Immobilization of different biomolecules by atomic force microscopy
© Breitenstein et al; licensee BioMed Central Ltd. 2010
Received: 4 January 2010
Accepted: 17 May 2010
Published: 17 May 2010
Micrometer resolution placement and immobilization of probe molecules is an important step in the preparation of biochips and a wide range of lab-on-chip systems. Most known methods for such a deposition of several different substances are costly and only suitable for a limited number of probes. In this article we present a flexible procedure for simultaneous spatially controlled immobilization of functional biomolecules by molecular ink lithography.
For the bottom-up fabrication of surface bound nanostructures a universal method is presented that allows the immobilization of different types of biomolecules with micrometer resolution. A supporting surface is biotinylated and streptavidin molecules are deposited with an AFM (atomic force microscope) tip at distinct positions. Subsequent incubation with a biotinylated molecule species leads to binding only at these positions. After washing streptavidin is deposited a second time with the same AFM tip and then a second biotinylated molecule species is coupled by incubation. This procedure can be repeated several times. Here we show how to immobilize different types of biomolecules in an arbitrary arrangement whereas most common methods can deposit only one type of molecules. The presented method works on transparent as well as on opaque substrates. The spatial resolution is better than 400 nm and is limited only by the AFM's positional accuracy after repeated z-cycles since all steps are performed in situ without moving the supporting surface. The principle is demonstrated by hybridization to different immobilized DNA oligomers and was validated by fluorescence microscopy.
The immobilization of different types of biomolecules in high-density microarrays is a challenging task for biotechnology. The method presented here not only allows for the deposition of DNA at submicrometer resolution but also for proteins and other molecules of biological relevance that can be coupled to biotin.
Bottom-up fabrication of defined nanostructures on solid surfaces requires immobilization of different addressable biomolecules as anchors. Nanometer scaled deposition of minute sample volumes was first introduced by Mirkin and co-workers [1, 2] and was realized by dip-pen nanolithography [3–5] where the tip of an atomic force microscope (AFM) is used to deposit reactive compounds directly on a surface.
However, it is difficult to use such lithographic methods for a fast and easy deposition of different biological compounds on the same carrier. So far no techniques were reported capable of deposing more than two kinds of biomolecules with a single tip. In addition, these biomolecules have to match the needs of the used spotting method. In the group of Klenerman [6, 7] a method for the controlled deposition of biomolecules using a scanning nanopipette was developed. They deposited biomolecules by electrophoretic flow applying a local voltage between the nanopipette and the surrounding medium that covers the functionalized surface. An alternative method with high spatial resolution is based on synthesis on the chip: Fodor and co-workers  developed a method to produce microarrays by repetitively uncovering photo-labile protecting groups on an activated silicon wafer with UV irradiation through a mask. Deprotection of the photolabile groups leads to coupling of the modified compounds. This method was commercialized by Affymetrix, who developed microarray feature sizes of 10 × 10 μm2 but is limited to oligonucleotides and peptides. However their length is restricted due to incomplete reactions . For higher quality and more versatility of biomolecule species, the deposition of presynthesized molecules is advantageous. Here we present a novel, universal technique that allows immobilizing different types of biomolecules in a well defined, high resolution pattern by using only one single AFM-tip. Chemical and fluidic properties of the molecules that have to be immobilized by this method may differ and do not have to match, as it is the case with other methods. This approach is a first step towards generating individually patterned nanostructures fixed on surfaces and allows the construction of DNA anchored structures.
The method presented is a microcontact printing, still it is highly flexible and pattern independent. The protocols and methods that are established in microcontact printing, e.g. , have recently been shown to be applicable to the preparation of microscopically small features  and, hence, could be combined with our approach for immobilizing several different biomolecules.
This work is aimed at the development of a universal method for the production of micrometer scaled arrays with several different immobilized biomolecules. For scaling down feature size and for greater flexibility an atomic force microscope (AFM) was used. The AFM-tip is utilized like a pen and allows small volume deposition of reactive compounds. A crucial prerequisite for the immobilization of different biomolecules is to avoid any cross contaminations. This can be achieved by either cleaning or replacing the tip. However, replacing would result in a decreased accuracy due to long distance-moving of the tip, whereas cleaning might precipitate cross contaminations and, furthermore, would result in decreased accuracy because of the additional movement. To solve this problem, neutravidin is used as a natural, highly reactive linker for biotinylated biomolecules and is deposited by a single AFM-tip. This results in two significant advantages: Besides an improved accuracy of spot positions, optimization and adaptation steps for deposition are reduced to a minimum, since only one chemical compound, neutravidin, is to be deposited.
Results and Discussion
A novel approach has been presented for the high resolution immobilization of multiple biomolecules on a solid glass support and within the same array. The unique feature of the method is that optimization of the spotting protocol can be reduced to just one spotting substance, regardless of what kind of biotinylated mixture of biomolecules is to be arranged. Two completely different species of molecules have been used to demonstrate the sequence of working steps: biotinylated fluorescence dyes and single stranded DNA. In addition to the flexibility of the whole process, the possibility to treat the surface prior to each spotting step simplifies the whole procedure considerably. The unaffected biochemical activity of the immobilized molecules was shown by hybridization of a mixture of fluorescently labeled complementary oligonucleotides. In general, the results pave the way for creating surface bound and well addressed nanostructures that are based on functional biomolecules.
