Advertisement

Characterization of the Chemical Reactivity and Selectivity of DNA Bases Through the Use of DFT-Based Descriptors

  • Vanessa Labet
  • Christophe MorellEmail author
  • Vincent Tognetti
  • Olga A. Syzgantseva
  • Laurent Joubert
  • Nelly Jorge
  • André Grand
  • Jean Cadet
Chapter
Part of the Topics in Heterocyclic Chemistry book series (TOPICS, volume 38)

Abstract

In this chapter, the use of conceptual DFT descriptors for understanding the occurrence and likely mechanisms of formation of DNA lesions is reviewed. After a synthetic presentation of the principal DFT-based descriptors, the global reactivity and selectivity of DNA bases are investigated from global and local descriptors. Then, the formation of several DNA lesions is studied including cytosine compound deamination, intra-strand DNA cross-links, and pyrimidine dimer photoproducts. It appears from the use of the global and local DFT-based descriptors that most of the experimental facts can be theoretically rationalized.

Keywords

Descriptors of chemical reactivity Conceptual DFT DNA damage Cytosine deamination Cyclobutane pyrimidine dimers Pyrimidine (6–4) pyrimidone photoproducts Tandem base lesions Purine 5′,8-cyclonucleosides Dual descriptors 

Notes

Acknowledgments

All the authors thank INSERM: “This research has benefited from ITMO cancer of Aviesan within the framework Plan Cancer 2009–2013.” Cette recherche a bénéficié de l’aide de l’ITMO cancer d’Aviesan dans le cadre du Plan Cancer 2009–2013.

