Skip to main content
SpringerLink
Log in

Insight on the interaction of polychlorobiphenyl with nucleic acid–base

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

The interaction between one polychlorobiphenyl (3,3′,4,4′,-tetrachlorobiphenyl, coded PCB77) and the four DNA nucleic acid–base is studied by means of quantum mechanics calculations in stacked conformations. It is shown that even if the intermolecular dispersion energy is the largest component of the total interaction energy, some other contributions play a non negligible role. In particular the electrostatic dipole-dipole interaction and the charge transfer from the nucleobase to the PCB are responsible for the relative orientation of the monomers in the complexes. In addition, the charge transfer tends to flatten the PCB, which could therefore intercalate more easily between DNA base pairs. From these seminal results, we predict that PCB could intercalate completely between two base pairs, preferably between Guanine:Cytosine pairs.

Molecular orbital interaction diagram of stacked PCB77 and Adenine.

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

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Jimenez B, Wright C, Kelly M, Startin JR (1996) Levels of PCDDs, PCDFs and non-ortho PCBs in dietary supplement fish oil obtained in spain. Chemosphere 32:461–467

    Article  CAS  Google Scholar 

  2. Kurokowa Y, Matsueda T, Nakamura M, Takada S, Fukamachi K (1996) Characterization of non-ortho coplanar PCBs, polychlorinated dibenzo-p-dioxines and dibenzofurans in the atmosphere. Chemosphere 32:491–500

    Article  Google Scholar 

  3. Morgan DP, Roan CC (1971) Absorption, storage, and metabolic conversion of ingested DDT and DDT metabolites in man. Arch Environ Health 22:301–308

    CAS  Google Scholar 

  4. Kimbrough RD (1995) Polychlorinated biphenyls (PCBs) and human health: an update. Crit Rev Toxicol 25:133–163

    Article  CAS  Google Scholar 

  5. Faroon OM, Keith S, Jones D, De Rosa C (2001) Carcinogenic effects of polychlorobiphenyls. Toxicol Ind Health 17:41–62

    Article  CAS  Google Scholar 

  6. Safe SH (1994) Polychlorinated biphenyls (PCBs): environnemental impact, biochemical and toxic responses, and implications for risk assessment. Crit Rev Toxicol 24:87–149

    Article  CAS  Google Scholar 

  7. Preston BD, Miller JA, Miller EC (1984) Reactions of 2,2′,5,5′-tetrachlorobiphenyl 3,4-oxide with methionine, cysteine and glutathione in relation to the formation of methylthio-metabolites of 2,2′,5,5′-tetrachlorobiphenyl in the rat and mouse. Chem Biol Interact 50:289–312

    Article  CAS  Google Scholar 

  8. Narbonne JF, Daubeze M (1980) In vitro binding hexachlorobiphenyl to DNA and proteins. Toxicology 16:173–175

    Article  CAS  Google Scholar 

  9. Poland A, Glover E, Kende AS (1976) Stereospecific high binding affinity of 2,3,7,8-teratchlorodibenzo-p-dioxin by cytosols. Evidence that the binding species is a receptor for induction of aryl hydrocarbon hydroxylase. J Biol Chem 251:4936–4946

    CAS  Google Scholar 

  10. Cheney BV, Tolly T (1979) Electronic factor affecting receptor binding of binding of dibenzo-p-dioxins and dibenzofurans. Int J Quant Chem 16:87–110

    Article  CAS  Google Scholar 

  11. Parthasarathi R, Padmanabhan J, Sbramanian V, Maiti B, Chattaraj PK (2003) J Phys Chem A 107:10346–10352

    Article  CAS  Google Scholar 

  12. Yoshimura H, Yoshihara S, Ozawa N, Miki M (1979) Possible correlation between induction modes of hepatic enzymes by PCBs and their toxicity in rats. Ann NY Acad Sci 320:179–192

    CAS  Google Scholar 

  13. Jimenez B, Hernandez LM, Eljarrat E, Rivera J, Gonzalez MJ (1996) Level of PCDDs, PCDFs, and non-ortho PCBs in serum samples of non-exposed individuals living in Madrid (Spain). Chemosphere 33:2403–2410

    Article  CAS  Google Scholar 

  14. Tanabe S, Kannan N, Wakimoto T, Tatsukawa R (1987) Method for the determination of three toxic nonortho chlorine substituted coplanar PCBs in environmental samples at part-per-trillion levels. Int J Environ Anal Chem 29:199–213

    Article  CAS  Google Scholar 

  15. Faqi AS, Dalsenter PR, Merker HJ, Chahoud I (1998) Effects on developmental landmarks and reproductive capability of 3,3′,4,4′-tetrachlorobiphenyl and 3,3′,4,4′-pentachlorobiphenyl in offspring of rats exposed during pregnancy. Hum Exp Toxicol 17:365–372

