Modified Silicon Wafer Research Articles

On the Importance of Silane Infusion Order on the Microscopic and Macroscopic Properties of Multifunctional Charge Gradients.

Four multicomponent charge gradients containing acidic and basic functionalities were prepared via sol–gel processes and the controlled-rate infusion (CRI) method to more clearly understand how preparation conditions influence macroscopic properties. CRI is used to form gradients by infusing reactive alkoxysilanes into a glass vial housing a vertically oriented modified silicon wafer. The concentration and time of infusion of the silane solutions were kept constant. Only the sequence of infusion of the silane solutions was changed. The first set of samples was prepared by initially infusing a solution containing 3-aminopropyltriethoxysilane (APTES) followed by a mercaptopropyltrimethoxysilane (MPTMS) solution. The individual gradients were formed either in an aligned or opposed fashion with respect to the initial gradient. The second set of samples was prepared by infusing the MPTMS solution first followed by the APTES solution, again in either an aligned or opposed fashion. To create charge gradients (NH3+, SO3–), the samples were immersed into H2O2. The extent of modification, the degree of protonation of the amine, and the thicknesses of the individual layers were examined by X-ray photoelectron spectroscopy (XPS) and spectroscopic ellipsometry. The wettability of the individual gradients was assessed via static contact angle measurements. The results demonstrate the importance of infusion order and how it influences the macroscopic and microscopic properties of gradient surfaces including the surface concentration, packing density, degree of protonation, and ultimately wettability. When the gradient materials are prepared via infusion of the APTES sol first, it results in increased deposition of both the amine and thiol groups as evidenced by XPS. Interestingly, the total thickness evaluated from ellipsometry was independent of the infusion order for the aligned gradients, indicative of significant differences in the film density. For the opposed gradients, however, the infusion of APTES first leads to a significantly thicker composite film. Furthermore, it also leads to a more pronounced gradient in the protonation of the amine, which introduces a very different surface wettability. The use of aminosilanes provides a viable approach to create gradient surfaces with different functional group distributions. These studies demonstrate that the controlled placement of functional groups on a surface can provide a new route to prepare gradient materials with improved performance.

Polymer Brushes via Surface-Initiated Electrochemically Mediated ATRP: Role of a Sacrificial Initiator in Polymerization of Acrylates on Silicon Substrates.

Silicon wafers as semiconductors are essential components of integrated circuits in electronic devices. For this reason, modification of the silicon surface is an important factor in the manufacturing of new hybrid materials applied in micro- and nanoelectronics. Herein, copolymer brushes of hydrophilic poly(2-hydroxyethyl acrylate) (PHEA) and hydrophobic poly(tert-butyl acrylate) (PtBA) were grafted from silicon wafers via simplified electrochemically mediated atom transfer radical polymerization (seATRP) according to a surface-initiated approach. The syntheses of PHEA-b-PtBA copolymers were carried out with diminished catalytic complex concentration (successively 25 and 6 ppm of Cu). In order to optimize the reaction condition, the effect of the addition of a supporting electrolyte was investigated. A controlled increase in PHEA brush thickness was confirmed by atomic force microscopy (AFM). Various other parameters including contact angles and free surface energy (FSE) for the modified silicon wafer were presented. Furthermore, the effect of the presence of a sacrificial initiator in solution on the thickness of the grafted brushes was reported. Successfully fabricated inorganic–organic hybrid nanomaterials show potential application in biomedicine and microelectronics devices, e.g., biosensors.

Semiempirical Peak Fitting Guided by ab Initio Calculations of X-ray Photoelectron Spectroscopy Narrow Scans of Chemisorbed, Fluorinated Silanes.

Here, we address the issue of finding correct CF2/CF3 area ratios from X-ray photoelectron spectroscopy (XPS) C 1s narrow scans of materials containing -CH2CH2(CF2)nCF3 (n = 0, 1, 2, ...) moieties. For this work, we modified silicon wafers with four different fluorosilanes. The smallest had a trifluoropropyl (n = 0) moiety, followed by nonafluorohexyl (n = 3), tridecafluoro (n = 5), and finally, heptadecafluoro (n = 7) moieties. Monolayer deposition of the fluorosilanes was confirmed by spectroscopic ellipsometry, wetting, and XPS. Analysis of the trifluoropropyl (n = 0) surface and a sample of polytetrafluoroethylene provided pure-component XPS spectra for -CF3 and -(CF2)n- moieties, respectively. Initial XPS C 1s peak fitting, which follows the literature precedent, was not entirely adequate. To address this issue, six different fitting approaches with increasing complexity and/or input from the Hartree-Fock theory (HF) were considered. Ultimately, we show that by combining HF results with empirical analyses, we obtain more accurate CF2/CF3 area ratios while maintaining high-quality fits.