References

  1. 1.
    Lindahl T (1993) Nature 362:709–715CrossRefGoogle Scholar
  2. 2.
    Cadet J (1994) In: Hemminki K, Dipple A, Shuker DEG, Kadlubar FF, Segerbäck D, Bartsch H (eds) DNA adducts, identification and biological significance. IARC Scientific Publication, Lyon, pp 125–245Google Scholar
  3. 3.
    Gentil A, Cabrak-Neto JB, Mariage-Samson R, Margot A, Imbach J-L, Rayner B, Sarasin A (1992) J Mol Biol 227:981CrossRefGoogle Scholar
  4. 4.
    Carell T, Brandmayr C, Hienzch A, Müller M, Pearson D, Reiter V, Thoma I, Thumbs P, Wagner M (2012) Angew Chem Int Ed 51:7110CrossRefGoogle Scholar
  5. 5.
    Branco MR, Ficz G, Reik W (2012) Nat Rev Genet 13:7Google Scholar
  6. 6.
    Kkriaucionis S, Heintz N (2009) Science 324:929CrossRefGoogle Scholar
  7. 7.
    Tahliani M, Koh KP, Shen YH, Pastor WA, Bandukwala H, Brudno Y, Agarawal S, Iyer LM, Liu DR, Aravind L, Rao A (2009) Science 324:930CrossRefGoogle Scholar
  8. 8.
    Shapiro R, Klein RS (1966) Biochemistry 5:2358CrossRefGoogle Scholar
  9. 9.
    Lindahl T, Lindahl B (1974) Biochemistry 13:3405CrossRefGoogle Scholar
  10. 10.
    Shen JC, Rideout WM III, Jones PA (1994) Nucleic Acids Res 22:972CrossRefGoogle Scholar
  11. 11.
    Lindahl T (1982) Ann Rev Biochem 51:61CrossRefGoogle Scholar
  12. 12.
    Neddermann P, Jiricny J (1993) J Biol Chem 268:21218Google Scholar
  13. 13.
    Cadet J, Loft S, Olinski R, Evans MD, Bialkowski K, Wagner JR, Dedon PC, Moeller P, Greenberg MM, Cooke MS (2012) Free Radic Res 46:367CrossRefGoogle Scholar
  14. 14.
    Murphy MP (2009) Biochem J 417:1CrossRefGoogle Scholar
  15. 15.
    Ferguson LR (2010) Mutat Res 690:3CrossRefGoogle Scholar
  16. 16.
    Park JB (2003) Exp Mol Med 35:325CrossRefGoogle Scholar
  17. 17.
    von Sonntag C (2006) Free-radical-induced DNA damage and its repair – a chemical perspective. Springer, Berlin/Heidelberg/New YorkCrossRefGoogle Scholar
  18. 18.
    Cadet J, Douki T, Ravanat J-L (2010) Free Radic Biol Med 49:9–21CrossRefGoogle Scholar
  19. 19.
    Cadet J, Ravanat J-L, TavernaPorro M, Menoni H, Angelov D (2012) Cancer Lett 327:5CrossRefGoogle Scholar
  20. 20.
    Dedon PC (2008) Chem Res Toxicol 21:206CrossRefGoogle Scholar
  21. 21.
    Cadet J, Wagner J-R (2013) Cold Spring Harb Perspect Biol 5:a012559CrossRefGoogle Scholar
  22. 22.
    Beckman JS, Beckman TW, Chen J, Marshall PA, Freeman BA (1990) Proc Natl Acad Sci U S A 87:1620CrossRefGoogle Scholar
  23. 23.
    Denicola A, Freeman BA, Trujillo M, Radi R (1996) Arch Biochem Biophys 333:49CrossRefGoogle Scholar
  24. 24.
    Medinas DB, Cerchario G, Trindale DF, Augusto O (2007) IUBMB Life 59:255CrossRefGoogle Scholar
  25. 25.
    Crean C, Uvaydov Y, Geacintov N, Shafirovich V (2008) Nucleic Acids Res 36:742CrossRefGoogle Scholar
  26. 26.
    Perrier S, Hau J, Gasparutto D, Cadet J, Favier A, Ravanat J-L (2006) J Am Chem Soc 128:5703CrossRefGoogle Scholar
  27. 27.
    Cadet J, Douki T, Ravanat J-L (2008) Acc Chem Res 41:1075CrossRefGoogle Scholar
  28. 28.
    Madugundu GS, Wagner JR, Cadet J, Kropachev K, Yun BH, Geacintov NE, Shafirovich V (2013) Chem Res Toxicol 26:1031–1033Google Scholar
  29. 29.
    Cadet J, Ravanat J-L, Martinez GR, Medeiros MH, Di Mascio P (2006) Photochem Photobiol 82:1219CrossRefGoogle Scholar
  30. 30.
    Epe B (2012) Photochem Photobiol Sci 11:98CrossRefGoogle Scholar
  31. 31.
    Cadet J, Sage E, Douki T (2005) Mutat Res 571:3CrossRefGoogle Scholar
  32. 32.
    Cadet J, Mouret S, Ravanat J-L, Douki T (2012) Photochem Photobiol 88:1048CrossRefGoogle Scholar
  33. 33.
    Courdavault S, Baudouin C, Charveron M, Canghilem B, Favier A, Cadet J, Douki T (2005) DNA Repair (Amst) 4:836CrossRefGoogle Scholar
  34. 34.
    Wallace SS, Murphy DL, Sweasy JB (2012) Cancer Lett 327:73CrossRefGoogle Scholar
  35. 35.
    Friedberg EC (2001) Nat Rev Cancer 1:22CrossRefGoogle Scholar
  36. 36.
    Heil K, Pearson D, Carell T (2011) Chem Soc Rev 40:4271CrossRefGoogle Scholar
  37. 37.
    Budden T, Bowden NA (2013) Int J Mol Sci 14:1132CrossRefGoogle Scholar
