Skip to main content
Log in

Interactions between Al12X (X = Al, C, N and P) nanoparticles and DNA nucleobases/base pairs: implications for nanotoxicity

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

Abstract

The interactions between neutral Al12X(I h ) (X = Al, C, N and P) nanoparticles and DNA nucleobases, namely adenine (A), thymine (T), guanine (G) and cytosine (C), as well as the Watson−Crick base pairs (BPs) AT and GC, were investigated by means of density functional theory computations. The Al12X clusters can tightly bind to DNA bases and BPs to form stable complexes with negative binding Gibbs free energies at room temperature, and considerable charge transfers occur between the bases/BPs and the Al12X clusters. These strong interactions, which are also expected for larger Al nanoparticles, may have potentially adverse impacts on the structure and stability of DNA and thus cause its dysfunction.

Adenine–thymine complex with aluminium Al12X nanoparticle

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

Access this article

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
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Fischer HC, Chan WC (2007) Nanotoxicity: the growing need for in vivo study. Curr Opin Biotechnol 18:565–571

    Article  CAS  Google Scholar 

  2. Lubick N (2008) Risks of nanotechnology remain uncertain. Environ Sci Technol 42:1821–1824

    Article  CAS  Google Scholar 

  3. Buzea C, Pacheco II, Robbie K (2007) Nanomaterials and nanoparticles: sources and toxicity. Biointerphases 2:MR17–MR71

    Article  Google Scholar 

  4. Ray PC, Yu H, Fu PP (2009) Toxicity and environmental risks of nanomaterials: challenges and future needs. J Environ Sci Health C Environ Carcinog Ecotoxicol Rev 27:1–35

    Article  CAS  Google Scholar 

  5. Bouwmeester H, Dekkers S, Noordam MY, Hagens WI, Bulder AS, De Heer C, Ten Voorde SECG, Wijnhoven SWP, Marvin HJP, Sips AJAM (2009) Review of health safety aspects of nanotechnologies in food production. Regul Toxicol Pharm 53:52–62

    Article  CAS  Google Scholar 

  6. Jones CF, Grainger DW (2009) In vitro assessments of nanomaterial toxicity. Adv Drug Deliv Rev 61:438–456

    Article  CAS  Google Scholar 

  7. Hillegass JM, Arti S, Lathrop SA, MacPherson MB, Fukagawa NK, Mossman BT (2010) Assessing nanotoxicity in cells in vitro. Wiley Interdiscip Rev Nanomed Nanobiotechnol 2:219–231

    Article  CAS  Google Scholar 

  8. Dhawan A, Sharma V (2010) Toxicity assessment of nanomaterials: methods and challenges. Anal Bioanal Chem 398:589–605

    Article  CAS  Google Scholar 

  9. Hu YL, Gao JQ (2010) Potential neurotoxicity of nanoparticles. Int J Pharm 394:115–121

    Article  CAS  Google Scholar 

  10. Fadeel B, Garcia-Bennett AE (2010) Better safe than sorry: Understanding the toxicological properties of inorganic nanoparticles manufactured for biomedical applications. Adv Drug Deliv Rev 62:362–374

    Article  CAS  Google Scholar 

  11. Aillon KL, Xie Y, El-Gendy N, Berkland CJ, Forrest ML (2009) Effects of nanomaterial physicochemical properties on in vivo toxicity. Adv Drug Deliv Rev 61:457–466

    Article  CAS  Google Scholar 

  12. Shvedova AA, Kagan VE, Fadeel B (2010) Close encounters of the small kind: adverse effects of man-made materials interfacing with the nano-cosmos of biological systems. Annu Rev Pharmacol Toxicol 50:63–88

    Article  CAS  Google Scholar 

  13. Balbus JM, Maynard AD, Colvin VL, Castranova V, Daston GP, Denison RA, Dreher KL, Goering PL, Goldberg AM, Kulinowski KM, Monteiro-Riviere NA, Oberdörster G, Omenn GS, Pinkerton KE, Ramos KS, Rest KM, Sass JB, Silbergeld EK, Wong BA (2007) Meeting report: hazard assessment for nanoparticles—report from an interdisciplinary workshop. Environ Health Perspect 115:1654–1659

