Skip to main content
SpringerLink
Log in

Thermochemical properties of some vinyl chloride-induced DNA lesions: detailed view from NBO & AIM analysis

  • Original Research
  • Published:
Structural Chemistry Aims and scope Submit manuscript

Abstract

Etheno-damaged DNA adducts such as 3,N 4-ethenocytosine, N 2,3-ethenoguanine, and 1,N 2-ethenoguanine are associated with carcinogenesis and cell death. These inevitable damages are counteracted by glycosylase enzymes, which cleave damaged nucleobases from DNA. Escherichia coli alkyl purine DNA glycosylase is the enzyme responsible for excising damaged etheno adducts from DNA in humans. In an effort to understand the intrinsic properties of these molecules, we examined gas-phase acidity values and proton affinities (PA) of multiple sites of these molecules as well as equilibrium tautomerization and base pairing properties by quantum mechanical calculations. We also used calculations to compare the acidic and basic properties of these etheno adduct with those of the normal bases—cytosine and guanine nucleobases. We hypothesize that alkyl DNA glycosylase may cleave certain damaged nucleobases as anions and that the active site may take advantage of a nonpolar environment to favor deprotonated cytosine or guanine as a leaving group versus damaged nucleobases.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Scheme 1
Scheme 2
Fig. 1
Fig. 2
Fig. 3
Scheme 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

Notes

  1. Presented at the proceeding for the ACS spring meeting 2010, the division of Organic Chemistry, Biologically–related Molecules & Processes.

References

  1. Nguyen MT, Chandra AK, Zeegers-Huyskens T (1998) J Chem Soc Faraday Trans 94:1277

    Article  CAS  Google Scholar 

  2. Chandra AK, Nguyen MT, Uchimaru T, Zeegers-Huyskens T (1999) J Phys Chem A 103:8853

    Article  CAS  Google Scholar 

  3. Saenger W (1984) Principles of nucleic acid structure. Springer, New York

    Book  Google Scholar 

  4. Dianov G, Sedgwick B, Daly G, Olsson M, Lovett S, Lindahl T (1994) Nucleic Acids Res 22:993

    Article  CAS  Google Scholar 

  5. Savva R, McAuley-Hecht K, Brown T, Pearl L (1995) Nature 373:487

    Article  CAS  Google Scholar 

  6. Radzicka A, Wolfenden R (1995) Science 267:90

    Article  CAS  Google Scholar 

  7. Lee JK, Houk KN (1997) Science 276:942

    Article  CAS  Google Scholar 

  8. Lundegaard C, Jensen KF (1999) Biochemistry 38:3327

    Article  CAS  Google Scholar 

  9. Lindahl T (1993) Nature 362:709

    Article  CAS  Google Scholar 

  10. Loeb LA (1989) Cancer Res 49:5489

    CAS  Google Scholar 

  11. Mullaart E, Lohman PH, Berends F, Vijg J (1990) Mutat Res 237:189

    Article  CAS  Google Scholar 

  12. Creech JL, Johnson MN (1974) J Occup Med 16:150

    Google Scholar 

  13. Laib RJ (1986) In: Singer B, Bartsch H (eds) The role of cyclic nucleic acid adducts in carcinogenesis and mutagenesis. IARC Scientific Publication No 70. Oxford University Press, London, pp 101–108

  14. Battaglia R, Conacher HBS, Page BD (1990) Food Addit Contam 7:477

    Article  CAS  Google Scholar 

  15. Ough CS (1976) J Agric Food Chem 24:323

    Article  CAS  Google Scholar 

  16. Kronberg L, Sjoholm R, Karlsson S (1992) Chem Res Toxicol 5:852

    Article  CAS  Google Scholar 

  17. Guengerich FP, Crawford WM, Watanabe PG (1979) Biochemistry 18:5177

    Article  CAS  Google Scholar 

  18. Ames BN, Gold LS (1991) Mutat Res 250:3

    Article  CAS  Google Scholar 

  19. Marnett LJ, Burcham PC (1993) Chem Res Toxicol 6:771

    Article  CAS  Google Scholar 

  20. Christians FC, Newcomb TG, Loeb LA (1995) Prev Med 24:329

    Article  CAS  Google Scholar 

  21. Lawley PD (1989) Mutat Res 213:3

    Article  CAS  Google Scholar 

  22. Bartsch H, Barbin A, Marion MJ, Nair J, Guichard Y (1994) Drug Metab Rev 26:349

    Article  CAS  Google Scholar 

  23. Barbin A (1999) Role of etheno DNA adducts in carcinogenesis induced by vinyl chloride in rats. IARC Scientific Publications, Lyon

