Electron-induced damage of biotin studied in the gas phase and in the condensed phase at a single-molecule level

New Journal of Physics

Volumn 15, Issue , 2013, Pages

  Keller, Adrian ^a,b   Kopyra, Janina ^c   Gothelf, Kurt V ^b   Bald, Ilko ^b,d,e  

^a INSTITUTE OF ION BEAM PHYSICS AND MATERIALS RESEARCH   (Germany)

^b AARHUS UNIVERSITY   (Denmark)

^c SIEDLCE UNIVERSITY OF NATURAL SCIENCES AND HUMANITIES   (Poland)

^d UNIVERSITY OF POTSDAM   (Germany)

^e BAM FEDERAL INSTITUTE FOR MATERIALS RESEARCH AND TESTING   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DISSOCIATION YIELD; DISSOCIATIVE ELECTRON ATTACHMENT; INTERMOLECULAR BINDING; INTERMOLECULAR HYDROGEN; RADIATION EXPERIMENT; SECONDARY ELECTRONS; SINGLE MOLECULE LEVEL; VAN DER WAALS BONDS;

ELECTRON ENERGY ANALYZERS; GENE EXPRESSION; HYDROGEN BONDS; MOLECULES; PHOTODISSOCIATION; PROTEINS; VAN DER WAALS FORCES;

COENZYMES;

EID: 84883415926     PISSN: 13672630     EISSN: None     Source Type: Journal    
DOI: 10.1088/1367-2630/15/8/083045     Document Type: Article

References (66)

