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Review

A review on techniques to fabricate silicon oxide arraysfor biomolecules patterning

K. Sathiyaraj, M. Harshiny, B. Nazeema Banu, K. Rajendran, S. Kumaran ⇑Department of Biotechnology, Periyar Maniammai University, Thanjavur, India

a r t i c l e i n f o

Article history:Received 24 January 2011Received in revised form 22 March 2011Accepted 28 March 2011Available online 3 April 2011

Keywords:Silicon oxidePatterningOxidationSAMBiochip

a b s t r a c t

The development of methods for pattern proteins and otherfunctional molecules on the surfaces with nanoscale accuracy isindispensable to take advantage of their properties in ultrasensitiveand/or high-density devices. Several methods are used to fabricateorganized micro/nanohierarchical structures on a surface and givethe ability of molecules to self-assemble by using the mutual rec-ognition properties. However, the supramolecular organization isdifficult to extend from nano- to mesoscopic length scales or doesnot allow accurate placement of the desired structures on a specificregion of an inhomogeneous surface. This paper reviews the differ-ent techniques used to fabricate nano/millimeter range patterns onSiO2/Si substrates and local chemical grafting to perform successfulattachment of biomolecules on predetermined areas.

� 2011 Elsevier Ltd. All rights reserved.

Contents

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5822. Fabrication methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 582

2.1. Electrical method – tip based and parallel oxidation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5822.2. Optical method – UV and laser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5842.3. Mechanical method – imprint and lift off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 585

3. Attachment of functional molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5884. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 589

0749-6036/$ - see front matter � 2011 Elsevier Ltd. All rights reserved.doi:10.1016/j.spmi.2011.03.014

⇑ Corresponding author. Address: Department of Biotechnology, Periyar Maniammai University, Vallam, Thanjavur 613 403,Tamil Nadu, India. Mobile: +91 9944960860; fax: +91 4362 264660.

E-mail address: [email protected] (S. Kumaran).

Superlattices and Microstructures 49 (2011) 581–590

Contents lists available at ScienceDirect

Superlattices and Microstructures

j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o ca t e / s u p e r l a t t i c es


Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 590References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 590

1. Introduction

Patterning of proteins and other functional biomolecules on solid substrates is a fundamental re-search in developing biosensors and in vivo implantations. Silicon (Si) is used in sensing applicationsdue to its moderate price (with respect to gold) and easy to fabricate nano/micro oxide dots for pat-terning of biomolecules by functionalizing the surface [1–4]. Biomolecules can be patterned at prede-termined positions on silicon and signals may be retrieved during the ligand–receptor or antigen–antibody/DNA–DNA binding proteins, etc. Si also has drastic change in their electrical and opticalmodules at miniature structures, which allows for effective transduction modes to retrieve the signalas to function as biosensors [5,6]. Beyond the biosensor application, these fabricated structures areapplicable in drawing circuits for ICs (integrated circuits), optical gratings as polarizer in PICs (pho-tonic integrated circuits), gate oxide sandwich for transistors, etc.

There are many methods to fabricate well controlled nanostructures, such as oxidation [7–19], la-ser [20–22], ultraviolet [23–25], etching [20,22], and imprint [26,27]. We are working on fabrication ofsilicon oxide using AFM anodic oxidation and a copper wire assisted homemade setup. Here, we like toreview the advantages as well as disadvantages of the above mentioned methods and the selection ofthe method according to their application. In this study, fabrication techniques are divided by thephysical concepts behind it, such as electrical method (local oxidation), optical method (UV and laser)and mechanical method (imprint and lift off).

2. Fabrication methods

2.1. Electrical method – tip based and parallel oxidation

Local oxidation process is an electrochemical process, where AFM tip (i.e. cathode) and siliconsubstrate (i.e. anode) with water meniscus as medium, the electric field produces oxidation onthe surface under the water meniscus. This technique was first performed with scanning tunnelingmicroscopy (STM) and later it was performed using atomic force microscopy (AFM) [7], AFM localanodic oxidation is a highly versatile direct-write method to fabricate well-defined nanometricoxide structures [8].