Reusable Silicon-Based Surface-Enhanced Raman Scattering Ratiometric Aptasensor with High Sensitivity, Specificity, and Reproducibility.

Rapid, sensitive, and accurate detection of adenosine triphosphate (ATP), the primary energy molecule, is critical for the elucidation of its unique roles in cell signaling and many cellular reactions. Up to date, a major challenge is still remaining for fabricating surface-enhanced Raman scattering (SERS) aptamer sensors (aptasensors) suitable for accurate and reliable quantification of ATP. Herein, we develop the ratiometric silicon SERS aptasensor for ATP detection, which is made of uniform silver nanoparticles (Ag NPs)-modified silicon wafer (Ag NPs@Si), followed by the functionalization with double-stranded DNA (dsDNA I). The dsDNA I is formed by the aptamer and its complementary DNA (cDNA), which contains two independent segments (e.g., 5'-Cy3-labeled DNA-C1, 3'-ROX-labeled DNA-C2). In the presence of ATP, ROX-DNA-C2 is dissociated from dsDNA I due to the formation of aptamer/ATP complex, leading to the attenuation of ROX signals, and meanwhile, Cy3 signals remain constant ascribed to the formation of dsDNA II caused by the supplementation of aptamer. As a result, ratiometric signals of the ratio of ROX intensity to Cy3 intensity (IROX/ICy3) can be achieved. Of particular significance, the developed ATP aptasensor features excellent reproducibility [e.g., the relative standard deviation (RSD) is less than ∼4%, comparable or superior to that of previously reported aptasensors], ultrahigh sensitivity [e.g., the detection of limit (LOD) reaches 9.12 pM, lower than that of other reported ATP SERS aptasensors], as well as good recyclability (e.g., ∼9.3% of RSD values of ratiometric signals within three cycles).

PS-b-PMMA/PLA blends for nanoporous templates with hierarchical and tunable pore size

Blends of poly(styrene)-block-poly(methyl methacrylate) (PS-b-PMMA) and poly(lactide) (PLA) were deposited in the form of thin films on the surface of modified silicon wafers and exposed to tetrahydrofuran (THF) vapor annealing. It was shown that in specific experimental conditions, a core-shell morphology consisting in cylinders with a PMMA shell and a PLA core, within a continuous matrix of PS, was formed. In this case, PLA naturally segregated in the core of the PMMA cylinders, minimizing the PS/PLA interaction, which constitutes the most incompatible pair (the interaction strength between the various components was confirmed in thin films of the corresponding polymer blends). Compared to other block copolymer/homopolymer blends described in the literature, this system exhibits unexpected high increase of the characteristic lengths of the system (center-to-center distance and diameter). This was attributed to a partial solubilization of the PLA in the PMMA corona (the two polymers are highly compatible), inducing an enhanced level of PS and PLA stretching caused by the strong repulsion between these two polymers. The selective extraction of the PLA yielded to porous domains with small dimensions (6±2.5nm), reaching the performances that are currently attained in highly incompatible block polymers with low molecular weight. Further PMMA removal revealed a second porosity level, with higher pores diameter and center-to-center distance compared to the neat PS-b-PMMA system. This work highlights how PS-b-PMMA, that currently represents one of the industrial standards nanoporous template precursors, can be modified in an easy and costless approach using PLA homopolymer addition.

Modifying Surface Fluctuations of Polymer Melt Films with Substrate Modification.

