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J. Phys. Chem. C 2007, 111, 17032-17037
Adsorption and Self-Assembly of Oligodeoxynucleotides onto a Mica Surface Zolta´ n Ba´ lint,† Krisztina Nagy,# Ilona Laczko´ ,† Sa´ ndor Bottka,‡ Gergely A. Ve´ gh,† Zsolt Szegletes,† and Gyo1 rgy Va´ ro´ *,† Institute of Biophysics, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary, H-6726, Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary, H-6726, and Department of Medical Physics and Biophysics, UniVersity of Szeged, Szeged, Hungary ReceiVed: June 7, 2007; In Final Form: August 7, 2007
Atomic force microscopy has been used to study the specific structures of oligodeoxynucleotides (ODN) dried onto a freshly cleaved muscovite mica surface. The nucleotides have an important role in biology as the building blocks of the information coding DNA. To fulfill this task, the nucleotides must have specific self-assembling properties. The appearance of self-assembly was monitored as a function of different external factors, such as the concentration of the ODN, pH of the solution, and the composition of the surface material. At low ODN concentrations, around 20 nM, fiber-like formations appeared. At a rather high ODN concentration, around 400 nM, a network-like structure was seen. These formations appear only when the pH of the solution falls to between 3.3 and 4. Several surfaces were investigated, but the self-assembly of the ODN was observed only in the case of mica surfaces.
Introduction The study of the nucleic acids, the building blocks of DNA, which stores and transmits genetic information, is important to understand the organization of prebiotic polymers, leading to the appearance of life. The ability to bind DNA to a surface allowed this to be one of the first biological materials to be investigated by atomic force microscope (AFM),1 and it is even now intensively studied.2-6 Single-, double-, and triple-stranded DNA molecules deposited on mica surfaces were observed.2,3 In recent years, numerous observations have reinforced the hypothesis of a surface-mediated origin of life.7,8 The high affinity of DNA for mineral surfaces, such as montmorillonite clay or mica, makes this observation very plausible. Self-assembly is recognized as a very efficient method of nanotechnology.9 Self-assembling of the λ-DNA was observed on a silanized mica surface.10 The self-assembly of twodimensional DNA crystals has been intensively investigated as a tool to create nanocircuits.9,11,12 Recently a 2D fractal dimension method was introduced to study highly disordered structures of immobilized oligonucleotides (ODN).13 AFM is an important tool in the study of the tertiary conformation of ODN and DNA in different environments relevanttobiologicalexperimentsandbiotechnicalapplications.14-18 Allemand and co-workers showed that specific binding of DNA can be achieved on a great variety of surfaces by judicious choice of pH. At pH around 5.5 the DNA is more likely to bind onto hydrophobic surfaces by an extremity rather than by a midsegment.4 Recently, a simple method was established to assemble an ODN monolayer onto unoxidized crystalline silicon. The method consists of two steps.19 First, a monolayer of a spacer is * Corresponding author. E-mail:
[email protected]. † Institute of Biophysics, Biological Research Center of the Hungarian Academy of Sciences. ‡ Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences. # University of Szeged.
deposited via cathode electrografting, and then the ODN was anchored to it, through amidation in aqueous solution. By studying the adsorption of the ODN to highly oriented pyrolytic graphite (HOPG), different adsorption patterns were observed, depending on the molecular mass or the hydrophobic character of the individual bases and on the secondary structure.6 Adsorption to a gold surface was also investigated.5 Self-aggregation of ODN or DNA onto a mica surface in the presence of different cations (K+, Mg2+, Ni2+, etc.) was intensively studied.20,21 Formation of a complex was described between the DNA and gold nanoparticles, promoting development of novel methods of nanoparticles self-assembly on DNA templates.22 By using polymer-functionalized DNA deposited and dried onto a polycarbonate-coated glass substrate and using a special technique, formation of nanowires was observed with AFM.23 This was an important step toward the construction of functional nanodevices using DNA and other biomolecules. In the present work we investigate the conditions for selfassembly of the ODN onto mica surfaces. This could be relevant in nanobiotechnical applications. The observation that the nucleic acid bases and ODN adsorb onto muscovite mica surfaces, which are very similar to the earlier described montmorillonite clay, may contribute to the understanding of the origin of life.7,8,24 Experimental Methods 18mer ODN with the sequence 5′ GAGCTGCACGCTGCCGTC 3′ was synthesized with an Expedite 8909 synthesizer (Applied Biosystems). Double HPLC purification was performed on a Kromasil 100-C18 250 × 10 mm ID column, using acetonitrile-triethylammonium acetate mixtures at pH 7 as eluent, resulting in the triethylammonium salt of ODN. The complementary strands of the ODN, 18mer oligo-dA, and oligo-T sequences were also synthesized. Fifty microliters of a 5 to 500 nM aqueous solution of ODN was dropped onto a freshly cleaved 15 × 15 mm2 muscovite
10.1021/jp074400l CCC: $37.00 © 2007 American Chemical Society Published on Web 10/12/2007
Oligodeoxynucleotides on a Mica Surface
J. Phys. Chem. C, Vol. 111, No. 45, 2007 17033
Figure 1. Formation of the oligonucletide complexes. (a and b) The height image of the surface after drying 50 µL of 20 nM, pH 3.5-4 ODN on a 15 × 15 mm2 mica surface. (c) The height profile along the line drawn on b. (d and e) The height image and the height profile of the mica surface, when high purity water was dried on it.
mica surface (Grade V-1 Muscovite, SPI Supplies Division Structure Probe Inc., West Chester, PA), if not otherwise mentioned, and dried for 1 h under a continuous flow of highly purified air. For the sample preparation, high purity water and hydrochloric acid were purchased (Sigma-Aldrich, Buchs, Switzerland). AFM measurements were performed with an MFP-3D atomic force microscope head and Molecular Force Probe 3D controller (Asylum Research, Santa Barbara, CA). The driver program MFP-3D Xop was written in IGOR Pro software (version 5.03, Wavemetrics, Lake Oswego, OR). The measurements were carried out with AC240 rectangular silicon cantilevers, with tetrahedral tips (Olympus, Optical Co. Ltd. Tokyo, Japan). The nominal properties of the cantilever: resonant frequency 70 kHz, spring constant 2 N/m, tip radius
