Radiolysis Of DNA Research Articles

Extending Quantum Chemistry of Bound States to Electronic Resonances.

Electronic resonances are metastable states with finite lifetime embedded in the ionization or detachment continuum. They are ubiquitous in chemistry, physics, and biology. Resonances play a central role in processes as diverse as DNA radiolysis, plasmonic catalysis, and attosecond spectroscopy. This review describes novel equation-of-motion coupled-cluster (EOM-CC) methods designed to treat resonances and bound states on an equal footing. Built on complex-variable techniques such as complex scaling and complex absorbing potentials that allow resonances to be associated with a single eigenstate of the molecular Hamiltonian rather than several continuum eigenstates, these methods extend electronic-structure tools developed for bound states to electronic resonances. Selected examples emphasize the formal advantages as well as the numerical accuracy of EOM-CC in the treatment of electronic resonances. Connections to experimental observables such as spectra and cross sections, as well as practical aspects of implementing complex-valued approaches, are also discussed.

Comments on the mechanisms of action of radiation protective agents: basis components and their polyvalence.

PurposeThese comments suggest a division of radiation protective agents on the grounds of their mechanism of action that increase the radio resistance of an organism.ConclusionGiven below is the division of radiation protective agents on the basis of their mechanism of action into 3 groups: 1) Radiation protective agents, with the implementation of radiation protective action taking place at the cellular level in the course of rapidly proceeding radiation-chemical reactions. At the same time, when the ionizing radiation energy is absorbed, these agents partially neutralize the “oxygen effect” as a radiobiological phenomenon, especially in the radiolysis of DNA; 2) Radiation protective agents that exert their effect at the system level by accelerating the post-radiation recovery of radiosensitive tissues through activation of a number of pro-inflammatory signaling pathways and an increase in the secretion of hematopoietic growth factors, including their use as mitigators in the early period after irradiation prior to the clinical development of acute radiation syndrome (ARS). 3) Radiomodulators including drugs and nutritional supplements that can elevate the resistance of the organism to adverse environmental factors, including exposure to ionization by means of modulating the gene expression through a hormetic effect of small doses of stressors and a “substrate” maintenance of adaptive changes, resulting in an increased antioxidant protection of the organism. Radiation protective agents having polyvalence in implementation of their action may simultaneously induce radioprotective effect by various routes with a prevalence of basis mechanisms of the action.

Comments to the Mechanism of Protective and Pharmacological Action of Radioprotectors from the Family of Aminothiols

This review evaluates a characteristic features of the mechanism of radiation protective action of aminothiols hence their pharmacological properties and their difference fro m the rest of antio xidants. Over the years, extensive experimental stud- ies of radiation protective agents from aminothiols series were completed by discovery of radioprotectors cystamine and amifostine used in medical p ractice. Characteristic features of the mechanism o f radiation protective act ion of aminothiols un- like other antio xidants are potential chance of the development of comp lete neutralizat ion of o xygen effect as radiological phenomenon, first of all, in DNA radio lysis. This peculiar action of aminothiols is connected with their chemical structure be- ing able to squeeze DNA helix v ia diamine bond of aminothiol disulfide thereby decreasing availabilility of crit ical points o f DNA mo lecules to radicals of oxygen species. Positive charge of aminothiol molecules has an advantage for the development of high their concentration in negative DNA mo lecules. In addit ion, pharmacological properties of aminothiols can deierminate complex polyfunctional action that is significant for the radiation protection, including the in fluence to mitochondria respira- tion follo wing acute hypoxia, gene Mn-SOD expression, activity of the Tip60 acetylransferase, etc. However, the decrease of DNA damage by aminothiols is basic factor in their p rotective action. The properties of aminothiols t o block transaminase fol- lowing a develop ment of hypotension expand their application in clinical practice and the same thing is a cause for severe side effect. Character of aminothiol pharmad inamics is necessary to take into consideration in its repeated a pplication. The scheme of prophylactic application of aminothiols in radiotherapy and for potential victims of radiation accidents is analy zed.

Soft X-ray and low energy electron-induced damage to DNA under N2 and O2 atmospheres.

DNA damage induced by low energy electrons (LEEs) and soft X-rays is measured under dry nitrogen and oxygen at atmospheric pressure and temperature. Five-monolayer plasmid DNA films deposited on tantalum and glass substrates are exposed to Al K(α) X-rays of 1.5 keV in the two different environments. From the damage yields for DNA, G values are extracted for X-rays and LEEs. The G values for LEEs are 3.5 and 3.4 higher than those for X-ray photons under N(2) and O(2) atmospheres, respectively. Because most of the measured damage is in the form of single strand breaks (SSB), this result indicates a much higher effectiveness for LEEs relative to X-rays in causing SSB in both environments. The results indicate that the oxygen fixation mechanism, which is highly effective in increasing radiobiological effectiveness, under aerobic conditions, is operative on the type of damage created at the early stage of DNA radiolysis by LEEs.