  38. 38.
    Batista FZ, Kaina B, Menegheni R, Menck CFM (2009) Mutat Res 681:197CrossRefGoogle Scholar
  39. 39.
    Wang Y (2008) Chem Res Toxicol 21:276CrossRefGoogle Scholar
  40. 40.
    Belmadoui N, Boussicault F, Guerra M, Ravanat J-L, Chatgilialoglu C, Cadet J (2010) Org Biomol Chem 8:3211CrossRefGoogle Scholar
  41. 41.
    Chatgilialoglu C, Ferreri C, Terzidis MA (2011) Chem Soc Rev 40:1368CrossRefGoogle Scholar
  42. 42.
    Geerlings P, De Proft F, Langenaeker W (2003) Chem Rev 103:1793CrossRefGoogle Scholar
  43. 43.
    Chermette H (1999) J Comput Chem 20:129CrossRefGoogle Scholar
  44. 44.
    Ayers PW, Anderson JSM, Bartolotti JL (2005) Int J Quantum Chem 103:1793Google Scholar
  45. 45.
    Senet P (1996) J Chem Phys 105:6471CrossRefGoogle Scholar
  46. 46.
    Parr RG, Donnelly RA, Levy M, Palke WE (1978) J Chem Phys 68:3801CrossRefGoogle Scholar
  47. 47.
    Parr RG, Pearson RG (1983) J Am Chem Soc 105:7512CrossRefGoogle Scholar
  48. 48.
    Parr RG, Yang W (1984) J Am Chem Soc 106:4049CrossRefGoogle Scholar
  49. 49.
    Geerlings P, Sablon N, Fievez T, De Proft F (2010) Abs Papers Am Chem Soc 240:212Google Scholar
  50. 50.
    Fuentealba P, Parr RG (1991) J Chem Phys 94:5559CrossRefGoogle Scholar
  51. 51.
    Morell C, Grand A, Toro-Labbé A, Chermette H (2013) J Mol Model 19:2893–2900CrossRefGoogle Scholar
  52. 52.
    Iczkowski RP, Margrave JL (1961) J Am Chem Soc 83:3547CrossRefGoogle Scholar
  53. 53.
    Mulliken RS (1934) J Chem Phys 2:782CrossRefGoogle Scholar
  54. 54.
    Yang W, Parr RG (1985) Proc Natl Acad Sci U S A 82:6723CrossRefGoogle Scholar
  55. 55.
    Pearson RG (1983) J Am Chem Soc 85:3533CrossRefGoogle Scholar
  56. 56.
    Pearson RG (1987) J Chem Educ 64:561CrossRefGoogle Scholar
  57. 57.
    Parr RG, Zhou Z (1993) Acc Chem Res 26:256CrossRefGoogle Scholar
  58. 58.
    Parr R, von Szventpaly L, Liu S (1999) J Am Chem Soc 121:1992CrossRefGoogle Scholar
  59. 59.
    Klopman G (1968) J Am Chem Soc 90:223CrossRefGoogle Scholar
  60. 60.
    Salem L (1968) J Am Chem Soc 90:543CrossRefGoogle Scholar
  61. 61.
    Fukui K (1957) J Chem Phys 27:1247CrossRefGoogle Scholar
  62. 62.
    Fukui K (1987) Science 218:747CrossRefGoogle Scholar
  63. 63.
    Yang W, Mortier WJ (1986) J Am Chem Soc 108:5708CrossRefGoogle Scholar
  64. 64.
    Hocquet A, Toro-Labbé A, Chermette H (2004) J Mol Struct (THEOCHEM) 686:213CrossRefGoogle Scholar
  65. 65.
    Cadet J, Grand A, Morell C, Letelier JR, Montcada JL, Toro-Labbé A (2002) J Phys Chem A 107:5334CrossRefGoogle Scholar
  66. 66.
    Fievez T, Weckhuysen BM, De Proft F, Geerlings P (2009) J Phys Chem C 113:19905CrossRefGoogle Scholar
  67. 67.
    Muya JT, De Proft F, Geerlings P, Nguyen MT, Ceulemans A (2011) J Phys Chem A 115:9609Google Scholar
  68. 68.
    Sablon N, De Proft F, Geerlings P (2010) J Chem Phys Lett 1:1228CrossRefGoogle Scholar
  69. 69.
    Yang W, Cohen A, De Proft F, Geerlings P (2012) J Chem Phys 136:144110CrossRefGoogle Scholar
  70. 70.
    Sablon N, De Proft P, Sola M, Geerlings P (2012) Phys Chem Chem Phys 14:3960CrossRefGoogle Scholar
  71. 71.
    Morell C, Grand A, Toro-Labbé A (2005) J Phys Chem A 109:205CrossRefGoogle Scholar
  72. 72.
    Morell C, Grand A, Toro-Labbé A (2006) Chem Phys Lett 425:342CrossRefGoogle Scholar
  73. 73.
    Berkowitz M, Parr RG (1988) J Chem Phys 88:2554CrossRefGoogle Scholar
  74. 74.
    Ayers PW, Morell C, De Proft F, Geerling P (2007) Chem Eur J 13:8240CrossRefGoogle Scholar
  75. 75.
    Morell C, Labet V, Grand A, Ayers PW, Geerlings P, De Proft F, Chermette H (2009) J Chem Theory Comput 5:2274CrossRefGoogle Scholar
  76. 76.
    Morell C, Labet V, Ayers PW, Genovese L, Grand A, Chermette H (2011) J Phys Chem A 115:8032CrossRefGoogle Scholar
  77. 77.
    Tognetti V, Morell C, Ayers PW, Joubert L, Chermette H (2013) Phys Chem Chem Phys 15:14465–14475Google Scholar
  78. 78.
    Kumar V, Kishor S, Ramaniah LM (2012) J Mol Model 18:3969CrossRefGoogle Scholar