    Google Scholar 

  24. Basu AK, Wood ML, Niedernhofer LJ, Ramos LA, Essigmann JM (1993) Biochemistry 32:12793

    Article  CAS  Google Scholar 

  25. Moriya M, Zhang W, Johnson F, Grollman AP (1994) Natl Acad Sci USA 91:11899

    Article  CAS  Google Scholar 

  26. Levine RL, Yang IY, Hossain M, Pandya GA, Grollman AP, Moriya M (2000) Cancer Res 60:4098

    CAS  Google Scholar 

  27. Cheng KC, Preston BD, Cahill DS, Dosanjh MK, Singer B, Loeb LA (1991) Proc Natl Acad Sci USA 88:9974–9978

    Article  CAS  Google Scholar 

  28. Langouet S, Muller M, Guengerich FP (1997) Biochemistry 36:6069

    Article  CAS  Google Scholar 

  29. Akasaka S, Guengerich FP (1999) Chem Res Toxicol 12:501

    Article  CAS  Google Scholar 

  30. Speina E, Kierzek AM, Tudek B (2003) Mutat Res 531:205

    Article  CAS  Google Scholar 

  31. Stivers JT, Jiang YL (2003) Chem Rev 103:2729

    Article  CAS  Google Scholar 

  32. Berti PJ, McCann JAB (2006) Chem Rev 106:506–555

    Article  CAS  Google Scholar 

  33. Obrien PJ, Ellenberger T (2004) J Biol Chem 279:9750

    Article  CAS  Google Scholar 

  34. Singer B, Hang B (1997) Chem Res Toxicol 10:713

    Article  CAS  Google Scholar 

  35. Parikh SS, Walcher G, Jones GD, Slupphaug G, Krokan HE, Blackburn GM, Tainer JA (2000) Proc Natl Acad Sci USA 97:5083