Deposition of a plasma polymerized film on a silicon substrate substantially changes the fluctuations on the surface of a sufficiently thin melt polystyrene (PS) film atop the substrate. Surface fluctuation relaxation times measured with X-ray photon correlation spectroscopy (XPCS) for ca. 4Rg thick melt films of 131 kg/mol linear PS on hydrogen-passivated silicon (H-Si) and on a plasma polymer modified silicon wafer can both be described using a hydrodynamic continuum theory (HCT) that assumes the film is characterized throughout its depth by the bulk viscosity. However, when the film thickness is reduced to ∼3Rg, confinement effects are evident. The surface fluctuations are slower than predicted using the HCT, and the confinement effect for the PS on H-Si is larger than that for the PS on the plasma polymerized film. This deviation is due to a difference in the thicknesses of the strongly adsorbed layers at the substrate which are impacted by the substrate surface energy.

In situ surface enhanced Raman spectroscopy detection in high pressure solution

In situ surface enhanced Raman scattering (SERS) in solution was tested in this study at ambient temperature and high pressure (up to 978MPa) in a diamond-anvil cell, with the intent of resolving trace detection in high pressure conditions. The 4-chlorothiophenol solution was used as the analyte in our experiments. A silver nanoparticle layer, formed by chemical reduction and assembled on a poly (allylamine hydrochloride)-modified silicon wafer, was used as the substrate. There was an obvious rise in SERS intensity when the sample chamber was pressurized for the first time in the diamond-anvil cell. But then the intensity drop occurred with increasing pressure and all peaks have pressure-induced blue shift below 700MPa. The SERS intensity and Raman shift displayed irregular changes in the pressure range from 700MPa to 978MPa. The discovery of the survival of in situ high-pressure SERS in solution in the present study may make it a prospecting tool for the high-precision detection of analyte in high pressure conditions. Moreover, it could provide more information on the SERS mechanisms that have been puzzling us for decades.

Asymmetry of the free-standing polyelectrolyte multilayers

Free-standing polyelectrolyte multilayers (PEMs) triggered an intense research effort to develop functional capsules and membranes, nevertheless, the comprehensive understanding of the surface distinctions between the two sides of the free-standing PEMs has been rarely studied. In this paper, we demonstrate the asymmetric surface morphologies, compositions, surface charge and wetting properties of the free-standing PEMs made of alternating deposition of poly(diallyldimethylammonium chloride) (PDDA) and poly(styrenesulfonate) (PSS) on uncharged trimethoxy (octyl) silane modified silicon wafer (TMOS-Si) substrates. The growth behaviors (e.g., linear or exponential growth) of the (PDDA/PSS)n PEMs deposited on TMOS-Si substrates are similar to those deposited on negatively charged substrates except a slower evolution in morphology and thickness, evidenced by atomic force microscopy (AFM) and ellipsometry. The surface charge of the two sides can be tuned as+/+, −/-, and+/− by selecting the first and the terminate layer of the polyelectrolyte during the deposition process, indicated by X-ray photoelectron spectroscopy (XPS) and the surface zeta potential measured by spinning disk method. Further, water contact angle measurements exhibit a strong difference between the back side (the bottom side that was initially contacted with the substrate) (74±4°) and front side (33±2° and 48±3° for PDDA and PSS as the outmost layer, respectively) of the PEMs. The larger water contact angle of the back side is probably resulted from the orientation of the alkyl chains of the polyelectrolytes as the hydrophobic–hydrophobic interactions played significant roles in deposition of a polyelectrolyte onto an uncharged substrate. This paper may gain new insights on understanding surface properties of the PEMs.

Self-assembly of silver nanoparticles as high active surface-enhanced Raman scattering substrate for rapid and trace analysis of uranyl(VI) ions

A facile surface-enhanced Raman scattering (SERS) substrate based on the self-assembly of silver nanoparticles on the modified silicon wafer was obtained, and for the first time, an advanced SERS analysis method basing on this as-prepared substrate was established for high sensitive and rapid detection of uranyl ions. Due to the weakened bond strength of OUO resulting from two kinds of adsorption of uranyl species (“strong” and “weak” adsorption) on the substrate, the ν1 symmetric stretch vibration frequency of OUO shifted from 871cm−1 (normal Raman) to 720cm−1 and 826cm−1 (SERS) along with significant Raman enhancement. Effects of the hydrolysis of uranyl ions on SERS were also investigated, and the SERS band at ~826cm−1 was first used to approximately define the constitution of uranyl species at trace quantity level. Besides, the SERS intensity was proportional to the variable concentrations of uranyl nitrate ranging from 10−7 to 10−3molL−1 with an excellent linear relation (R2=0.998), and the detection limit was ~10−7molL−1. Furthermore, the related SERS approach involves low-cost substrate fabrication, rapid and trace analysis simultaneously, and shows great potential applications for the field assays of uranyl ions in the nuclear fuel cycle and environmental monitoring.