Review of DNA Radiolysis

Review of DNA Radiolysis

Modification of DNA radiolysis by DNA-binding proteins: structural aspects

Formation of specific complexes between proteins and their cognate DNA modulates the yields and the location of radiation damage on both partners of the complex. The radiolysis of DNA-protein complexes is studied for: (1) the Escherichia coli lactose operator-repressor complex, (2) the complex between DNA bearing an analogue of an abasic site and the repair protein Fpg of Lactococcus lactis. Experimental patterns of DNA damages are presented and compared to predicted damage distribution obtained using an improved version of the stochastic model RADACK. The same method is used for predicting the location of damages on the proteins. At doses lower than a threshold that depends on the system, proteins protect their specific binding site on DNA while at high doses, the studied complexes are disrupted mainly through protein damage. The loss of binding ability is the functional consequence of the amino-acids modification by OH* radicals. Many of the most probably damaged amino acids are essential for the DNA-protein interaction and within a complex are protected by DNA.

Radiolysis of DNA–protein complexes

We discuss here modifications of DNA and protein radiolysis due to the interaction of these two partners in specific complexes. Experimental patterns of frank strand breaks (FSB) and alkali revealed breaks (ARB) obtained for DNA lac operator bound to the lac repressor and for a DNA containing an abasic site analog bound to the formamidopyrimidine-DNA glycosylase are reported. Experimental data are compared to predicted damage distribution obtained using the theoretical model RADACK.

The influence of dithiothreitol on DNA radiolysis in frozen aqueous solution:: an EPR study

The effect of a thiol, dithiothreitol (DTT), on DNA radiolysis at cryogenic temperatures was investigated by the EPR method. Dithiothreitol repairs up to 30% of DNA radicals, but an increase in the thiol concentration above 10 mM, even up to 1000 mM, does not further enhance the overall level of the repair process. The transfers of paramagnetic centres from both the guanine radical cation, and the allyl radical of thymine, to thiol were observed, while products generated via the reductive pathway remained unaffected.

ESR study of the chemical damage in the direct radiolysis of DNA by 60Co gamma and 5.6 Mev protons: the effect of the mono and bifunctional complexation to Pt(II)

ESR study of the chemical damage in the direct radiolysis of DNA by 60Co gamma and 5.6 Mev protons: the effect of the mono and bifunctional complexation to Pt(II)

Radiolysis of DNA in the presence of a protein studied by HPL-gel chromatography

The influence of bovine serum albumin (BSA) on the radiolysis of double-stranded DNA was studied by measuring the loss of highly polymerized DNA with HPL-gel chromatography. The scavenger capacity of BSA for OH-radicals kBSA \\[BSA] was kept constant at 7.8 105 s1, when DNA (0.1 mg/ml) was irradiated under different gas conditions (air, N2 and N2 O), at pH 7 and 5 and with different ionic conditions. The resulting protein radicals react with DNA producing DNAprotein crosslinks and DNA double-strand breaks. The yield and the kind of DNA damage depend on the nature of the protein radicals and their association with DNA. High phosphate concentration prevents the association of BSA with DNA and causes a reduction of the protection by BSA against double-strand breakage of DNA. Radiolysis in the presence of BSA in perchlorate solution leads to more strand breakage and less protein crosslinking than in phosphate solution because perchlorate is more chaotropic than phosphate. Changing the pH from 7 to 5 increases the protection by BSA against DNA strand breakage.

The effect of serum albumin on the radiolysis of DNA studied by constant field electrophoresis and compared to alterations caused by low molecular weight OH scavengers

After radiolysis of calf thymus DNA in 10 2 mo ldm 3 phosphate buffer at pH 7 under N2, N2 O and air the yields of double-strand breaks (dsb) have been determined by constant field electrophoresis. Double-strand (dsb) breaks were formed according to a linear-quadratic relationship with dose showing a lower G-value under aerobic than under anaerobic conditions (G (air) 1.4 nmolJ1; G (N2) 2.1 nmol J 1; G (N2O) 4.9 nmolJ1). To test the reliability of this system the effect of low molecular weight OH scavengers which were already used in comparable work with plasmid DNA were studied. The results with plasmid DNA and calf thymus DNA obtained by different techniques of electrophoresis agreed quite well. Under N2 more protection was obtained with ethanol than with DMSO or with t-butanol. Under air, double-strand breakage was further decreased and reached the same level with all of these scavengers. Furthermore the constant field electrophoresis gives similar results as the low-angle light scattering technique for radiation induced double strand breakage of calf thymus DNA. When BSA was used at the same scavenger capacity as the low molecular weight scavengers, the protection against double strand breakage was less if radiolysis was carried out in the presence of proteins. Under anaerobic conditions the protection factor was 13 in the presence of BSA, while with DMSO or t-butanol this factor was about 100 and with ethanol 300. In contrast to the low molecular weight OH scavengers oxygen enhanced radiation-induced double-strand breakage with BSA. It is assumed that protein peroxyl radicals may cause strand breakage.

