Abstract
The interaction between nanoparticles (NPs) and DNA plays an important role in the genotoxicity of NPs, and it is imperative to characterize the nano/DNA interactions and explore the underlying chemical mechanisms. In this chapter, we demonstrated systematic experimental approaches based on atomic force microscope (AFM), coupled with modeling computation to probe the binding activity of NPs with DNA and the putative genotoxicity. Using quantum dots (QDs) as a model NP, we examined the binding kinetics, binding isotherm, binding specificity, and binding mechanisms of NPs to DNA with the application of AFM. We further assessed the binding affinity between NPs and DNA by calculating their interaction energy on the basis of Derjaguin-Landau-Verwey-Overbeek (DLVO) models. The modeling results of binding affinity were validated by the NPs/DNA binding images experimentally derived by AFM. The investigation of the relationship between the binding affinity of five NPs ((QDs (+), QDs (−), silver NPs, hematite NPs, and gold NPs) for DNA with their inhibition effects on DNA replication indicated that NPs with a high binding affinity for DNA molecules exhibited higher inhibition on DNA replication. The methodology employed in this study can be extended to study the interaction of other NPs with DNA, which is anticipated to benefit the future design of safe NPs, as well as the toxicological investigations of NPs.
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References
An HJ, Jin B (2012) Prospects of nanoparticle-DNA binding and its implications in medical biotechnology. Biotechnol Adv 30:1721–1732
An HJ, Liu QD, Ji QL, Jin B (2010) DNA binding and aggregation by carbon nanoparticles. Biochem Biophys Res Commun 393:571–576
Nel AE, Madler L, Velegol D, Xia T, Hoek EMV, Somasundaran P, Klaessig F, Castranova V, Thompson M (2009) Understanding biophysicochemical interactions at the nano-bio interface. Nat Mater 8:543–557
Yang WJ, Shen CC, Ji QL, An HJ, Wang JJ, Liu QD, Zhang ZZ (2009) Food storage material silver nanoparticles interfere with DNA replication fidelity and bind with DNA. Nanotechnology 20:0851-02
Allen MJ, Bradbury EM, Balhorn R (1997) AFM analysis of DNA-protamine complexes bound to mica. Nucleic Acids Res 25:2221–2226
Alonso-Sarduy L, Roduit C, Dietler G, Kasas S (2011) Human topoisomerase II-DNA interaction study by using atomic force microscopy. FEBS Lett 585:3139–3145
Hansma HG (2001) Surface biology of DNA by atomic force microscopy. Annu Rev Phys Chem 52:71–92
Lyubchenko YL, Shlyakhtenko LS (2009) AFM for analysis of structure and dynamics of DNA and protein-DNA complexes. Methods 47:206–213
Pastre D, Hamon L, Sorel I, Le Cam E, Curmi PA, Pietrement O (2010) Specific DNA-protein interactions on mica investigated by atomic force microscopy. Langmuir 26:2618–2623
Tessmer I, Moore T, Lloyd RG, Wilson A, Erie DA, Allen S, Tendler SJB (2005) AFM studies on the role of the protein RdgC in bacterial DNA recombination. J Mol Biol 350:254–262
An H, Jin B (2011) DNA exposure to buckminsterfullerene (C-60): toward DNA stability, reactivity, and replication. Environ Sci Tech 45:6608–6616
Li KG, Zhang W, Chen YS (2013) Quantum dot binding to DNA: single-molecule imaging with atomic force microscopy. Biotechnol J 8(1):110–116
Zhang W, Yao Y, Chen YS (2011) Imaging and quantifying the morphology and nanoelectrical properties of quantum dot nanoparticles interacting with DNA. J Phys Chem C 115:599–606
Butt H-J, Graf K, Kappl M (2003) Physics and chemistry of interfaces. Wiley-VCH, Weinheim
Butt HJ, Cappella B, Kappl M (2005) Force measurements with the atomic force microscope: technique, interpretation and applications. Surf Sci Rep 59: 1–152
Considine RF, Drummond CJ (2001) Surface roughness and surface force measurement: a comparison of electrostatic potentials derived from atomic force microscopy and electrophoretic mobility measurements. Langmuir 17:7777–7783
Zhang W, Stack AG, Chen YS (2011) Interaction force measurement between E. coli cells and nanoparticles immobilized surfaces by using AFM. Colloids Surf B Biointerfaces 82:316–324
Blanchard BJ, Thomas VL, Ingram VM (2002) Mechanism of membrane depolarization caused by the Alzheimer A beta 1–42 peptide. Biochem Biophys Res Commun 293:1197–1203
Oh YJ, Jo W, Yang Y, Park S (2007) Biofilm formation and local electrostatic force characteristics of Escherichia coli O157: H7 observed by electrostatic force microscopy. Applied Physics Letters 90:143901–143903
Sun L, Wang JJ, Bonaccurso E (2010) Nanoelectronic properties of a model system and of a conjugated polymer: a study by Kelvin probe force microscopy and scanning conductive torsion mode microscopy. J Phys Chem C 114:7161–7168
Zhang W, Hughes J, Chen YS (2012) Impacts of hematite nanoparticle exposure on biomechanical, adhesive, and surface electrical properties of Escherichia coli cells. Appl Environ Microbiol 78:3905–3915