1. Green N M, Anfinsen C B, Edsall J T and Frederic M R 1975 Advances in Protein Chemistry (New York: Academic) pp 85-133
2. Sun X J, Tolbert L P and Hildebrand J G 1995 Using laser-scanning confocal microscopy as a guide for electron-microscopic study - a simple method for correlation of light and electron-microscopy J. Histochem. Cytochem. 43 329-35
3. Wang J, Xu D K, Kawde A N and Polsky R 2001 Metal nanoparticle-based electrochemical stripping potentiometric detection of DNA hybridization Anal. Chem. 73 5576-81 (Pubitemid 33108570)
4. Willard D M, Carillo L L, Jung J and Van Orden A 2001 CdSe-ZnS quantum dots as resonance energy transfer donors in a model protein-protein binding assay Nano Lett. 1 469-74 (Pubitemid 33673968)
5. Leduc C, Ruhnow F, Howard J and Diez S 2007 Detection of fractional steps in cargo movement by the collective operation of kinesin-1 motors Proc. Natl Acad. Sci. USA 104 10847-52 (Pubitemid 47175189)
6. Connolly S and Fitzmaurice D 1999 Programmed assembly of gold nanocrystals in aqueous solution Adv. Mater. 11 1202-5
7. Lee J, Govorov A O, Dulka J and Kotov N A 2004 Bioconjugates of CdTe nanowires and Au nanoparticles: plasmon-exciton interactions, luminescence enhancement and collective effects Nano Lett. 4 2323-30 (Pubitemid 40002363)
8. Hoff J D, Cheng L J, Meyhofer E, Guo L J and Hunt A J 2004 Nanoscale protein patterning by imprint lithography Nano Lett. 4 853-7 (Pubitemid 38716339)
9. Bui H, Onodera C, Kidwell C, Tan Y, Graugnard E, Kuang W, Lee J, Knowlton W B, Yurke B and Hughes W L 2010 Programmable periodicity of quantum dot arrays with DNA origami nanotubes Nano Lett. 10 3367-72
10. Ko S H, Gallatin G M and Liddle J A 2012 Nanomanufacturing with DNA origami: factors affecting the kinetics and yield of quantum dot binding Adv. Funct. Mater. 22 1015-23
11. Eskelinen A-P, Kuzyk A, Kaltiaisenaho T K, Timmermans M Y, Nasibulin A G, Kauppinen E I and Torma P 2011 Assembly of single-walled carbon nanotubes on DNA-origami templates through streptavidin-biotin interaction Small 7 746-50
12. Voigt N V et al 2010 Single-molecule chemical reactions on DNA origami Nature Nanotechnol. 5 200-3
13. Helmig S, Rotaru A, Arian D, Kovbasyuk L, Arnbjerg J, Ogilby P R, Kjems J, Mokhir A, Besenbacher F and Gothelf K V 2010 Single molecule atomic force microscopy studies of photosensitized singlet oxygen behavior on a DNA origami template ACS Nano 4 7475-80
14. Keller A, Bald I, Rotaru A, Cauet E, Gothelf K V and Besenbacher F 2012 Probing electron-induced bond cleavage at the single-molecule level using DNA origami templates ACS Nano 6 4392-9
15. Zempleni J 2005 Uptake, localization, and noncarboxylase roles of biotin Annu. Rev. Nutr. 25 175-96 (Pubitemid 41208999)
16. Hassan Y I and Zempleni J 2006 Epigenetic regulation of chromatin structure and gene function by biotin J. Nutr. 136 1763-5 (Pubitemid 43973573)
17. Peters D M, Griffin J B, Stanley J S, Beck M M and Zempleni J 2002 Exposure to UV light causes increased biotinylation of histones in Jurkat cells Am. J. Physiol. - Cell Physiol. 283 C878-84
18. Rodriguez-Melendez R, Griffin J B and Zempleni J 2004 Biotin supplementation increases expression of the cytochrome P(450)1B1 gene in Jurkat cells, increasing the occurrence of single-stranded DNA breaks J. Nutr. 134 2222-8 (Pubitemid 39201589)
19. Kothapalli N, Sarath G and Zempleni J 2005 Biotinylation of K12 in histone H4 decreases in response to DNA double-strand breaks in human JAr choriocarcinoma cells J. Nutr. 135 2337-42 (Pubitemid 41429587)
20. Baccarelli I, Bald I, Gianturco F A, Illenberger E and Kopyra J 2011 Electron-induced damage of DNA and of its components: experiments and theoretical modellings Phys. Rep. 508 1-44
21. Nguyen J, Ma Y, Luo T, Bristow R G, Jaffray D A and Lu Q-B 2011 Direct observation of ultrafast-electron-transfer reactions unravels high effectiveness of reductive DNA damage Proc. Natl Acad. Sci. USA 108 11778-83