Comparative study of DNA radiolysis by fast neutrons and γ-rays

The effect of fast neutrons on cells is different from that of gamma-rays: the relative (to gamma) biological effect (RBE) is higher than one and the oxygen enhancement ratio (OER) is lower than that of gamma-rays. We searched for differences between the effects of the two radiations on DNA, the critical target of radiations. Using a model plasmid DNA we observed that for the same absorbed dose, fast neutrons induce twice fewer single strand breaks (SSB) and 1.5 more double strand breaks (DSB) than gamma-rays. A transition metal ion, the Cu++, is a better sensitizer of DNA breakage with fast neutrons than with gamma-rays. In anoxia, cysteamine, a positively charged thiol, is a better radioprotector against neutrons than against gamma-rays. In presence of cysteamine, the OER is lower for neutrons than for gamma-rays. These results are discussed in terms of different physical properties of the two types of radiation.

DNA radiolysis. Mapping of the gene regulation domains

Ionizing radiations induce strand breaks and modifications of nucleotides (base and/or sugar) in DNA. In aerated solution, the damages are mainly due to the attack of DNA by the hydroxyl radicals (OH ·) issued from the radiolysis of water. The lesions occur at every nucleotides along the DNA molecule. For γ-rays, β-rays and fast neutrons, we have determined at each nucleotide the probability of strand breakage at neutral pH and the probability of base and sugar modification leading also to strand breakage after an alkaline treatment. The method of sequencing gel electrophoresis was used for this purpose. We have shown that the probability of getting a radiation induced damage at a given nucleotide is modulated by: i) the chemical nature of this nucleotide, ii) the local conformation determined by the sequence of nucleotides and by DNA strandedness (single or double stranded), iii) the type of structure to which the nucleotide belongs (right-handed B- or left-handed Z-DNA) and iv) the presence of proteins specifically (e.g. repressors) or nonspecifically (histones or histone-like) bound to DNA. Therefore, radiolysis may be a convenient tool for mapping gene regulation domains in which DNA is often in non-canonical B forms or is in interaction with regulatory proteins.

Radiolysis of DNA studied by HPL-gel chromatography.

Radiolytic loss of highly polymerized calf thymus DNA was measured by HPL-gel chromatography. Irradiation of DNA in 10(-2) mol dm-3 sodium phosphate under N2 and air caused the same loss. Under N2O this loss was doubled showing that the reactions of OH radicals mainly lead to strand breakage. The stability of the double helix is decisive for the yield of double strand breaks. In this work the radiation-induced degradation was altered by different sodium phosphate concentration, by substituting phosphate for perchlorate and by changing the temperature in the radiolysis of DNA under air. A decrease of the strength of non-covalent bonds in DNA always leads to an increase of degradation of DNA. Radiosensitivity of DNA is higher at pH 7 than at pH 9 or 5.

Radioprotection of DNA by a DNA-binding protein: MC1 chromosomal protein from the archaebacterium Methanosarcina sp. CHTI55.

The archaebacterial chromosomal protein MC1 binds tightly and unspecifically to DNA; binding protects DNA against radiolysis by fast neutrons. At low covering of pBR322 plasmid DNA, one bound protein protects some 50 attack sites (phosphate-sugar moieties) against both single (ssb) and double strand breaks (dsb). At high covering of plasmid, protection against dsb becomes almost complete, although about half of the attack sites remain accessible to ssb. DNA restriction fragments were used to investigate the organization of the complexes, and its consequences on DNA radiolysis. Sequencing gel electrophoresis of the radiolytically-broken fragments are almost regular in the absence of protein, showing that breakage occurs at every base. In the presence of the protein, a periodic protection pattern is observed. The period of 11 base pairs is interpreted as the minimum distance between two adjacent MC1 proteins.

ESR study of the direct radiolysis of DNA, DNA-histones and DNA-intercalators complexes

The nature of the radicals contributing to the room temperature spectrum of irradiated “dry” DNA, with special reference to the central structure, is discussed, and the thesis of their ionic origin tested by irradiation experiments with intercalators. The mechanism of spin transfer protein→DNA has been investigated through a comparative ESR study on the DNA-histones complex, the structureless random molecular mixture of the DNA-histones and the neat components. The yield of spin transfer is enhanced in the random mixture, presumably because of the greater efficiency of molecular contacts. Evidence of the scavenging of electrons by the thymine and cytosine bases, as a key mechanism for the spin transfer, has been obtained.