Sugimura et al. [9–11] have performed local oxidation with different self assembled monolayersformed on silicon (Fig. 1a). In this research work, authors have performed local oxidation for differentreaction time (0–50 s) and observed that oxide dot height increased with increase in reaction time

Fig. 1. (a) Schematic of AFM tip based lithography, (b) lateral force and (c) topography of fabricated dot [9].

582 K. Sathiyaraj et al. / Superlattices and Microstructures 49 (2011) 581–590


(Fig. 1b and c). Anodic oxidation formation on surface occurred after degradation of monolayer, whereadsorbed water leads to degradation of monolayer and promotes anodization on silicon. In thisresearch, it has been proved that the oxidation well prolonged after complete degradation ofmonolayer but it is not clear at which reaction time maximum size of oxide dot can be formed atthe given condition [12,13]. Sugimura et al. [9–11] have studied the size and growth of oxide dotfor different time duration but does not mentioned the maximum limit of oxidation at a particularposition.

Jegadesan et al. [14] have used AFM anodic oxidation on PMMA (poly(methyl methacrylate))monolayer coated on silicon wafer and optimized the changes with different bias voltages (�4 to�11 V) at 0.5 lm s�1 scan rate. Fig. 2 shows the oxidation pattern with both raised (low voltages�4 and �5 V) and grooved patterns (high voltage �11 V). Interesting result was obtained; at �7 Vthe pattern has both, raised and grooved patterns. They also studied the stability of patterned afterseveral days by AFM imaging and confirmed the pattern remains same as fabricated. Jagadeesanet al. [14] have shown some interesting result as at �7 V both raised and grooved patters can beobtained but the reason is not clearly stated.

Suzuki et al. [15], Shanmugam et al. [16], and Martínez et al. [17] have performed AFM localoxidation to fabricated silicon oxide patterns on silicon substrate and with various surface modifiedsilicon substrate (Figs. 3 and 4). Authors have concluded that fabrication of oxide dots on different sur-faces provides different surface charge polarization, which is useful for uniform patterning of differentbiomolecules.

Tip-based AFM local oxidation is a suitable method for fabrication of submicron/nanometersizedoxide structures, but it has inherent limitation such as time consumption for large-area fabrication[17]. Humidity plays major role in AFM local oxidation; it may be harmful to circuits in AFM. In orderto pattern the biomolecules in millimeter/micrometer range, researchers developed upscaled tech-niques for large-area patterning [18].

Conductive stamping using digital video disc (DVD) as a cathode is one of the techniques to patternin millimeter range [18,19]. In this technique to enhance the conductivity of DVD, thin metallic films(5 nm Cr and 50 nm Au) are formed by electron beam evaporation. Sacrificial PMMA layer was coatedon silicon substrate to produce regular and homogeneous patterns. This stamp and substrate wereintroduced into a home-made parallel oxidation instrument and bias voltage was applied with relativehumidity of 70% (Fig. 5) to get parallel SiO2 tracks.

Equipments such as sputter coating, chemical vapor deposition, pulsed laser depositions arerequired to coat thin metallic films on stamps to achieve high conductivity. Hence, we have assembledhomemade set up for large area patterning using commercial copper wire (submitted). In homemadesetup, we have optimized bias voltage as 25 V for 4 min to fabricating oxide dots (micrometer range)

Fig. 2. Raised and grooved patterns due to ramping the tip to different voltage [14].

K. Sathiyaraj et al. / Superlattices and Microstructures 49 (2011) 581–590 583


and it is easy to maintain the relative humidity around 60–70%. We are looking to improve this setupby controlling with microprocessor controller units and ionizer for produce humidity to fabricate welldefined patterns on predetermined positions.

2.2. Optical method – UV and laser

Photon (light energy) incident on a surface, excite the surface atom electrons to take part in theoxidation reaction. This fundamental phenomenon of laser beam reaction is a mechanochemicaloxidation method used to fabricate silicon oxide on silicon [20–22]. Qiao et al. [20] and Hosono andTokura [21] have irradiated silicon surface using laser source to fabricate oxide line on silicon withdifferent laser powers (Fig. 6), at 8 W silicon surface was melted and spreads, whereas at 2.5 W nochange observed. Protrusions are formed at 4 W and KOH etching is carried out to control the width

Fig. 3. Protocal for (a) negative and (b) positive patterning of protein [15].

