Lithuanian Journal of Physics article / Lietuvos fizikos žurnalo straipsnis

[PDF] http://dx.doi.org/10.3952/lithjphys.48306

Open access article / Atviros prieigos straipsnis

Lith. J. Phys. 48, 287–297 (2008)

SCANNING PROBE MICROSCOPIC AND OPTICAL DETECTION OF DNA INTEGRATION WITHIN MULTICOMPONENT STRUCTURES ON Si SURFACES
V. Bukauskas, J. Babonas, A. Rėza, J. Sabataitytė, I. Šimkienė, and A. Šetkus
Semiconductor Physics Institute, A. Goštauto 11, LT-01108 Vilnius, Lithuania
E-mail: setkus@pfi.lt

Received 9 May 2008; revised 13 June 2008; accepted 18 September 2008

Self-arrangement of DNA based structures on clean mica and modified Si surfaces is investigated by means of scanning probe microscope (SPM) and spectroscopic ellipsometry (SE) method. DNA strands are deposited from a colloidal solution on solid surfaces at room temperature. Surfaces of solid substrates and biomolecular structures are additionally modified by Ag nanoparticles. The self-arranged surface structures are visualized by SPM. The effect of the multicomponent structures on the optical response of complex hybrid structures is studied. Changes in the optical response of the hybrid samples are related to the contributions of self-assembled DNA-based structures and Ag nanoparticles on the Si surfaces. Binding of Ag nanoparticles to the DNA strands and formation of well-ordered structures on the surfaces with DNA are discussed.

Keywords: biomolecular structures, surface, self-assemblage, optical properties, scanning probe microscopy

PACS: 68.37.Ps, 78.68.+m, 81.07.Pr, 81.16.Dn

DNR SĄSAJOS SU DAUGIAKOMPONENČIAIS DARINIAIS Si PAVIRŠIUJE TYRIMAS SKENUOJANČIOJO ZONDO MIKROSKOPU IR OPTINIAIS METODAIS
V. Bukauskas, J. Babonas, A. Rėza, J. Sabataitytė, I. Šimkienė, A. Šetkus
Puslaidininkių fizikos institutas, Vilnius, Lietuva

Darinių su DNR molekulėmis susitvarkymas ant švaraus žėručio ir specialiai apdoroto Si paviršių yra tirtas skenuojančiojo zondo mikroskopu (SZM) ir spektroskopine elipsometrija (SE). Kambario temperatūroje DNR junginiai nusodinami ant kietojo paviršiaus iš koloidinių tirpalų. Kietieji padėklai su biomolekulėmis taip pat padengiami Ag nanodalelių sluoksniu. Savitvarkių darinių paviršiaus atvaizdas gaunamas naudojant įvairius SZM režimus. Taip pat tiriama optinio atsako priklausomybė nuo daugiakomponenčio hibridinio darinio sandaros. Specifiniai pokyčiai, stebimi optiniame atsake, atsiranda dėl DNR molekulių ir Ag nanodalelių susijungimo savitvarkiame hibridiniame darinyje ant Si paviršiaus. Aptariamos tvarkingai ant kietojo paviršiaus susirikiavusių darinių charakteristikos, siejant jas su DNR ir Ag nanodalelių susijungimo ypatumais.

