Radiation damage to DNA in DNA–protein complexes

Spotheim-Maurizot, M.; Davidkova, Maria

doi:10.1016/j.mrfmmm.2011.02.003

Cited by 47 publications

(34 citation statements)

References 49 publications

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“…an oestrogen response elementreceptor complex (Stísová et al, 2006) and a DNA glycosylase and its abasic DNA target site (Gillard et al, 2004)]. In these studies, the main damaging species is predicted to be the oxidizing hydroxyl radical produced through solvent irradiation, which is known to add to double covalent bonds within both DNA and RNA bases to induce strand breaks and base modification (Spotheim-Maurizot & Davídková , 2011;Chance et al, 1997). It was suggested that physical screening of DNA by protein shielded the DNA-protein interaction sites from radical damage, yielding an extended life-dose for the nucleoprotein complex compared with separate protein and DNA constituents at RT.…”

Section: Discussionmentioning

confidence: 99%

RNA protects a nucleoprotein complex against radiation damage

Bury

McGeehan

Antson

et al. 2016

Acta Cryst Sect D Struct Biol

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Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 Å ) than the previous systematic specific damage study on a protein-DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a singlestranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiationinduced Lys and Phe disordering upon RNA binding directly from the electron density. IntroductionWith the wide use of high-flux third-generation synchrotron sources, radiation damage (RD) has once again become a dominant reason for the failure of structure determination using macromolecular crystallography (MX) in experiments conducted both at room temperature and under cryocooled conditions (100 K). Significant progress has been made in recent years in understanding the inevitable manifestations of X-ray-induced RD within protein crystals, and there is now a body of literature on possible strategies to mitigate the effects of RD (e.g. Zeldin, Brockhauser et al., 2013;Bourenkov & Popov, 2010). However, there is still no general consensus within the field on how to minimize RD during MX data collection, and debates on the dependence of RD progression on incident X-ray energy (Shimizu et al., 2007; Liebschner et ISSN 2059-7983 al., 2015) and the efficacy of radical scavengers (Allan et al., 2013) have yet to be resolved.RD manifests in two forms. Global radiation damage is observed within reciprocal space as the overall decay of the summed intensity of reflections detected within the diffraction pattern as dose increases (Garman, 2010;Murray & Garman, 2002). Dose is defined as the a...

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Section: Discussionmentioning

confidence: 99%

RNA protects a nucleoprotein complex against radiation damage

Bury

McGeehan

Antson

et al. 2016

Acta Cryst Sect D Struct Biol

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“…DNA/RNA oxidation by · OH radical remains a field of active research. [25][26][27][28][29] Therefore, accurate determinations of the spectroscopic features of the radical products are relevant to unambiguously recognize such species in the experiments.…”

Section: The Journal Of Chemical Physics 139 071101 (2013)mentioning

confidence: 99%

Communication: Electronic UV-Vis transient spectra of the ·OH reaction products of uracil, thymine, cytosine, and 5,6-dihydrouracil by using the complete active space self-consistent field second-order perturbation (CASPT2//CASSCF) theory

Francés‐Monerris

Merchán

Roca‐Sanjuán

2013

The Journal of Chemical Physics

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“…These results suggest that the irradiated and recovered bacteria were as virulent as the non-irradiated cells in terms of capacity to produce enterotoxins. It has been reported that the irradiation has direct effect on DNA binding protein and sugar bases due to the effect of OH • (30) of which the role of DNA binding protein has been clearly stipulated in previously reported work (29). When the protein which function as the ligand of DNA and has a critical function including the DNA repair is damaged due to the effect of irradiation we expected to see loss of integrity of the DNA double strand beyond the ordinary identification by PCR.…”

Section: Resultsmentioning

confidence: 91%

“…In this study up to 10 kGy of γ-irradiation was found to be not enough to eliminate B. cereus from food, also the survived bacteria after γ-irradiation were able to multiply again when favorable condition is provided. On the other hand, higher doses of γ-irradiation have been reported to have negative impact on the quality parameters of these food products (19,29). Hence it can be suggested that γ-irradiation up to 10 kGy may affect the quality of the vegetables without necessarily eliminating the contaminating B. cereus.…”

Section: Resultsmentioning

confidence: 99%

Resistance of Bacillus cereus and its enterotoxin genes in ready-to-eat foods to γ-irradiation

Mtenga

Kassim

Lee

et al. 2012

Food Sci Biotechnol

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This study was investigated the resistance of Bacillus cereus ATCC 13752 and its enterotoxin coding genes in cereals, vegetables, and tryptic soy broth to γ-irradiation. Screening for enterotoxin coding genes, viability test, PCR analysis, measurement of DNA concentration, cellular constituents release, SEM, and antibiotic sensitivity tests were performed after irradiation at 0, 1.5, 3, 5, 7, 10, and 15 kGy. Thirty % of strains screened possessed all enterotoxins genes. At 10 kGy B. cereus viable cell count was reduced by 4 logCFU/mL. B. cereus in vegetables and broth demonstrated higher susceptibility than those in cereals. Enterotoxins coding genes could be identified in the γ-irradiated cells, antibiotic sensitivity profile was not affected. Concentration of DNA containing enterotoxin coding genes was reduced and release of cellular constituent was highest at 15 kGy. γ-Irradiation up to 10 kGy did not eliminate B. cereus neither affected their enterotoxins coding genes from ready-to-eat food.

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Radiation damage to DNA in DNA–protein complexes

Cited by 47 publications

References 49 publications

RNA protects a nucleoprotein complex against radiation damage

RNA protects a nucleoprotein complex against radiation damage

Communication: Electronic UV-Vis transient spectra of the ·OH reaction products of uracil, thymine, cytosine, and 5,6-dihydrouracil by using the complete active space self-consistent field second-order perturbation (CASPT2//CASSCF) theory

Resistance of Bacillus cereus and its enterotoxin genes in ready-to-eat foods to γ-irradiation

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