    Article  Google Scholar 

  14. Ostrowski AD, Martin T, Conti J, Hurt I, Harthorn BH (2009) Nanotoxicology: characterizing the scientific literature, 2000-2007. J Nanopart Res 11:251–257

    Article  CAS  Google Scholar 

  15. Bosi S, Feruglio L, Ros TD, Spalluto G, Gregoretti B, Terdoslavich M, Decorti G, Passamonti S, Moro S, Prato M (2004) Hemolytic effects of water-soluble fullerene derivatives. J Med Chem 47:6711–6715

    Article  CAS  Google Scholar 

  16. Zhao X, Striolo A, Cummings PT (2005) C60 binds to and deforms nucleotides. Biophys J 89:3856–3862

    Article  CAS  Google Scholar 

  17. Zhao X (2008) Interaction of C60 derivatives and ssDNA from simulations. J Phys Chem C 112:8898–8906

    Article  CAS  Google Scholar 

  18. Shukla MK, Leszczynski J (2009) Fullerene (C60) forms stable complex with nucleic acid base guanine. Chem Phys Lett 469:207–209

    Article  CAS  Google Scholar 

  19. Shukla MK, Dubey M, Zakar E, Namburu R, Czyznikowska Z, Leszczynski J (2009) Interaction of nucleic acid bases with single-walled carbon nanotube. Chem Phys Lett 480:269–272

    Article  CAS  Google Scholar 

  20. Shukla MK, Dubey M, Zakar E, Namburu R, Leszczynski J (2010) Interaction of nucleic acid bases and Watson-Crick base pairs with fullerene: computational study. Chem Phys Lett 493:130–134

    Article  CAS  Google Scholar 

  21. Shukla MK, Dubey M, Zakar E, Namburu R, Leszczynski J (2010) Density functional theory investigation of interaction of zigzag (7,0) single-walled carbon nanotube with Watson-Crick DNA base pairs. Chem Phys Lett 496:128–132

    Article  CAS  Google Scholar 

  22. Mazzuca D, Russo N, Toscano M, Grand A (2006) On the interaction of bare and hydrated aluminum ion with nucleic acid bases (U, T, C, A, G) and monophosphate nucleotides (UMP, dTMP, dCMP, dAMP, dGMP). J Phys Chem B 110:8815–8824

    Article  CAS  Google Scholar 

  23. Bedrov D, Smith GD, Davande H, Li L (2008) Passive transport of C60 fullerenes through a lipid membrane: a molecular dynamics simulation study. J Phys Chem B 112:2078–2084

    Article  CAS  Google Scholar 

  24. Shang J, Ratnikova TA, Anttalainen S, Salonen E, Ke PC, Knap HT (2009) Experimental and simulation studies of a real-time polymerase chain reaction in the presence of a fullerene derivative. Nanotechnology 20:415101

    Article  Google Scholar 

  25. Redmill PS, McCabe C (2010) Molecular dynamics study of the behavior of selected nanoscale building blocks in a gel-phase lipid bilayer. J Phys Chem B 114:9165–9172

    Article  CAS  Google Scholar 

  26. Perl DP, Gajdusek DC, Garruto RM, Yanagihara RT, Gibbs CJ (1982) Intraneuronal aluminum accumuation in amyotrophic lateral sclerosis and Parkinsonism-dementia of Guam. Science 217:1053–1055

    Article  CAS  Google Scholar 

  27. De Broe ME, Coburn JW (1990) Aluminium and renal failure. Dekker, New York

    Book  Google Scholar 

  28. Guillard O, Fauconneau B, Olichon D, Dedieu G, Deloncle R (2004) Hyperaluminemia in a woman using an aluminum-containing antiperspirant for 4 years. Am J Med 117:956–959

    Article  Google Scholar 

  29. Foncin JF (1987) Alzheimer’s disease and aluminum. Nature 326:136

    Article  CAS  Google Scholar 

  30. Kawahara M (2005) Effects of aluminum on the nervous system and its possible link with neurodegenerative diseases. J Alzheimers Dis 8:171–182