Muller DJ, Dufrene YF (2011) Atomic force microscopy: a nanoscopic window on the cell surface. Trends in Biology 21:433–498
Dhawan A, Sharma V (2010) Toxicity assessment of nanomaterials: methods and challenges. Anal Bioanal Chem 398:589–605
Li HX, Rothberg L (2004) Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles. Proc Natl Acad Sci U S A 101:14036–14039
Gill R, Zayats M, Willner I (2008) Semiconductor quantum dots for bioanalysis. Angew Chem Int Ed 47:7602–7625
Medintz IL, Uyeda HT, Goldman ER, Mattoussi H (2005) Quantum dot bioconjugates for imaging, labelling and sensing. Nat Mater 4:435–446
Michalet X, Pinaud FF, Bentolila LA, Tsay JM, Doose S, Li JJ, Sundaresan G, Wu AM, Gambhir SS, Weiss S (2005) Quantum dots for live cells, in vivo imaging, and diagnostics. Science 307:538–544
Qi LF, Gao XH (2008) Emerging application of quantum dots for drug delivery and therapy. Expert Opin Drug Deliv 5:263–267
Green M, Howman E (2005) Semiconductor quantum dots and free radical induced DNA nicking. Chem Commun (Camb) 1:121–123
Leung C, Maradan D, Kramer A, Howorka S, Mesquida P, Hoogenboom BW (2010) Improved Kelvin probe force microscopy for imaging individual DNA molecules on insulating surfaces. Appl Phys Lett 97:203703
Guthold M, Zhu XS, Rivetti C, Yang GL, Thomson NH, Kasas S, Hansma HG, Smith B, Hansma PK, Bustamante C (1999) Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase. Biophys J 77:2284–2294
Lyubchenko YL, Shlyakhtenko LS (1997) Visualization of supercoiled DNA with atomic force microscopy in situ. Proc Natl Acad Sci U S A 94:496–501
Stark M, Moller C, Muller DJ, Guckenberger R (2001) From images to interactions: high-resolution phase imaging in tapping-mode atomic force microscopy. Biophys J 80:3009–3018
Mahtab R, Harden HH, Murphy CJ (2000) Temperature- and salt-dependent binding of long DNA to protein-sized quantum dots: thermodynamics of “inorganic protein”-DNA interactions. J Am Chem Soc 122:14–17
Mahtab R, Sealey SM, Hunyadi SE, Kinard B, Ray T, Murphy CJ (2007) Influence of the nature of quantum dot surface cations on interactions with DNA. J Inorg Biochem 101:559–564
Zhao YD, Xu Q, Wang JH, Wang Z, Yin ZH, Yang Q (2008) Interaction of CdTe quantum dots with DNA. Electrochem Commun 10:1337–1339
Yang Y, Sass LE, Du CW, Hsieh P, Erie DA (2005) Determination of protein-DNA binding constants and specificities from statistical analyses of single molecules: MutS-DNA interactions. Nucleic Acids Res 33:4322–4334
Winter RB, Berg OG, Vonhippel PH (1981) Diffusion-driven mechanisms of protein translocation on nucleic-acids. 3. The Escherichia-coli-Lac repressor-operator interaction – kinetic measurements and conclusions. Biochemistry 20:6961–6977
Schofield MJ, Brownewell FE, Nayak S, Du CW, Kool ET, Hsieh P (2001) The Phe-X-Glu DNA binding motif of MutS – the role of hydrogen bonding in mismatch recognition. J Biol Chem 276:45505–45508
Harries D (1998) Solving the Poisson-Boltzmann equation for two parallel cylinders. Langmuir 14: 3149–3152
Manning GS (2006) The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force. Biophys J 91:3607–3616
Derjaguin B, Sidorenkov G (1941) Thermoosmosis at ordinary temperatures and its analogy with the thermomechanical effect in helium II. C R Acad Sci De L Urss 32:622–626
Hoek EMV, Agarwal GK (2006) Extended DLVO interactions between spherical particles and rough surfaces. J Colloid Interface Sci 298:50–58
Verwey EJW, Overbeek JTG, van Nes K (1948) Theory of the stability of lyophobic colloids; the interaction of sol particles having an electric double layer. Elsevier Pub. Co., New York
Li KG, Chen YS (2012) Evaluation of DLVO interaction between a sphere and a cylinder. Colloids Surf A Physicochem Eng Asp 415:218–229
Schellman JA, Stigter D (1977) Electrical double-layer, zeta potential, and electrophoretic charge of double-stranded DNA. Biopolymers 16:1415–1434
Sharp KA, Honig B (1990) Electrostatic interactions in macromolecules – theory and applications. Annu Rev Biophys Biophys Chem 19:301–332
Stigter D (1977) Interactions of highly charged colloidal cylinders with applications to double-stranded DNA. Biopolymers 16:1435–1448
Li G, Levitus M, Bustamante C, Widom J (2005) Rapid spontaneous accessibility of nucleosomal DNA. Nat Struct Mol Biol 12:46–53
Mi LJ, Wen YQ, Pan D, Wang YH, Fan CH, Hu J (2009) Modulation of DNA polymerases with gold nanoparticles and their applications in hot-start PCR. Small 5:2597–2600
Chaloupka K, Malam Y, Seifalian AM (2010) Nanosilver as a new generation of nanoproduct in biomedical applications. Trends Biotechnol 28:580–588
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Li, K., Du, S., Van Ginkel, S., Chen, Y. (2014). Atomic Force Microscopy Study of the Interaction of DNA and Nanoparticles. In: Capco, D., Chen, Y. (eds) Nanomaterial. Advances in Experimental Medicine and Biology, vol 811. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-8739-0_6
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