    Article  CAS  Google Scholar 

  36. Seeberg E, Eide L, Bjoras M (1995) Trends Biochem Sci 20:391

    Article  CAS  Google Scholar 

  37. Habraken Y, Carter CA, Kirk MC, Ludlum DB (1991) Cancer Res 51:499

    CAS  Google Scholar 

  38. Matijasevic Z, Sekiguchi M, Ludlum DB (1992) Proc Natl Acad Sci USA 89:9331

    Article  CAS  Google Scholar 

  39. Habraken Y, Carter CA, Sekiguchi M, Ludlum DB (1991) Carcinogenesis 12:1971

    Article  CAS  Google Scholar 

  40. Mertz E, Krishtalik LJ (2000) Proc Natl Acad Sci USA 97:2081

    Article  CAS  Google Scholar 

  41. Jordan F, Li H, Brown A (1999) Biochemistry 38:6369

    Article  CAS  Google Scholar 

  42. Simonson T, Brooks CL (1996) J Am Chem Soc 118:8452

    Article  CAS  Google Scholar 

  43. Gilson MK, Honig BH (1986) Biopolymers 25:2097

    Article  CAS  Google Scholar 

  44. Lowry TH, Richardson KS (1987) Mechanism and theory in organic chemistry. Harper & Row, New York

    Google Scholar 

  45. McEwen WK (1936) J Am Chem Soc 58:1124

    Article  CAS  Google Scholar 

  46. Kurinovich MA, Lee JK (2000) J Am Chem Soc 122:6258

    Article  CAS  Google Scholar 

  47. Yurenko PY, Zhurakivsky RO, Ghomi M, Samijlenko PS, Hovorun DM (2007) J Phys Chem B 111:6263

    Article  CAS  Google Scholar 

  48. Yurenko PY, Zhurakivsky RO, Ghomi M, Samijlenko PS, Hovorun DM (2007) J Phys Chem B 111:9655

    Article  CAS  Google Scholar 

  49. Yurenko PY, Zhurakivsky RO, Ghomi M, Samijlenko PS, Hovorun DM (2008) J Phys Chem B 112:1240

    Article  CAS  Google Scholar 

  50. Spartan ‘06V102’, Wavefunction, Inc., Irvine

  51. Becke AD (1993) J Chem Phys 98:5648

    Article  CAS  Google Scholar 

  52. Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785

    Article  CAS  Google Scholar 

  53. Reed AE, Weinhold F (1985) J Chem Phys 83:1736

    Article  CAS  Google Scholar 

  54. Reed AE, Weinstock RB, Weinhold F (1985) J Chem Phys 83:735

    Article  CAS  Google Scholar 

  55. Reed AE, Weinhold F (1983) J Chem Phys 78:4066

    Article  CAS  Google Scholar 

  56. Foster JP, Weinhold F (1980) J Am Chem Soc 102:7211

    Article  CAS  Google Scholar 

  57. Yurenko PY, Zhurakivsky RO, Ghomi M, Samijlenko PS, Hovorun DM (2011) J Biomol Struct Dyn 1:51

    Article  Google Scholar 

  58. Yurenko PY, Zhurakivsky RO, Ghomi M, Samijlenko PS, Hovorun DM (2007) Chem Phys Lett 447:140

    Article  CAS  Google Scholar 

  59. Shishkin VO, Palamarchuk GV, Gorb L, Leszczynski J (2006) J Phys Chem B 110:4413

    Article  CAS  Google Scholar 

  60. Samijlenko PS, Yurenko PY, Stepanyugin VA, Hovorun DM (2010) J Phys Chem B 114:1454

    Article  CAS  Google Scholar 

  61. Bader RFW (1998) J Phys Chem A 102:7314

    Article  CAS  Google Scholar 

  62. Pakiari AH, Eskandari K (2006) J Mol Struct 759:51

    CAS  Google Scholar 

  63. Abboud JLM, Mó O, De Paz JLG, Yáñez M, Esseffar MM, Bouab W, El-Mouhtadi M, Mokhlisse R, Ballesteros E, Herreros M, Homan H, Lopez-Mardomingo C, Notario R (1993) J Am Chem Soc 115:12468

    Article  CAS  Google Scholar 

  64. Rozas I, Alkorta I, Elguero J (2000) J Am Chem Soc 122:11154

    Article  CAS  Google Scholar 

  65. Espinosa E, Molins E, Lecomte C (1998) Chem Phys Lett 285:170

    Article  CAS  Google Scholar 

  66. Shishkin VO, Palamarchuk VG, Gorb L, Leszczynski J (2008) Chem Phys Lett 452:198

    Article  CAS  Google Scholar 

  67. Matta FC, Castillo N, Boyd JR (2006) J Phys Chem B 110:563

    Article  CAS  Google Scholar 

  68. Bader RFW (2002) AIM2000 program package, Ver. 2.0. McMaster University, Hamilton

  69. Kosenkov D, Kholod Y, Gorb L, Shishkin O, Hovorun DM, Mons M, Leszczynski J (2009) J Phys Chem B 113:6140

    Article  CAS  Google Scholar 

  70. Mons M, Piuzzi F, Dimicoli I, Gorb L, Leszczynski J (2006) J Phys Chem A 110:38

    Article  Google Scholar 

  71. Gorb L, Kaczmare A, Gorb A, Sadle AJ, Leszczynski J (2005) J Phys Chem B 109:13770

    Article  CAS  Google Scholar 

  72. Katritzky AR, Karelson M (1991) J Am Chem Soc 113:1561

    Article  CAS  Google Scholar 

  73. Ha TK, Gunthard HH (1993) J Am Chem Soc 115:11939

    Article  CAS  Google Scholar 

  74. Ha TK, Keller HJ, Gunde R, Gunthard HH (1999) J Phys Chem A 103:6612

    Article  CAS  Google Scholar 

  75. Nir E, Janzen C, Imhof P, Kleinermanns K, De Vries MS (2001) J Chem Phys 115:4604

    Article  CAS  Google Scholar 

  76. Nir E, Muller M, Grace LI, De Vries MS (2002) Chem Phys Lett 355:59

    Article  CAS  Google Scholar 

  77. Rejnek J, Hanus M, Labelac M, Ryjacek F, Hobza P (2005) Phys Chem Chem Phys 7:2006

    Article  CAS  Google Scholar 

  78. Plutzer C, Kleinermanns K (2002) Phys Chem Chem Phys 4:4877

    Article  Google Scholar 

  79. Shukla MK, Leszczynski J (2006) Chem Phys Lett 429:261

    Article  CAS  Google Scholar 

  80. Kosenkov D, Gorb L, Shishkin O, Sponer V, Leszczynski J (2008) J Phys Chem B 112:150

    Article  CAS  Google Scholar 

  81. Mons M, Dimicoli I, Piuzzi F, Tardivel B, Elhanine M (2002) J Phys Chem A 106:5088

    Article  CAS  Google Scholar 

  82. Trygubenko A, Bogdan TV, Rueda M, Orozco M, Luque FJ, Sponer J, Slavıcek P, Hobza P (2002) Phys Chem Chem Phys 4:4192