Bypassing Protein Corona Issue on Active Targeting: Zwitterionic Coatings Dictate Specific Interactions of Targeting Moieties and Cell Receptors.

Surface functionalization strategies for targeting nanoparticles (NP) to specific organs, cells, or organelles, is the foundation for new applications of nanomedicine to drug delivery and biomedical imaging. Interaction of NPs with biological media leads to the formation of a biomolecular layer at the surface of NPs so-called as "protein corona". This corona layer can shield active molecules at the surface of NPs and cause mistargeting or unintended scavenging by the liver, kidney, or spleen. To overcome this corona issue, we have designed biotin-cysteine conjugated silica NPs (biotin was employed as a targeting molecule and cysteine was used as a zwitterionic ligand) to inhibit corona-induced mistargeting and thus significantly enhance the active targeting capability of NPs in complex biological media. To probe the targeting yield of our engineered NPs, we employed both modified silicon wafer substrates with streptavidin (i.e., biotin receptor) to simulate a target and a cell-based model platform using tumor cell lines that overexpress biotin receptors. In both cases, after incubation with human plasma (thus forming a protein corona), cellular uptake/substrate attachment of the targeted NPs with zwitterionic coatings were significantly higher than the same NPs without zwitterionic coating. Our results demonstrated that NPs with a zwitterionic surface can considerably facilitate targeting yield of NPs and provide a promising new type of nanocarriers in biological applications.

High-precision drop shape analysis (HPDSA) of quasistatic contact angles on silanized silicon wafers with different surface topographies during inclining-plate measurements: Influence of the surface roughness on the contact line dynamics

Contact angles and wetting of solid surfaces are strongly influenced by the physical and chemical properties of the surfaces. These influence quantities are difficult to distinguish from each other if contact angle measurements are performed by measuring only the advancing θa and the receding θr contact angle. In this regard, time-dependent water contact angles are measured on two hydrophobic modified silicon wafers with different physical surface topographies. The first surface is nearly atomically flat while the second surface is patterned (alternating flat and nanoscale rough patterns) which is synthesized by a photolithography and etching procedure. The different surface topographies are characterized with atomic force microscopy (AFM), Fourier transform infrared reflection absorption spectroscopy (FTIRRAS) and Fourier transform infrared attenuated total reflection spectroscopy (FTIR-ATR). The resulting set of contact angle data obtained by the high-precision drop shape analysis approach is further analyzed by a Gompertzian fitting procedure and a statistical counting procedure in dependence on the triple line velocity. The Gompertzian fit is used to analyze overall properties of the surface and dependencies between the motion on the front and the back edge of the droplets. The statistical counting procedure results in the calculation of expectation values E(p) and standard deviations σ(p) for the inclination angle φ, contact angle θ, triple line velocity vel and the covered distance of the triple line dis relative to the first boundary points XB,10. Therefore, sessile drops during the inclination of the sample surface are video recorded and different specific contact angle events in dependence on the acceleration/deceleration of the triple line motion are analyzed. This procedure results in characteristically density distributions in dependence on the surface properties. The used procedures lead to the possibility to investigate influences on contact angles more in detail.

Hybrid silicon/P3HT solar cells based on an interfacial modification with a molecular thiophene layer

Hybrid photovoltaic (PV) devices based on a poly(3-hexylthiophene) (P3HT) layer and chemically modified silicon wafers with thiophene groups are reported for the first time. The chemical modification was performed by linking thiophene units directly onto silicon atoms at the n-type silicon wafer surface. To achieve the silicon modification, two-step, chlorination/alkylation reactions were used to convert Si–H into Si–thiophene bonds. Such interfacial modification increased the compatibility and the physical contact between the organic and inorganic phases as well as it promoted a more favorable alignment of band-edge energies. Thus, the hybrid photovoltaic devices based on n-Si/thiophene/P3HT achieved a power conversion efficiency of 8.0% (under simulated air mass 1.5 solar irradiation at 100 mW cm−2), which was higher than the device containing the silicon wafer with terminal Si–H bonds.