Fig. 4. Silicon surface (a) covered by thin layer of native silicon dioxide, (b) silicon dioxide patterns fabricated by localoxidation, (c) functionalized with APTES and (d) functionalized with OTS [17].



of protrusion (Fig. 6d). Qiao et al. [20] have studied the etching effect on track width and also studiedthe oxide line formation on etched surface.

Shin et al. [22] have used laser to obtain both the patterns due to back-side illumination and front-side illumination (Fig. 7). In this work, a thin metallic film is deposited in between transparentsubstrate and Indium tin oxide (ITO) film. Laser beam incident on the transparent side creates athermo-elastic force on the metal film which makes to detach metal coating with ITO and form animpression on the transparent substrate. Pre-coating of silicon oxide thin layer on silicon substrateand irradiating the film by laser treatment will induce the bonding between silicon oxide and siliconproduces a well defined pattern according to laser parameters.

UV photolithography is commonly used to fabricate groove and rise by exposing the photo resistover the substrate to UV through a mask to transfer its pattern on the substrate (followed by etchingor uniform metal coatings) [23–25]. Commercial UV masks are available, but it is a tedious procedureto positioning the masks. Wang et al. [24] approached a new mask-less method (Fig. 8a) to prepareordered silica nanopatterns. In this research, polystyrene-b-poly(dimethylsiloxane) (PS-b-PDMS)block copolymers were spin coated on silicon wafer and annealed under tetrahydrofuran (THF) or ace-tone vapor. PDMS has higher interaction than PS with silicon, PS component was easily removed byUV/O3 irradiation and PDMS converted into silicon oxide. A wide range of inorganic films withwell-ordered nanostructures was prepared and X-ray photoelectron spectroscopy (XPS) confirmsthe presence of silicon oxide.

2.3. Mechanical method – imprint and lift off

Patterning using lithographic techniques requires one of the key steps to make contact for position-ing the active layers at predetermined position on the substrate. Soft lithography (micro-contactprinting and lift off) has few significant advantages such as low cost and ability to transfer a particular

Fig. 5. Schematic of parallel local oxidation process [18].

Fig. 6. AFM image of lines on wafer at different laser powers (a) 8 W, (b) 4 W, (c) 2.5 W and (d) with KOH etching [21].



Fig. 7. Optical profiler image of patterned Au (top) and ITO (bottom) films [22].

Fig. 8. (a) Schematic diagram of the steps to generate silicon oxide spheres. AFM height image of the polymer layer (b) beforeUV irradiation, (c) after UV irradiation and (d) acetone annealed UV irradiated surface [24].



self-assembled monolayer (SAM) pattern with nanometer resolution. Martínez et al. [17] have exploitedthis advantages by using print-based method such as lithography-controlled dewetting. In thiswork, a soft stamp inked with molecules to be patterned is lightly pressed against a silicon surfacefunctionalized with aminopropyltriethoxysilane (APTES) (Fig. 9a). The nanoscale liquid meniscusformed between protrusion of stamp and the substrate leads to the selective deposition of molecules(Fig. 9b and c). Number of molecules deposited per line width determines the meniscus size and it canbe controlled by the applied load. These nanopatterns are stable at room temperature and ambientpressure.

Scavia et al. [26] performed micro contact printing, as a first step poly-3(hexylthiophene) (P3HT)layer is fabricated on OTS functionalized silicon oxide and PDMS layer is coated over P3HT. Finallythe P3HT layer is printed onto the new substrate and then the PDMS layer is detached from P3HTlayer. Stress effects and nanolevel defects due to stress are determined by repeating this procedurewith different elongation ratio and stress direction. Structural change in AFM image (Fig. 10) also clo-sely agrees to the change in elongation ratio and stress effect (stress pressure).

Fig. 9. (a) Scheme of pattern large areas of a silicon surface with nanoscale features made of ferritin molecules, (b) parallel arrayof single ferritin molecules and (c) AFM image of the single-molecule ferritin lines (the inset shows the line diameter) [17].