References / Nuorodos

[1] I. Willner, B. Willner, and E. Katz, Biomolecule–nanoparticle hybrid systems for bioelectronic applications, Bioelectrochem. 70, 2–11 (2007),
http://dx.doi.org/10.1016/j.bioelechem.2006.03.013
[2] T. Liedl, T.L. Sobey, and F.C. Simmel, DNA-based nanodevices, Nanotoday 2, 36–41 (2007),
http://dx.doi.org/10.1016/S1748-0132(07)70057-9
[3] F.L. Yap and Y. Zhang, Protein and cell micropatterning and its integration with micro / nanoparticles assembly, Biosensors Bioelectron. 22, 775–788 (2007),
http://dx.doi.org/10.1016/j.bios.2006.03.016
[4] Q. Huo, A perspective on bioconjugated nanoparticles and quantum dots, Colloids Surf. B 59, 1–10 (2007),
http://dx.doi.org/10.1016/j.colsurfb.2007.04.019
[5] H.R. Luckarift, S. Balasubramanian, S. Paliwal, G.R. Johnson, and A.L. Simonian, Enzyme-encapsulated silica monolayers for rapid functionalization of a gold surface, Colloids Surf. B 58, 28–33 (2007),
http://dx.doi.org/10.1016/j.colsurfb.2006.08.013
[6] D.N. Woolfson and M.G. Ryadnov, Peptide-based fibrous biomaterials: Some things old, new and borrowed, Curr. Opinion Chem. Biol. 10, 559–567 (2006),
http://dx.doi.org/10.1016/j.cbpa.2006.09.019
[7] A. Wu, W. Cheng, Z. Li, J. Jiang, and E. Wang, Electrostatic-assembly metallized nanoparticles network by DNA template, Talanta 68, 693–699 (2006),
http://dx.doi.org/10.1016/j.talanta.2005.05.024
[8] C. Peng, Yo. Song, G. Wei, W. Zhang, Z. Li, and W.-F. Dong, Self-assembly of λ-DNA networks/Ag nanoparticles: Hybrid architecture and active-SERS substrate, J. Colloid Interface Sci. 317, 183–190 (2008),
http://dx.doi.org/10.1016/j.jcis.2007.09.017
[9] V. Lavalley, P. Chaudouet, and V. Stambouli, An atomic force microscopy study of DNA hairpin probes monolabelled with gold nanoparticle: Grafting and hybridization on oxide thin films, Surf. Sci. 601, 5424–5432 (2007),
http://dx.doi.org/10.1016/j.susc.2007.09.015
[10] S. Basu, S. Jana, S. Pande, and T. Pal, Interaction of DNA bases with silver nanoparticles: Assembly quantified through SPRS and SERS, J. Colloid Interface Sci. 321, 288–293 (2008),
http://dx.doi.org/10.1016/j.jcis.2008.02.015
[11] A. Mougin, V.G. Babak, F. Palmino, E. Beche, F. Baros, D.J. Hunting, L. Sanche, and M. Fromm, TDAB-induced DNA plasmid condensation on the surface of a reconstructed boron doped silicon substrate, Surf. Sci. 602, 142–150 (2008),
http://dx.doi.org/10.1016/j.susc.2007.09.058
[12] K. Kalyanasundaram and M. Grätzel, Applications of functionalized transition metal complexes in photonic and optoelectronic devices, Coord. Chem. Rev. 177, 347–414 (1998),
http://dx.doi.org/10.1016/S0010-8545(98)00189-1
[13] J. Kobayashi, T. Hinoue, and H. Watarai, Study of adsorption of water-soluble porphyrin at glass–solution interface in the presence of cationic surfactant admicelles by means of total internal reflection spectroscopy, Bull. Chem. Soc. Jpn. 71, 1847–1855 (1998),
http://dx.doi.org/10.1246/bcsj.71.1847
[14] S.B. Lei, J. Wang, Y.H. Dong, C. Wang, L.J. Wan, and C.L. Bai, STM and XRD studies of the adsorption and assembling structures of phthalocyanine and porphyrin, Surf. Interface Anal. 34, 767–771 (2002),
http://dx.doi.org/10.1002/sia.1407
[15] Q. Weiping, X. Bin, Y. Danfeng, L. Yihua, W. Lei, W. Chunxiao, Y. Fang, L. Zhuhong, and W. Lu, Site-directed immobilization if immunoglobulin G on 3-aminopropyltriethoxysilane modified silicon wafer surfaces, Mater. Sci. Eng. C 8–9, 475–480 (1999),
http://dx.doi.org/10.1016/S0928-4931(99)00015-6
[16] R. Šustavičiūtė, I. Šimkienė, J. Sabataitytė, A. Rėza, A. Kindurys, R. Tamaševičius, and J. Babonas, Formation and investigation of porous SiO2 films on Si, Lithuanian J. Phys. 44, 465–476 (2004),
http://dx.doi.org/10.3952/lithjphys.44608
[17] F.J. Giessibl, Advances in atomic force microscopy, Rev. Mod. Phys. 75, 949–983 (2003),