22. Boudaiffa B, Cloutier P, Hunting D, Huels M A and Sanche L 2000 Resonant formation of DNA strand breaks by low-energy (3-20 eV) electrons Science 287 1658-60 (Pubitemid 30127768)
23. Martin F, Burrow P D, Cai Z L, Cloutier P, Hunting D and Sanche L 2004 DNA strand breaks induced by 0-4 eV electrons: the role of shape resonances Phys. Rev. Lett. 93 068101
24. Huels M A, Boudaiffa B, Cloutier P, Hunting D and Sanche L 2003 Single, double and multiple double strand breaks induced in DNA by 3-100 eV electrons J. Am. Chem. Soc. 125 4467-77 (Pubitemid 36418694)
25. Abdoul-Carime H and Sanche L 2004 Alteration of protein constituents induced by low-energy (< 40 eV) electrons: III. The aliphatic amino acids J. Phys. Chem. B 108 457-64
26. Abdoul-Carime H, Gohlke S and Illenberger E 2004 Conversion of amino-acids by electrons at subexcitation energies Phys. Chem. Chem. Phys. 6 161-4
27. Kopyra J, Szamrej I, Abdoul-Carime H, Farizon B and Farizon M 2012 Decomposition of methionine by low energy electrons Phys. Chem. Chem. Phys. 14 8000-4
28. Alizadeh E et al 2011 Bond dissociation of the dipeptide dialanine and its derivative alanine anhydride induced by low energy electrons J. Chem. Phys. 134 054305
29. Gschliesser D, Vizcaino V, Probst M, Scheier P and Denifl S 2012 Formation and decay of the dehydrogenated parent anion upon electron attachment to dialanine Chem. Eur. J. 18 4613-9
30. Abdoul-Carime H and Illenberger E 2004 Degradation of vitamin C by low-energy electrons Chem. Phys. Lett. 390 481-4
31. Abdoul-Carime H, Gohlke S and Illenberger E 2004 Site-specific dissociation of DNA bases by slow electrons at early stages of irradiation Phys. Rev. Lett. 92 168103
32. Ptasinska S, Denifl S, Grill V, Maerk T D, Scheier P, Gohlke S, Huels M A and Illenberger E 2005 Bond-selective H-ion abstraction from thymine Angew. Chem. Int. Edn Engl. 44 1647-50
33. Denifl S et al 2007 Influence of functional groups on the site-selective dissociation of adenine upon low-energy electron attachment Angew. Chem. Int. Edn Engl. 46 5238-41 (Pubitemid 47051299)
34. Bald I, Dabkowska I and Illenberger E 2008 Probing biomolecules by laser-induced acoustic desorption: electrons at near zero electron volts trigger sugar-phosphate cleavage Angew. Chem. Int. Edn Engl. 47 8518-20
35. Bald I, Kopyra J, Dabkowska I, Antonsson E and Illenberger E 2007 Low energy electron-induced reactions in gas phase 1,2,3,5-tetra-O-acetyl-b-DD- ribofuranose: a model system for the behavior of sugar in DNA J. Chem. Phys. 126 074308
36. Konig C, Kopyra J, Bald I and Illenberger E 2006 Dissociative electron attachment to phosphoric acid esters: the direct mechanism for single strand breaks in DNA Phys. Rev. Lett. 97 018105 (Pubitemid 44026377)
37. Bald I, Kopyra J and Illenberger E 2006 Selective excision of C5 from D-ribose in the gas phase by low-energy electrons (0-1 eV): implications for the mechanism of DNA damage Angew. Chem. Int. Edn Engl. 45 4851-5 (Pubitemid 44179130)
38. Kopyra J 2012 Low energy electron attachment to the nucleotide deoxycytidine monophosphate: direct evidence for the molecular mechanisms of electron-induced DNA strand breaks Phys. Chem. Chem. Phys. 14 8287-9
39. Rothemund P W K 2006 Folding DNA to create nanoscale shapes and patterns Nature 440 297-302
40. Tørring T, Voigt N V, Nangreave J, Yan H and Gothelf K V 2011 Chem. Soc. Rev. 40 5636-46
41. Andersen E S et al 2009 Self-assembly of a nanoscale DNA box with a controllable lid Nature 459 73-6
42. Han D, Pal S, Yang Y, Jiang S, Nangreave J, Liu Y and Yan H 2013 DNA Gridiron nanostructures based on four-arm junctions Science 339 1412-5
43. Alizadeh E and Sanche L 2012 Precursors of solvated electrons in radiobiological physics and chemistry Chem. Rev. 112 5578-602
44. Martin I, Skalicky T, Langer J, Abdoul-Carime H, Karwasz G, Illenberger E, Stano M and Matejcik S 2005 Low energy electron driven reactions in single formic acid molecules (HCOOH) and their homogeneous clusters Phys. Chem. Chem. Phys. 7 2212-6 (Pubitemid 40758462)
