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

Journal of Molecular Modeling - Tập 18 - Trang 559-568 - 2011
Peng Jin1,2, Yongsheng Chen3, Shengbai B. Zhang4, Zhongfang Chen2
1Wuhan Center for Magnetic Resonance, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
2Department of Chemistry, University of Puerto Rico, San Juan, USA
3School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, USA
4Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, USA

Tóm tắt

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.

Tài liệu tham khảo

Fischer HC, Chan WC (2007) Nanotoxicity: the growing need for in vivo study. Curr Opin Biotechnol 18:565–571 Lubick N (2008) Risks of nanotechnology remain uncertain. Environ Sci Technol 42:1821–1824 Buzea C, Pacheco II, Robbie K (2007) Nanomaterials and nanoparticles: sources and toxicity. Biointerphases 2:MR17–MR71 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 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 Jones CF, Grainger DW (2009) In vitro assessments of nanomaterial toxicity. Adv Drug Deliv Rev 61:438–456 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 Dhawan A, Sharma V (2010) Toxicity assessment of nanomaterials: methods and challenges. Anal Bioanal Chem 398:589–605 Hu YL, Gao JQ (2010) Potential neurotoxicity of nanoparticles. Int J Pharm 394:115–121 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 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 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 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 Ostrowski AD, Martin T, Conti J, Hurt I, Harthorn BH (2009) Nanotoxicology: characterizing the scientific literature, 2000-2007. J Nanopart Res 11:251–257 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 Zhao X, Striolo A, Cummings PT (2005) C60 binds to and deforms nucleotides. Biophys J 89:3856–3862 Zhao X (2008) Interaction of C60 derivatives and ssDNA from simulations. J Phys Chem C 112:8898–8906 Shukla MK, Leszczynski J (2009) Fullerene (C60) forms stable complex with nucleic acid base guanine. Chem Phys Lett 469:207–209 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 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 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 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 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 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 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 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 De Broe ME, Coburn JW (1990) Aluminium and renal failure. Dekker, New York 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 Foncin JF (1987) Alzheimer’s disease and aluminum. Nature 326:136 Kawahara M (2005) Effects of aluminum on the nervous system and its possible link with neurodegenerative diseases. J Alzheimers Dis 8:171–182 Braydich-Stolle LK, Speshock JL, Castle A, Smith M, Murdock RC, Hussain SM (2010) Nanosized aluminum altered immune function. ACS Nano 4:3661–3670 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 Frisch MJ et al (2004) Gaussian 03, Gaussian, Inc., Wallingford CT 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 De Heer WA (1993) The physics of simple metal clusters: experimental aspects and simple models. Rev Mod Phys 65:611–676 Khanna SN, Jena P (1992) Assembling crystals from clusters. Phys Rev Lett 69:1664–1667 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 Kumar V, Bhattacharjee S, Kawazoe Y (2000) Silicon-doped icosahedral, cuboctahedral, and decahedral clusters of aluminum. Phys Rev B 61:8541–8547 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 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 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 Zhao Y, Truhlar DG (2008) Density functionals with broad applicability in chemistry. Acc Chem Res 41:157–167 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 Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105:2999–3094 Reed AE, Curtiss LA, Weinhold F (1988) Intermolecular interactions from a natural bond orbital donor-acceptor viewpoint. Chem Rev 88:899–926 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 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 Laaksonen L (1992) A graphics program for the analysis and display of molecular dynamics trajectories. J Mol Graph 10:33–34 Bergman DL, Laaksonen L, Laaksonen A (1997) Visualization of solvation structure in liquid mixtures. J Mol Graph Model 15:301–306 Lippert B (2000) Multiplicity of metal ion binding patterns to nucleobases. Coord Chem Rev 200–202:487–516 Hud NV (2009) Nucleic acid–metal ion interactions. RSC, Cambridge 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 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 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 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 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 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 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 Mo Y (2006) Probing the nature of hydrogen bonds in DNA base pairs. J Mol Model 12:665–672 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 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