shell systems (here cation doublet state) is largely spin contaminated and as a result the calculated IPs were found to be quite high. In this context, Crespo-Hernandez et al. used projected MP2 (PMP2) method for the calculation of IPs of DNA bases, see Table 1.1. Recently, Yang et al. measured the ionization potentials of mono-, di-, and trinucleotide anions of A, T, G, and C using photodetachment–photoelectron (PD–PE) spectroscopy, and they found that 2'-deoxyguanosine 5'-monophosphate anion (dGMP^-) has the lowest ionization potential among all the DNA nucleotides. In their study, the electron detachment occurred from a π orbital of guanine base on dGMP^-; however, for the other three nucleotide anions, the lowest ionization takes place from the phosphate group. This observation is likely valid for the gas phase but is not relevant to solutions where thesolvation of thephosphate group makes it the DNA componentof highest IE. Furthermore, it is well known that bases are the sites of the lowest ionization in DNA from numerous experimental studies, and the presence of solvation and counterions near the phosphate groups when included show this to be the case by theory.</p> <p>There are several factors such as base pairing, base stacking, and solvation in DNA that significantly affect the ionization potential of bases in DNA. It is well known that solvation lowers the ionization potentials of bases by several electron volts when compared to the corresponding gas-phase values. In a study, Kim et al. have found that ionization potentials of adenine and thymine decrease with the increasing number of hydrating water molecules and hydration by three water molecules decrease the ionization potentials of A and T by 0.7 eV than their gas-phase values. Recently, the vertical ionization potentials of A, T, G, and C in aqueous medium was calculated by Close using polarized continuum model (PCM) and the projected MP2/6-31++G(<i>d, p</i>) and B3LYP/6-31++G(<i>d, p</i>) methods. After solvation energy correction of the electron (-1.3 eV), both the methods gave similar values of ionization potentials of guanine 4.77 (4.71), adenine 5.08 (5.05), cytosine 5.24 (5.32), and thymine 5.36 (5.41) (the numbers in parentheses are the PCM-B3LYP calculated values). These calculated values use a unusual standard state for the ejected electron. An electron in water at the conduction band edge (<i>V</i>₀) is employed as the final electron state not the gas-phase electron, and this lowers the IP by 1.3 eV. Without this correction the corresponding IP_vet values at B3LYP/6-31++G(<i>d, p</i>) level of calculation are 6.01 (G), 6.35 (A), 6.62 (C), and 6.71 (T).</p> <p>The ionization potentials of DNA bases in GC and AT hydrogen-bonded base pairs were calculated by Colson et al. using HF/3-21G and HF/6-31G(<i>d</i>)//HF/3-21G methods in Koopmans' approximations which were further refined by Li et al. using the B3LYP method and the 6-31G(<i>d</i>) basis set (Hutter and Clark and Bertran et al.). The calculated IP_vert for GC and AT base pairs, by Li et al., were found to be 7.23 and 7.80 eV; however, the zero-point energy (ZPE)-corrected adiabatic IP of GC and AT were found to be 6.90 and 7.68 eV, respectively. The IP_adia values of GC and AT pairs due to Li et al. are in good agreement (within 0.2 eV) with those earlier calculated by Hutter and Clark and Bertran et al.</p> <p>The effect of hydration on the ionization potential of GC and AT base pairs was studied by Colson et al. using HF/3-21G and HF/6-31+G(<i>d</i>)//HF/3-21G methods and Koopmans' approximation. In the calculation, they used four water molecules to solvate the base pairs; and the calculated IP<i>vert</i> of GC and AT base pairs, at HF/3-31G level of theory, were found to be 7.80 and 8.59 eV, respectively. However, the corresponding IP_adia, calculated at the HF/6-31+G(<i>d</i>)//HF/3-21G level of theory, was found to be 6.53 and 7.45 eV. Strangely, these values were higher than the corresponding gas-phase ionization potential values of the GC and AT base pairs. Each water molecule acting as a hydrogen-bond donor to the base increases the IP, while each water molecule in the hydrogen-bond acceptor configuration with the base lowers the IP. Therefore, it seems that four water molecules in the calculation of Colson et al. were not enough to fully account for the solvation shell surrounding The base pairs, and most of the waters act as hydrogen-bonddonors. Recently, Barnett et al. studied the duplex DNA <i>d</i>(5'-(G)<i>n</i> -3'), for <i>n</i> = 2, 3, considering the crystallographic structures, counterions (Na⁺) near the phosphate group, and solvating water molecules. Their calculated values of vertical and adiabatic IPs are substantially lower than expected, perhaps as a result of the involvement of nonequilibrium conformations in local minima which place counterions in sites to lower the IPs. The ionization potentials of base pairs in the stacked conformation have also been studied theoretically. The vertical ionization potential of stacked bases and base-paired dinucleotides were calculated by Sugiyama and Saito using 3-21G* and 6-31G* levels within Koopmans' approximation. With 6-31G* level of theory, the ionization potentials of G, GG, GGG, and GGGG were found to be 7.75, 7.28, 7.07, 6.98. The above discussion clearly shows that base pairing, stacking, hydration, and the local environment significantly affect the ionization potentials of the DNA bases, usually by lowering values.</p> <br> <p><b>1.2.2. Acid and Base Properties of Ionized DNA Bases and Base Pairs</b></p> <p>Following radiation, the one-electron-oxidized purines (G^•+, A^•+) and one-electron-reduced pyrimidines (C^•-, T^•-) in DNA become quite reactive in comparison to their neutral forms. The oxidized purines become stronger acids and undergo deprotonation reactions, whereas the reduced pyrimidines become stronger bases and undergo protonation reactions. A competitive reaction to deprotonation for DNA base cation radicals is theaddition of hydroxyl ions that form base hydroxyl adducts. This can lead tobiologically significant damages such as 8-oxoG. In addition, electron–hole transfer and intra-base-pair proton transfer reactions also occur. This intra-base pair proton (H⁺) transfer in DNA can slow or stop charge transfer processes in DNA. Such proton transfer process strongly depends on the pKa value of the base radical ion involved. Steenken first considered the proton transfer reactions between base-pair ion radicals from experimental measurements on nucleoside ion radicals and concluded that acidity of the complementary oxidized purine base and basicity of the radical anion (pyrimidine base) would affect the extent of such a proton transfer process. Experimental values of the p<i>K_a</i> of G^•+, A^•+, C^•+, and T^•+ are 3.9, < 1 (strong acid), ~4.0, and 3.6. On the other hand, the p<i>K_a</i> of C^•- and T^•- were reported to be as &#8805 13.0 (strong base) and &#8805 6.9, respectively.
(Continues...) Excerpted from Radical and Radical Ion Reactivity in Nucleic Acid Chemistry by Michael D. Greenberg. Copyright © 2009 by John Wiley & Sons, Ltd. Excerpted by permission of John Wiley & Sons.
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Comprehensive coverage of radical reactive intermediates in nucleic acid chemistry and biochemistry