http://dx.doi.org/10.1103/RevModPhys.75.949
[18] B. Anczykowski, B. Gotsmann, H. Fuchs, J.P. Cleveland, and V.B. Elings, How to measure energy dissipation in dynamic mode atomic force microscopy, Appl. Surf. Sci. 140, 376–382 (1999),
http://dx.doi.org/10.1016/S0169-4332(98)00558-3
[19] M. Argaman, R. Golan, N.H. Thomson, and H.G. Hansma, Phase imaging of moving DNA molecules and DNA molecules replicated in the atomic force microscope, Nucleic Acids Res. 25, 4379–4384 (1997),
http://dx.doi.org/10.1093/nar/25.21.4379
[20] B. Gady, D. Schleef, R. Reifenberger, D. Rimai, and L.P. DeMejo, Identification of electrostatic and van der Waals interaction forces between a micrometer-size sphere and a flat substrate, Phys. Rev. B 53, 8065–8070 (1996),
http://dx.doi.org/10.1103/PhysRevB.53.8065
[21] M. Lee, W. Lee, and F.B. Prinz, Geometric artefact suppressed surface potential measurements, Nanotechnol. 17, 3728–3733 (2006),
http://dx.doi.org/10.1088/0957-4484/17/15/019
[22] R.W. Stark, N. Naujoks, and A. Stemmer, Multifrequency electrostatic force microscopy in the repulsive regime, Nanotechnol. 18, 065502-1–7 (2007),
http://dx.doi.org/10.1088/0957-4484/18/6/065502
[23] G.-J. Babonas, A. Niilisk, A. Reza, A. Matulis, and A. Rosental, Spectroscopic ellipsometry of TiO₂/Si, Proc. SPIE 5122, 50–55 (2003),
http://dx.doi.org/10.1117/12.515700
[24] R. Tamaševičius, I. Šimkienė, A. Rėza, I. Blažys, and G.J. Babonas, Magnetic circular dichroism of iron porphyrin, Proc. SPIE 6596, 65961E-1–6 (2007),
http://dx.doi.org/10.1117/12.726514
[25] D. Bedeaux and J. Vlieger, Optical Properties of Surfaces (Imperial College Press, Singapore, 2004),
http://dx.doi.org/10.1142/p327
[26] SOPRA database,
http://www.sopra-sa.com/
[27] M. Kobayashi, K. Sumitomo, and K. Torimitsu, Real-time imaging of DNA–streptavidin complex formation in solution using a high-speed atomic force microscope, Ultramicroscopy 107, 184–190 (2007),
http://dx.doi.org/10.1016/j.ultramic.2006.07.008
[28] F. Moreno-Herrero, P. Herrero, F. Moreno, J. Colchero, C. Gomez-Navarro, J. Gomez-Herrero, and A.M. Bar, Topographic characterization and electrostatic response of M-DNA studied by atomic force microscopy, Nanotechnol. 14, 128–133 (2003),
http://dx.doi.org/10.1088/0957-4484/14/2/305
[29] B. Choi, H.-H. Lee, S. Jin, S. Chun, and S.-H. Kim, Characterization of the optical properties of silver nanoparticle films, Nanotechnol. 18, 075706-1–5 (2007),
http://dx.doi.org/10.1088/0957-4484/18/7/075706
[30] U. Kreibig and M. Vollmer, Optical Properties of Metal Clusters (Springer, Berlin, 1995),
http://dx.doi.org/10.1007/978-3-662-09109-8
[31] B.I. Kankia, Optical absorption assay for strand-exchange reactions in unlabeled nucleic acids, Nucleic Acid Res. 32, e154-1–6 (2004),
http://dx.doi.org/10.1093/nar/gnh152
[32] N.K. Sahoo, S. Thakur, M. Senthilkumar, D. Bhattacharyya, and N.C. Das, Reactive electron beam evaporation of gadolinium oxide optical thin films for ultraviolet and deep ultraviolet laser wavelengths, Thin Solid Films 440, 155–168 (2003),
http://dx.doi.org/10.1016/S0040-6090(03)00678-3
[33] N.K. Sahoo, S. Thakur, and R.B. Tokas, Fractals and superstructures in gadolinia thin film morphology: Influence of process variables on their characteristic parameters, Thin Solid Films 503, 85–95 (2006),
http://dx.doi.org/10.1016/j.tsf.2005.11.107
[34] S. Jakops, A. Duparre, and H. Truckenbrodt, AFM and light scattering measurements of optical thin films for applications in the UV spectral region, Int. J. Machine Tools Manufact. 38, 733–739 (1998),
http://dx.doi.org/10.1016/S0890-6955(97)00125-9
[35] X. Kuang and Z. Zhu, Fractal analysis and simulation of surface roughness of ceramic particles for composite materials, Appl. Composite Mater. 4, 69–81 (1997),
http://dx.doi.org/10.1023/A:1008824606064