Lhuillier et al. [27] performed imprint method to produce ordered pattern on Si/SiO2 substrate(Fig. 11). PMMA was spin coated on Si/SiO2 substrate and the mould is pressed against the substrateas softening the PMMA by heating. Then the mould is lifted up at 0.5 mm/min by slowly decreasingthe temperature and the remaining resist was removed using O2 plasma. OctadecylTriMethoxySilane(OTMS) monolayer is deposited on the SiO2/Si surface to form covalent Si–O–Si bonds which havestrong affinity to attach nanoparticles. Onoe and Takeuchi [28] performed a different attempt toproduce SiO2 microplates array by performing etching on Si–SiO2–Si and used lift off method tosupport the pattering of biomolecules on the fabricated microplates.

3. Attachment of functional molecules

An appealing model is provided by ferritin, which is a cage-shaped biomolecule that accommo-dates an iron oxyhydroxide nanoparticle [17]. Several methods have been developed or applied to pat-tern ferritin molecules [15–17]. We have patterned ferritin molecules on predetermined silicon oxide

Fig. 10. Effect of mechanical pressure by AFM height images for (a) no pressure case, (b) 0.3 N/cm2 and (c) 0.6 N/cm2 [26].

Fig. 11. Schematic representation combining NIL and CVD [27].



dots by two methods such as positive and negative patterning with silane group surface modificationand in this work we have concluded positive patterning is a suitable method for ferritin moleculeimmobilization [15,16]. Martínez et al. [17] have studied the immobilization of ferritin moleculeson silicon oxide dots and array under different pH of the immobilization solution and concluded pH6 was suitable pH for immobilization of ferritin molecule on silane group silicon oxide. Accordingto the discussion above positive patterning and immobilization of ferritin on silane at pH 6 will besophisticated way to fabricate ferritin biotemplates for lab-on-chip application [14–17].

Lhuillier et al. [27], Mesquida and Stemmer [29], Blanco et al. [30] and Ressier et al. [31] havedeposited nano particles (NPs) on ordered silicon oxide surface for biological analyzing devices. Inmost of published work, OTS has been used to modify the surface for attachment of particles but OTMShas superior property than OTS, since OTMS provides a long carbon chain which may increase the vander Waals attraction and adherence of biomolecules easily due to its high density. Here, Lhuillier et al.[27] and Ressier et al. [31], used this superior property of OTMS and attached nano particles on thepredetermined positions with higher density (Fig. 12a).

Blanco et al. [30] fabricated a multiprotein microarray of different immunoglobulin G (IgG) anti-bodies and biotinylated bovine serum albumin (biotin-BSA) and a collagen microarray on silicon diox-ide substrates (Fig. 12b) and fluorescence confirms the expected protein content of the spots attachedto the correct location of the microarray by using electric droplet lithography (EDL).

Tang et al. [25] and Onoe and Takeuchi [28] have studied the cell interaction on ordered SiO2 pat-terns. The whole cells were cultured from suitable media and then the whole cells are allowed foradherence on the micro patterns with suitable conditions and incubation time. Whereas, Onoe andTakeuchi [28] have initiated a new way of mobile patterned microplates for whole cells attachmentand the whole cell mounted microplates can be released by physical method by using glass needlewithout any chemical treatment.

4. Conclusion

Advantages and disadvantages of various techniques used to fabricate silicon oxide array have beenreviewed, classified on the basics of their physical concepts. We have concluded that electrical meth-ods such as AFM anodic oxidation and parallel array oxidation will give well defined structures thanthe optical and mechanical methods, due to its controlled contact during reaction and direct writingproperty. Whereas, each method has its own advantage and disadvantages, researchers should select a

Fig. 12. (a) An AFM picture of an OTMS micrometric square array [27] and (b) Fabrication of a multiprotein microarray by usingEDL [30].



suitable method according to their application. Uniform patterning achieved by using chemical treat-ments such as masking, etching, SAM layer formation and selection methods for patterning based onthe property of biomolecules with suitable chemical grafting for successful attachment is also brieflyreviewed.

Acknowledgments

K.S. sincerely acknowledges DBT Project BT/PR10018/NNT/28/95/2007 for financial assistance andDST Nanomission Infrastructure Project #SR/NM/PG-05/2008⁄. K.S. acknowledges Professor TatsuoYoshinobu, Tohoku University, Japan for introducing this research area.

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