The Wiley Series on Reactive Intermediates in Chemistry and Biology investigates reactive intermediates from the broadest possible range of disciplines. The contributions in each volume offer readers fresh insights into the latest findings, emerging applications, and ongoing research in the field from a diverse perspective.

The chemistry and biochemistry of reactive intermediates is central to organic chemistry and biochemistry, and underlies a significant portion of modern synthetic chemistry. Radical and Radical Ion Reactivity in Nucleic Acid Chemistry provides the only comprehensive review of the chemistry and biochemistry of nucleic acid radical intermediates.

With contributions by world leaders in the field, the text covers a broad range of topics, including:

• A discussion of the relevent theory

• Ionization of DNA

• Nucleic acid sugar radicals

• Nucleobase radicals

• Halopyrimidines

• Oxidative, reductive, and low energy electron transfer

• Electron affinity sensitizers

• Photochemical generative of reactive oxygen species

• Reactive nitrogen species

• Electrochemical oxidation of nucleic acids

• Enediyne rearrangements

• DNA photochemistry

• Phenoxyl radicals

A unique compilation on the cutting edge of our understanding, Radical and Radical Ion Reactivity in Nucleic Acid Chemistry provides an unparalleled resource to student and professional researchers in such fields as organic chemistry, biochemistry, molecular biology, and physical chemistry, as well as the industries associated with these disciplines.