    Article  CAS  Google Scholar 

  83. Kryachko EK, Nguyen MT, Zeegers-Huyskens Th (2001) J Phys Chem A 105:1288

    Article  CAS  Google Scholar 

  84. Kryachko ES, Nguyen MT, Zeegers-Huyskens Th (2001) J Phys Chem A 105:1934

    Article  CAS  Google Scholar 

  85. Fogarasi G (2002) J Phys Chem A 106:1381

    Article  CAS  Google Scholar 

  86. Piacenza M, Grimme S (2004) J Comput Chem 25:83

    Article  CAS  Google Scholar 

  87. Yang Z, Rodgers MT (2004) Phys Chem Chem Phys 6:2749

    Article  CAS  Google Scholar 

  88. Tsolakidis A, Kaxiras E (2005) J Phys Chem A 109:2373

    Article  CAS  Google Scholar 

  89. Blackburn GM (1990) In: Blackburn GM, Gait MJ, Loakes JD, Williams DM (eds) Nucleic acids in chemistry and biology. IRL Press, Oxford

    Google Scholar 

  90. Sinden RR (1994) DNA structure and function. Academic Press, San Diego

    Google Scholar 

  91. Topal MD, Fresco JR (1976) Nature 263:285

    Article  CAS  Google Scholar 

  92. Sowers LC, Fazakerley GC, Eritja R, Kaplan BE, Goodman MF (1986) Proc Natl Acad Sci USA 83:5434

    Article  CAS  Google Scholar 

  93. Sowers LC, Goodman MF, Eritja R, Kaplan BE, Fazakerley GC (1989) J Mol Biol 205:437

    Article  CAS  Google Scholar 

  94. Crow JF (1993) Environ Mol Mutagen 21:122

    Article  CAS  Google Scholar 

  95. Orozco M, Hernandez B, Luque FJ (1998) J Phys Chem B 102:5228

    Article  CAS  Google Scholar 

  96. Berg JM, Tymoczko JL, Stryer L (2002) Biochemistry. W H Freeman, New York

    Google Scholar 

  97. Chase MW (1998) J Phys Chem Ref Data Monograph 9:1951

  98. NIST chemistry webbook (2003) NIST standard reference database number 69, March 2003, Mallard WG, Linstrom PJ (eds) National Institute of Standards and Technology, Gaithersburg. http://webbook.nist.gov

  99. Sharma S, Lee JK (2004) J Org Chem 69:7018

    Article  CAS  Google Scholar 

  100. Liu M, Li T, Amegayibor FS, Cardoso DS, Fu Y, Lee JK (2008) J Org Chem 73:9283

    Article  CAS  Google Scholar 

  101. Chen ECM, Chen ES (2000) J Phys Chem B 104:7835

    Article  CAS  Google Scholar 

  102. Chen ECM, Herder C, Chen ES (2006) J Mol Struct 798:126

    Article  CAS  Google Scholar 

  103. Dimitri A, Goodenough AK, Guengerich FP, Broyde S, Scicchitano AD (2008) J Mol Biol 375:353

    Article  CAS  Google Scholar 

  104. Guerra CF, Bickelhaupt FM, Snijders JG, Baerends EJ (1999) Chem Eur J 5:3581

    Article  CAS  Google Scholar 

Download references

Acknowledgments

Support from Sharif University of Technology is gratefully acknowledged.

Author information

Authors and Affiliations

  1. Department of Chemistry, Sharif University of Technology, P.O. Box 11365-9516, Tehran, Iran

    Zahra Aliakbar Tehrani, Hedieh Torabifard & Alireza Fattahi

Authors
  1. Zahra Aliakbar Tehrani
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hedieh Torabifard
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alireza Fattahi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alireza Fattahi.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Aliakbar Tehrani, Z., Torabifard, H. & Fattahi, A. Thermochemical properties of some vinyl chloride-induced DNA lesions: detailed view from NBO & AIM analysis. Struct Chem 23, 1987–2001 (2012). https://doi.org/10.1007/s11224-012-0026-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11224-012-0026-y

Keywords

Search

Navigation