In subsequent steps the spots may be used to immobilize a variety of arbitary molecular species in a single array. In contrast to gold-thiol chemistry, the glass remains accessible for all types of optical microscopy. The whole immobilization procedure can be performed on transparent as well as opaque surfaces. The solid glass support can be employed for many applications where a non-conductive, transparent surface is needed. The procedure is also interesting for other structuring methods like micro-contact printing. We expect that existing nanolithography methods can be upgraded using the presented method.
All experiments have been carried out with nanolithographic tools, such as standard AFM-tips and script-based execution. It would also be possible to modify this general procedure for microcontact printing methods to fulfill the needs of industrial mass production. Further investigations will aim to reduce feature size to the sub micrometer range to enable fabrication of DNA-based nano-structures.
Silanization and biotinylation
Glass slides (Menzel Gläser, Menzel GmbH & Co. KG, 38116 Braunschweig, Germany) were cleaned with ultrasound in acetone for 15 minutes and again in ethanol (acetone and ethanol were obtained from Carl Roth GmbH & Co. KG, Karlsruhe, Germany). After rinsing with ultrapure water, the slides were put into NaOH (10 M) for 1 minute and washed thoroughly with water. Drying was carried out in a centrifuge (Varifuge 3.0R, Heraeus) for 1 minute at 2 g. In vapor phase at 120°C the silanization with 3-Aminopropyltriethoxysilane (Fluka Chemie GmbH, 89552 Steinheim, Germany) was executed in a sealed beaker and finished after 60 minutes. Silanization was tested by contact angle measurements by the sessile-drop tangent method - contact angle system from Dataphysics OCA30. For biotinylation, Sulfo-NHS-Biotin (20 mg) (Thermo Scientific, IL 61101 USA) was dissolved in DMSO (1 mL) (Carl Roth GmbH & Co. KG) because of its low stability and moisture-sensitivity. The DMSO solved Sulfo-NHS-Biotin can be stored at -20°C with desiccant. Sulfo-NHS-Biotin (10 mL) solution was added to Na2HPO4 (100 mM, 21 mL), NaCl (150 mM) buffer at pH 7.4. Incubation of 5 silanized glass slides took place for 3 hours at room temperature. Slides were washed with PBS and rinsed with water. Blocking was carried out by incubating the glass slides in a freshly preparated, 0.1% (w/v) solution of blocking reagent CA from Applichem in 100 mM Tris-Cl. For cleaning, slides were washed three times for 5 minutes in Tris-Cl and finally rinsed with ultrapure water. NaOH, Na2HPO4, NaCl, PBS and blocking reagent CA were obtained from AppliChem GmbH, 64291 Dortmund, Germany.
Addressing the spotted neutravidin (Thermo Scientific, IL 61101 USA) was accomplished by incubation of the biotinylated substance that had to be immobilized. Biotinylated dyes (Dyomics GmbH, 67745 Jena, Germany) as well as the biotinylated oligonucleotides (Biomers.net GmbH, 89077 Ulm, Germany) were diluted in carbonate buffer pH 9.0 to a final concentration of 0.5 mM. Incubation time for binding was 5 minutes and was stopped by washing with 1× PBS-buffer and ultrapure water. Oligonucleotides were treated with additional hybridization of fluorescently marked ssDNA. Hybridization was carried out in the dark for 30 minutes at 37°C and 80% relative humidity. Sequences of the oligonucleotides (Niemeyer et al.): LcF5: 5'-cttatcgctttatgaccggacc-3' (5': Biotin); RcF6: 5'-caatgaaacactaggcgaggac-3' (5': Biotin) and RcF2: 5'-gtcggttctaagaaaatggcgg-3' (5': Biotin). The three fragments were diluted in TE-buffer (50 mM Tris-Cl, 100 mM NaCl, AppliChem GmbH) to a final concentration of 1 mM. Washing was carried out with PBS-buffer and stringent washing with ultrapure water.
The atomic force microscope CP-II from Veeco (Santa Barbara CA, 93117 USA) and AFM-tips from NanoSensors (NanoAndMore GmbH, 35578 Wetzlar, Germany): DT-CONTR (force constant: 0.2 N/m; resonance frequency: 13 kHz) was used. Movement of the AFM-tip and execution were controlled by the diNanolithography Software V.1.8. Approaching the biotinylated glass slide was achieved in contact mode with 3.4 mN contact force. The tip remained in contact for 4 seconds and changed to the next spotting positions by retraction. Ink was supplied by a hypodermic needle of Popper & Sons, Inc. (N.Y. 11040 USA).
Fluorescence microscopy was carried out with an upright epifluorescence microscope Olympus A BX51 (objective: UPlanFL N; 40×/0.75). Fluorescence detection was accomplished with the following filter-cube combinations: Cy3 and DY-547 detection: excitation filter (Ex) BP 545/25, dichromatic mirror (Dm) 565, emission filter (Em) LP 605/70; for Cy5 and DY-647 detection: Ex BP 620/60, Dm 660, Em BP 700/75; and for Atto495 detection: Ex BP 460 - 495, Dm 505, Em LP 510 - 550. For illumination a mercury arc lamp (100 W, OSRAM GmbH, 81543 München, Germany) was used. Image acquisition was carried out with a CCD camera from Finger Lakes Instrumentation (FLI, New York 14485 USA; CM10-ZME; 6.8 μm pixel pitch; 2184 × 1472 pixels) in combination with FLIGrab Software V1.10. Image editing was realized with ImageJ V1.42q.
We thank A. Christmann for technical assistance with the atomic force microscope and M. Schellhase for performing tests and her expertise in general spotting technology. We gratefully acknowledge critical commentary and reviewing the manuscript by A. Peukert. We like to thank the European Commission for the support of this work (contract no. STRP13775, project Nucan).
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