DNA Radiolysis by Fast Neutrons. II. Oxygen, Thiols and Ionic Strength Effects

Plasmid DNA was irradiated with fast neutrons, and the protection by cysteamine against strand breakage (ssb and dsb) was evaluated in the presence and absence of oxygen. In the absence of cysteamine no radiosensitizing effect of oxygen was observed. In anoxia the protection factors, PF(ssb) and PF(dsb) of 1 mM cysteamine (in 50 mM potassium phosphate solution) were lower than the PFs observed with gamma-irradiation. The results agree with the radical repair model, in which the thiol competes with the oxygen produced inside the anoxic neutron-irradiated system, according to the 'oxygen-in-the-track' hypothesis. At low ionic strength in air-saturated solutions, positively charged cysteamine protects more efficiently than negatively charged thiolactate. The dependence of the PFs on the charge of the thiol can be explained by the condensation of counter-ions and depletion of co-ions around DNA, predicted by Manning's theory. Based on the same theory, we propose here an explanation of the ionic strength or by thiolactate at low ionic strength is largely due to scavenging of OH. radicals in the bulk solution. At low ionic strength the PF(ssb) of cysteamine is higher for neutrons than for gamma-irradiation. This might suggest different primary lesions for the two types of irradiation.

DNA Radiolysis by Fast Neutrons

The effects of fast neutron irradiation on DNA were studied using DNA of the pBR322 plasmid (4362 base pairs), and the results compared to those obtained with 60Co gamma rays. Irradiation of the plasmid DNA in solution with a neutrons beam (p34+Be) of the CERI (CNRS Orléans) cyclotron (with a flat energy spectrum from 34 MeV to low energies) results in half the yield of single-strand breaks (ssb), and 1.5 times higher yield of double-strand breaks (dsb) for neutrons as compared to gamma-rays. Possible specificity of the neutron-induced breaks was examined: the scavenging of OH. radicals by 0.1 mol dm-3 ethanol inhibits all neutron-induced ssb, but only 85 per cent of the dsb. For gamma-irradiation, both ssb and dsb are completely inhibited in these conditions. These results suggest at least three different origins for neutron-induced dsb. The occurrence of around 30 per cent of dsb can be explained by a radical transfer mechanism (proposed by Siddiqi and Bothe (1987) for gamma-irradiation). Around 55 per cent of dsb may be due to the non-random distribution of radicals in high-density tracks of the secondary particles of neutrons, which results in a simultaneous attack of the two strands by OH. radicals. These first two processes are both OH.-mediated and thus are sensitive to ethanol. The direct effect of fast neutrons and their secondaries (recoil protons, alpha-particles and recoil nuclei) can account for the remaining 15 per cent of dsb, not inhibited by 0.1 mol dm-3 ethanol.

Radiolysis of DNA in aqueous solution in the presence of a scavenger: A kinetic model based on a nonhomogeneous reaction of OH radicals with DNA molecules of spherical or cylindrical shape

Two expressions are given for the survival dose of DNA exposed to high-energy radiation in aqueous solution in the presence of a scavenger. They are derived from a model where a diffusion controlled reaction of OH radicals occurs on the surface of the DNA macromolecules in competition with scavenging in the bulk of the solution. The DNA molecules are approximated either by spheres or by cylinders. The model based on molecules of spherical shape corresponds closely to that developed by van Rijn et al. [20]. Expressions obtained from the cylindrical model are used to account for the dependence on the scavenger concentration of some experimentally measured quantities, namely the survival dose and the G value for single-strand breaks upon Co gamma-irradiation of phi X174 DNA and polyadenylic acid, respectively.

Ultraviolet Difference Spectral Studies in the Gamma Radiolysis of DNA and Model Compounds. I. Aqueous Solutions of DNA Bases

Ultraviolet difference spectra of gamma-irradiated, air-saturated aqueous solutions of DNA bases vs. unirradiated solutions of the same bases are shown to be a very sensitive supplemental tool with which to investigate the yields, postirradiation kinetics, and general nature of DNA base radiation products. Irradiated pyrimidines yield difference spectra which are approximately negative mirror-images of the base absorption spectra in the near-UV, indicating loss of ring conjugation. Difference spectra of irradiated purines yield a more complex pattern containing a positive long-wavelength peak, interpreted as radiation-induced extension of conjugation of the pi electron system beyond that of the unirradiated purine. On the basis of the spectroscopic evidence from these studies, 8-hydroxyguanine appears to be the dominant UV-absorbing radiation product in air-saturated guanine solutions with a G-value of 0.3 molec (100 eV)-1. Difference spectral studies provide isosbestic points which can be used in testing proposed radiation products and their yields. Such spectral studies are a rapid, non-invasive, supplemental tool which can be employed in conjunction with other analytical techniques in radiation-chemical studies, and which is one of the few tools able to detect short-lived chemical intermediates observed in oxygenated solutions of irradiated purines.