    Article  CAS  Google Scholar 

  16. Gray LE Jr, Wolf C, Mann P, Price M, Cooper RL, Ostby J (1999) Adminstration of potentially antiangenic pesticides and toxic substances (dibutyl- and dielthyl hexyl phtalate, PCB169, and ethane dimethane sulfonate) during sexuel differentiation produces divers profiles of reproductive malformations in the male rate. Toxicol Ind Health 15:94–118

    Article  Google Scholar 

  17. Hong C, Bush B, Xiao J (1992) Coplanar PCBs in fish and mussels from marine and estuarine waters of New York states. Ecotoxicol Environ Safety 23:118–131

    Article  CAS  Google Scholar 

  18. Sargent S, Roloff B, Meisner L (1989) In vitro chromosome damage due to PCB interactions. Mutat Res 224:79–88

    Article  CAS  Google Scholar 

  19. Wasson JS, Huff JE, Loprieno N (1977) A review of the genetic toxicology of chlorinated dibenzo-p-dioxins. Mutat Res 47:141–160

    Article  Google Scholar 

  20. Poland A, Glover E (1980) 2,3,7,8-tetrachlorodibenzo-p-dioxin: segregation of toxicity with the Ah locus. Mol Pharmacol 17:86–94

    CAS  Google Scholar 

  21. Safe S (1986) Comparative toxicology and mechanism of action of polychlorinated dibenzofurans. Annu Rev Pharmacol Toxicol 26:371–399

    Article  CAS  Google Scholar 

  22. Swart M, Wijst TV, Guerra CF, Bickelhaupt FM (2007) π-π stacking tackled with density functional theory. J Mol Model 13:1245–1257

    Article  CAS  Google Scholar 

  23. Vosko SH, Wilk L, Nusair M (1980) Accurate spin-dependent electron liquid correlation energies for local spin density calculations: A critical analysis. Can J Phys 58:1200–1211

    Article  CAS  Google Scholar 

  24. Zimmerli U, Parrinello M, Koumoustsakos P (2004) Dispersion corrections to density functionals for water aromatic interactions. J Chem Phys 120:2693–2699

    Article  CAS  Google Scholar 

  25. Grimme S (2004) Accurate description of van der Waals complexes by density functional theory including empirical corrections. J Comput Chem 25:1463–1473

    Article  CAS  Google Scholar 

  26. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian03, revision B.05. Gaussian, Inc, Wallingford

    Google Scholar 

  27. Sponer J, Leszczynski J, Hobza P (1996) Nature of nucleic acid − base stacking: nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs. J Phys Chem 100:5590–5596

    Article  CAS  Google Scholar 

  28. Hobza P, Sponer J (1999) Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical Ab initio calculations. Chem Rev 99:3247–3276

    Article  CAS  Google Scholar 

  29. Sponer J, Florian J, Ng HL, Sponer JE, Spackova N (2000) Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)2 B↔A intermediate crystal structure. Nucleic Acids Res 28:4893–4902

    Article  CAS  Google Scholar 

  30. Swart M, Ehlers AW, Lammertsma K (2004) Performance of the OPBE exchange-correlation functional. Mol Phys 102:2467–2474

    Article  CAS  Google Scholar 

  31. Cassandra DM, Wetmore C, Wetmore SD (2009) Noncovalent interactions involving histidine: the effect of charge on π − π stacking and T-shaped interactions with the DNA nucleobases. J Phys Chem B 113:16046–16058

    Article  Google Scholar 

  32. Rutledge LR, Wheaton CA, Wetmore SD (2007) A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine. Phys Chem Chem Phys 9:497–509

    Article  CAS  Google Scholar 

  33. Mulliken RS (1955) Electronic population analysis on LCAO MO molecular wave functions I. J Chem Phys 23:1833–1840

    Article  CAS  Google Scholar 

Download references

Acknowledgments

SA is very thankful to the Algerian government for a bursary. AM and XA thank the Agence National de la Recherche for funding ANR-09-BLAN-0191-01 PhotoBioMet.

Author information

Authors and Affiliations

  1. Equipe de Chimie et Biochimie Théoriques, UMR 7565 CNRS UL, Université de Lorraine, BP 70239, 54506, Vandoeuvre-lès-Nancy, France

    Soraya Abtouche, Thibaut Very, Antonio Monari & Xavier Assfeld

  2. Centre de Recherche Scientifique et Technique en Analyses Physico – Chimiques, BP 248, Alger, RP, 16004, Algerie

    Soraya Abtouche

  3. Laboratoire Physico Chimie Théorique et Chimie Informatique, USTHB, BP 32 EL ALIA 16111 BAB EZZOUAR, Alger, Algerie

    Soraya Abtouche & Meziane Brahimi

Authors
  1. Soraya Abtouche
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Thibaut Very
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Antonio Monari
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Meziane Brahimi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xavier Assfeld
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xavier Assfeld.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(DOC 527 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Abtouche, S., Very, T., Monari, A. et al. Insight on the interaction of polychlorobiphenyl with nucleic acid–base. J Mol Model 19, 581–588 (2013). https://doi.org/10.1007/s00894-012-1580-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-012-1580-3

Keywords

Search

Navigation