    CAS  Google Scholar 

  31. Braydich-Stolle LK, Speshock JL, Castle A, Smith M, Murdock RC, Hussain SM (2010) Nanosized aluminum altered immune function. ACS Nano 4:3661–3670

    Article  CAS  Google Scholar 

  32. Pedersen DB, Simard B, Martinez A, Moussatova A (2003) Stabilization of an unusual tautomer of guanine: photoionization of Al-guanine and Al-guanine-(NH3)n. J Phys Chem A 107:6464–6469

    Article  CAS  Google Scholar 

  33. Frisch MJ et al (2004) Gaussian 03, Gaussian, Inc., Wallingford CT

  34. Pedersen DB, Zgierski MZ, Denommee S, Simard B (2002) Photoinduced charge-transfer dehydrogenation in a gas-phase metal-DNA base complex: Al-cytosine. J Am Chem Soc 124:6686–6692

    Article  CAS  Google Scholar 

  35. De Heer WA (1993) The physics of simple metal clusters: experimental aspects and simple models. Rev Mod Phys 65:611–676

    Article  Google Scholar 

  36. Khanna SN, Jena P (1992) Assembling crystals from clusters. Phys Rev Lett 69:1664–1667

    Article  CAS  Google Scholar 

  37. Gong XG, Kumar V (1993) Enhanced stability of magic clusters: a case study of icosahedral Al12X, X = B, Al, Ga, C, Si, Ge, Ti, As. Phys Rev Lett 70:2078–2081

    Article  CAS  Google Scholar 

  38. Kumar V, Bhattacharjee S, Kawazoe Y (2000) Silicon-doped icosahedral, cuboctahedral, and decahedral clusters of aluminum. Phys Rev B 61:8541–8547

    Article  CAS  Google Scholar 

  39. Akutsu M, Koyasu K, Atobe J, Hosoya N, Miyajima K, Mitsui M, Nakajima A (2006) Experimental and theoretical characterization of aluminum-based binary superatoms of Al12X and their cluster salts. J Phys Chem A 110:12073–12076

    Article  CAS  Google Scholar 

  40. Wang B, Zhao J, Shi D, Chen X, Wang G (2005) Density-functional study of structural and electronic properties of Al n N (n = 2–12) clusters. Phys Rev A 72:023204

    Article  Google Scholar 

  41. Zhao Y, Schultz NE, Truhlar DG (2006) Design of density functionals by combining the method of constraint satisfaction with parametrization for thermochemistry, thermochemical kinetics, and noncovalent interactions. J Chem Theor Comput 2:364–382

    Article  Google Scholar 

  42. Zhao Y, Truhlar DG (2008) Density functionals with broad applicability in chemistry. Acc Chem Res 41:157–167

    Article  CAS  Google Scholar 

  43. Henry DJ, Varano A, Yarovsky I (2008) Performance of numerical basis set DFT for aluminum clusters. J Phys Chem A 112:9835–9844, and references therein

    Article  CAS  Google Scholar 

  44. Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105:2999–3094

    Article  CAS  Google Scholar 

  45. Reed AE, Curtiss LA, Weinhold F (1988) Intermolecular interactions from a natural bond orbital donor-acceptor viewpoint. Chem Rev 88:899–926

    Article  CAS  Google Scholar 

  46. Boys SF, Bernardi F (1970) The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys 19:553–566

    Article  CAS  Google Scholar 

  47. Vázquez M-V, Martínez A (2008) Theoretical study of cytosine-Al, cytosine-Cu and cytosine-Ag (neutral, anionic and cationic). J Phys Chem A 112:1033–1039

    Article  Google Scholar 

  48. Laaksonen L (1992) A graphics program for the analysis and display of molecular dynamics trajectories. J Mol Graph 10:33–34

    Article  CAS  Google Scholar 

  49. Bergman DL, Laaksonen L, Laaksonen A (1997) Visualization of solvation structure in liquid mixtures. J Mol Graph Model 15:301–306