45. Kopyra J, Konig-Lehmann C, Szamrej I and Illenberger E 2009 Unusual features in electron attachment to chlorodifluoroacetic acid (CClF2COOH): Strong dissociative electron attachment near 0 eV and associative attachment at 0.75 eV Int. J. Mass Spectrom. 285 131-6
46. Kopyra J, Konig-Lehmann C and Illenberger E 2011 Low energy (0-10 eV) electron driven reactions in the halogenated organic acids CCl3COOH, CClF2COOH and CF3CHNH2COOH (trifluoroalanine) J. Chem. Phys. 135 124307
47. Scheer A M, Mozejko P, Gallup G A and Burrow P D 2007 Total dissociative electron attachment cross sections of selected amino acids J. Chem. Phys. 126 174301 (Pubitemid 46717780)
48. Gallup G A, Burrow P D and Fabrikant I I 2009 Electron-induced bond breaking at low energies in HCOOH and glycine: the role of very short-lived sigma(*) anion states Phys. Rev. A 79 042701
49. Ptasinska S, Denifl S, Mroz B, Probst M, Grill V, Illenberger E, Scheier P and Mark T D 2005 Bond selective dissociative electron attachment to thymine J. Chem. Phys. 123 124302 (Pubitemid 41407775)
50. Martin I, Langer J and Illenberger E 2008 Reactions in fluorinated acetic acid esters triggered by slow electrons: bond cleavages, hydrogen transfer reactions and loss of halocarbons Z. Phys. Chem. 222 1185-96
51. Vasil'ev Y V, Figard B J, Voinov V G, Barofsky D F and Deinzer M L 2006 Resonant electron capture by some amino acids and their methyl esters J. Am. Chem. Soc. 128 5506-15
52. McMillen D F and Golden D M 1982 Hydrocarbon bond-dissociation energies Annu. Rev. Phys. Chem. 33 493-532
53. Lide D (ed) 2002 CRC Handbook of Chemistry and Physics (Boca Raton, FL: CRC)
54. Muftakhov M V and Shchukin P V 2010 Resonant dissociative electron capture by the simplest amino acids and dipeptides Russ. Chem. Bull. 59 896-911
55. Kopyra J, Konig-Lehmann C and Illenberger E 2012 Low energy electron attachment to N-acetylglycine Chem. Phys. Lett. 550 47-51
56. Bald I, Dabkowska I, Illenberger E and Ingolfsson O 2007 Energy selective excision of CN - following electron attachment to hexafluoroacetone azine Phys. Chem. Chem. Phys. 9 2983-90
57. Hamann T, Edtbauer A, Ferreira da Silva F, Denifl S, Scheier P and Swiderek P 2011 Dissociative electron attachment to gas-phase formamide Phys. Chem. Chem. Phys. 13 12305
58. Koenig-Lehmann C, Kopyra J, Dabkowska I, Kocisek J and Illenberger E 2008 Excision of CN - and OCN - from acetamide and some amide derivatives triggered by low energy electrons Phys. Chem. Chem. Phys. 10 6954-61
59. Ptasinska S, Denifl S, Grill V, Mark T D, Illenberger E and Scheier P 2005 Bond - and site-selective loss of H - from pyrimidine bases Phys. Rev. Lett. 95 093201 (Pubitemid 41505841)
60. Kopyra J, Koenig-Lehmann C and Illenberger E 2009 On the absolute value for the cross section of dissociative electron attachment (DEA) to the DNA base thymine Int. J. Mass Spectrom. 281 89-91
61. Sailer W, Pelc A, Probst M, Limtrakul J, Scheier P, Illenberger E and Mark T D 2003 Dissociative electron attachment to acetic acid (CH3COOH) Chem. Phys. Lett. 378 250-6
62. Pelc A, Sailer W, Scheier P, Mark T D and Illenberger E 2004 Fragmentation of propanoic acid by subexcitation electrons Chem. Phys. Lett. 392 465-9
63. Baccarelli I, Gianturco F A, Grandi A, Sanna N, Lucchese R R, Bald I, Kopyra J and Illenberger E 2007 Selective bond breaking in b-d-ribose by gas-phase electron attachment around 8 eV J. Am. Chem. Soc. 129 6269-77 (Pubitemid 46786820)
64. Bernhardt P and Paretzke H G 2003 Calculation of electron impact ionization cross sections of DNA using the Deutsch-Mark and binary-encounter- Bethe formalisms Int. J. Mass Spectrom. 223 599-611
65. Mozejko P and Sanche L 2003 Cross section calculations for electron scattering from DNA and RNA bases Rad. Environ. Biophys. 42 201-11 (Pubitemid 37521287)
66. Dionne G F 1975 Origin of secondary-electron-emission yield-curve parameters J. Appl. Phys. 46 3347-51