  79. 79.
    Ciino P, Gomez-Paloma L, Barone V (2004) J Org Chem 69:7414CrossRefGoogle Scholar
  80. 80.
    Sivanesan D, Subramanian V, Nair BU (2001) J Mol Struct (THEOCHEM) 544:123CrossRefGoogle Scholar
  81. 81.
    Saha S, Wang F, MacNaughton JB, Moewes A, Chang DP (2008) J Synchrotron Radiat 15:151CrossRefGoogle Scholar
  82. 82.
    Saha S, Roy RK (2007) J Phys Chem B 111:9664CrossRefGoogle Scholar
  83. 83.
    Parthasarti R, Amutha R, Subramanian V, Nair BU, Ramasami T (2004) J Phys Chem A 108:3817CrossRefGoogle Scholar
  84. 84.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas O, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09, Revision A.02. Gaussian, WallingfordGoogle Scholar
  85. 85.
    Chamorro E, Perez P (2005) J Chem Phys 123:114107CrossRefGoogle Scholar
  86. 86.
    Box HC, Dawidzik JD, Budzinski EE (2001) Free Radic Biol Med 31:856CrossRefGoogle Scholar
  87. 87.
    Cadet J, Berger M, Douki T, Ravanat J-L (1997) Rev Physiol Biochem Pharmacol 131:1Google Scholar
  88. 88.
    Grand A, Morell C, Labet V, Cadet J, Eriksson LA (2007) J Phys Chem A 111:8968–8972CrossRefGoogle Scholar
  89. 89.
    Akin M (2010) Thesis of the Georgia Institute of Technology, AtlantaGoogle Scholar
  90. 90.
    Inostroza-Rivera R, Herrera B, Toro-Labbé A (2012) Comput Theor Chem 990:222CrossRefGoogle Scholar
  91. 91.
    Wagner JR, Cadet J (2010) Acc Chem Res 43:564CrossRefGoogle Scholar
  92. 92.
    Bellon S, Ravanat J-L, Gasparutto D, Cadet J (2002) Chem Res Toxicol 15:598CrossRefGoogle Scholar
  93. 93.
    Dizdaroglu M, Jaruga P, Rodriguez H (2001) Free Radic Biol Med 30:774CrossRefGoogle Scholar
  94. 94.
    Jaruga P, Birincioglu M, Rodriguez H, Dizdaroglu M (2001) Biochemistry 41:3703CrossRefGoogle Scholar
  95. 95.
    Zhang RB, Eriksson LA (2006) Chem Phys Lett 417:303–308CrossRefGoogle Scholar
  96. 96.
    Xerri B, Morell C, Grand A, Cadet J, Cimino P, Barone V (2006) Org Biomol Chem 4:3986–3992CrossRefGoogle Scholar
  97. 97.
    Labet V, Morell C, Grand A, Cadet J, Cimino P, Barone V (2008) Org Biomol Chem 6:3300CrossRefGoogle Scholar
  98. 98.
    Labet V, Grand A, Morell C, Cadet J, Eriksson LA (2008) Theor Chem Acc 120:429CrossRefGoogle Scholar
  99. 99.
    Douki T, Cadet J (2001) Biochemistry 40:2495CrossRefGoogle Scholar
  100. 100.
    Ehrlich M, Norris KF, Wang RY-H, Kuo KC, Gehrke CW (1986) Biosci Rep 6:387CrossRefGoogle Scholar
  101. 101.
    Slae S, Shapiro R (1978) J Org Chem 43:1721CrossRefGoogle Scholar
  102. 102.
    Douki T, Cadet J (1992) J Photochem Photobiol B 15:199CrossRefGoogle Scholar
  103. 103.
    Douki T, Cadet J (1994) Biochemistry 33:11942CrossRefGoogle Scholar
  104. 104.
    Frederico LA, Kunkel TA, Shaw BR (1990) Biochemistry 29:2532CrossRefGoogle Scholar
  105. 105.
    Labet V, Morell C, Cadet J, Eriksson LA, Grand A (2009) J Phys Chem A 113:2524CrossRefGoogle Scholar
  106. 106.
    Labet V, Morell C, Douki T, Cadet J, Eriksson LA, Grand A (2010) J Phys Chem A 114:1826CrossRefGoogle Scholar
  107. 107.
    Grand A, Cadet J, Eriksson LA, Labet V, Jorge NL, Schreiber ML, Douki T, Morell C (2012) Theor Chem Acc 131:1187CrossRefGoogle Scholar
  108. 108.
    Breneman CM, Wiberg KB (1990) J Comp Chem 11:361CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Vanessa Labet
    • 1
  • Christophe Morell
    • 2
    Email author
  • Vincent Tognetti
    • 3
  • Olga A. Syzgantseva
    • 3
  • Laurent Joubert
    • 3
  • Nelly Jorge
    • 4
  • André Grand
    • 5
  • Jean Cadet
    • 5
  1. 1.Sorbonne Universités, UPMC Univ Paris 6, MONARIS, UMR 8233ParisFrance
  2. 2.Université de Lyon 1, ISA, UMR 5280VilleurbanneFrance
  3. 3.Normandie Université, COBRA, UMR6014 & FR 3038, Université de Rouen, INSA Rouen, CNRSMont-Saint-Aignan CedexFrance
  4. 4.Área Fisicoquímica, Facultad de Ciencias Exactas y Naturales y AgrimensuraUNNECorrientesArgentina
  5. 5.CEA Grenoble -Institut Nanosciences et Cryogénie/SCIB/LAN (UMR-E n 3 CEA-UJF), CEA-GrenobleGrenoble Cedex 9France

Personalised recommendations