    Article  CAS  Google Scholar 

  50. Lippert B (2000) Multiplicity of metal ion binding patterns to nucleobases. Coord Chem Rev 200–202:487–516

    Article  Google Scholar 

  51. Hud NV (2009) Nucleic acid–metal ion interactions. RSC, Cambridge

    Google Scholar 

  52. Krasnokutski SA, Lei Y, Lee JS, Yang DS (2008) Pulsed-field ionization photoelectron and IR-UV resonant photoionization spectroscopy of Al-thymine. J Chem Phys 129:124309

    Article  Google Scholar 

  53. Moussatova A, Vázquez M-V, Martínez A, Dolgounitcheva O, Zakrzewski VG, Ortiz JV, Pedersen DB, Simard B (2003) Theoretical study of the structure and bonding of a metal-DNA base complex: Al-guanine. J Phys Chem A 107:9415–9421

    Article  CAS  Google Scholar 

  54. Robertazzi A, Platts JA (2005) Hydrogen bonding and covalent effects in binding of cisplatin to purine bases: ab initio and atoms in molecules studies. Inorg Chem 44:267–274

    Article  CAS  Google Scholar 

  55. Baker ES, Manard MJ, Gidden J, Bowers MT (2005) Structural analysis of metal interactions with the dinucleotide duplex, dCG.dCG, using ion mobility mass spectrometry. J Phys Chem B 109:4808–4810

    Article  CAS  Google Scholar 

  56. Pelmenschikov A, Zilberberg I, Leszczynski J, Famulari A, Sironi M, Raimondi M (1999) cis-[Pt(NH3)2]2+ coordination to the N7 and O6 sites of a guanine-cytosine pair: disruption of the Watson-Crick H-bonding pattern. Chem Phys Lett 314:496–500

    Article  CAS  Google Scholar 

  57. Zilberberg IL, Avdeev VI, Zhidomirov GM (1997) Effect of cisplatin binding on guanine in nucleic acid: an ab initio study. J Mol Struct THEOCHEM 418:73–81

    Article  CAS  Google Scholar 

  58. Robertazzi A, Platts JA (2005) Binding of transition metal complexes to guanine and guanine–cytosine: hydrogen bonding and covalent effects. J Biol Inorg Chem 10:854–866

    Article  CAS  Google Scholar 

  59. Mo Y (2006) Probing the nature of hydrogen bonds in DNA base pairs. J Mol Model 12:665–672

    Article  CAS  Google Scholar 

  60. Quinn JR, Zimmerman SC, Del Bene JE, Shavitt I (2007) Does the A•T or G•C base-pair possess enhanced stability? Quantifying the effects of CH•••O interactions and secondary interactions on base-pair stability using a phenomenological analysis and ab initio calculations. J Am Chem Soc 129:934–941

    Article  CAS  Google Scholar 

  61. Roca-Sanjuán D, Rubio M, Merchán M, Serrano-Andrés L (2006) Ab initio determination of the ionization potentials of DNA and RNA nucleobases. J Chem Phys 125:084302

    Article  Google Scholar 

Download references

Acknowledgments

This research has been supported in China by the National Science Foundation of China (Grant No. 20921004) and in the United States by the National Science Foundation (Grant EPS-1010094), the Institutional Research Fund of University of Puerto Rico, and the US Environmental Protection Agency (EPA Grant No. RD-83385601). We thank Computational Center for Nanotechnology Innovations (CCNI) and TeraGrid for providing computational resources.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Peng Jin or Zhongfang Chen.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

Supporting information available. The geometries and the relative energies of the optimized base/BP–Al12X complexes, the BSSE corrected binding energies and the binding Gibbs free energies at different temperatures of the base/BP–Al12X complexes, as well as the full citation of [33]. (DOC 17162 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Jin, P., Chen, Y., Zhang, S.B. et al. Interactions between Al12X (X = Al, C, N and P) nanoparticles and DNA nucleobases/base pairs: implications for nanotoxicity. J Mol Model 18, 559–568 (2012). https://doi.org/10.1007/s00894-011-1085-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-011-1085-5

Keywords

Navigation