Relevance of the Poly(ethylene glycol) Linkers in Peptide Surfaces for Proteases Assays

Poly(ethylene glycol)s (PEGs) with different lengths were used as linkers during the preparation of peptide surfaces for protease detection. In the first approach, the PEG monolayers were prepared using a "grafting to" method on 3-aminopropyltrietoxysilane (APTES)-modified silicon wafers. Protected peptides with a fluorescent marker were synthesized by Fmoc solid phase synthesis. The protected peptide structures enabled their site-specific immobilization onto the PEG surfaces. Alternatively, the PEG-peptide surface was obtained by immobilizing a PEG-peptide conjugate directly onto the modified silicon wafer. The surfaces (composition, grafting density, hydrophilicity, and roughness) were characterized by time-of-flight-secondary ion mass spectrometry (ToF-SIMS), X-ray photoelectron spectroscopy (XPS), contact angle (CA), and atomic force microscopy (AFM). Introducing the PEG linker between the peptide and surface increased their resistance toward nonspecific protein adsorption. The peptide surfaces were examined as analytical platforms to study the action of trypsin as a representative protease. The products of the enzymatic hydrolysis were analyzed by fluorescence spectroscopy, electrospray ionization-mass spectrometry (ESI-MS), and ToF-SIMS. Conclusions about the optimal length of the PEG linker for the analytical application of PEG-peptide surfaces were drawn. This work demonstrates an effective synthetic procedure to obtain PEG-peptide surfaces as attractive platforms for the development of peptide microarrays.

“Coffee ring” formation dynamics on molecularly smooth substrates with varying receding contact angles

A systematic study of “coffee-ring” formation dynamics was carried out using chemically and physically well-controlled substrates and colloids. Clean silicon wafers were reacted with tris(trimethylsiloxyl)chlorosilane in the vapor phase to yield molecularly smooth substrates with advancing and receding contact angles up to 84°/74° (θA/θR) and a constant hysteresis of 12±2°. Monodisperse gold nanoparticles (AuNPs) of 15nm in diameter were stabilized and functionalized with poly(vinyl alcohol) (PVOH) of 9nm in thickness in aqueous solution. The evolution of contact angle and contact diameter of water and colloid-containing drops on clean and modified silicon wafers was assessed as sessile drops evaporated. PVOH-AuNPs in the colloid-containing drop increase the energy barrier for contact line depinning and the pinning force. There are up to four drying stages for colloid-containing drops, initial pinning, depinning, secondary pinning, and final evaporation. The contribution of each stage to evaporation depends on substrate receding contact angle. It is established in this study that the secondary pinning is unique for colloid-containing drops and is only observed on substrates with receding contact angles greater than 35°. “Coffee rings” are formed on all modified silicon wafers, but not on clean silicon wafers with contact angles of 0°/0°.

Synthesis and characterisation of PEG-peptide surfaces for proteolytic enzyme detection.

Peptide surfaces were obtained by the covalent immobilisation of fluorescently labelled pentapeptides carboxyfluorescein–glycine–arginine–methionine–leucine–glycine, either directly or through a poly(ethylene glycol) (PEG) linker on modified silicon wafers. Each step during the preparation of the peptide surfaces was confirmed by several surface characterisation techniques. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) and X-ray photoelectron spectroscopy were used to determine the surface composition, the wafers philicity was measured by contact angle and atomic force microscopy was used to investigate the surface morphology. Exposure of the peptide surfaces to trypsin resulted in the release of a fluorescently labelled peptide product, which allowed the kinetics of the enzymatic reaction to be followed with the aid of fluorescence spectroscopy. The electrospray ionisation mass spectrometry analysis of the post-digestion solution confirmed that the pentapeptides attached to the solid support undergo specific trypsin hydrolysis at the C-terminus of the arginine residues. Detailed surface analyses before and after the enzyme action was performed using ToF-SIMS. Because of the limited accessibility of the short peptide directly attached to the surface, a quantitative yield of enzymatic hydrolysis was observed only in case when the peptide was bound through the PEG linker. The insertion of the PEG linker increased the number of immobilised peptides and the rate of enzymatic digestion which consequently improved the quality of the enzyme assays. The described approach may be used for different peptide sequences designed for other proteases. FigureMonitoring of trypsin hydrolysis on PEG-peptide surface Electronic supplementary materialThe online version of this article (doi:10.1007/s00216-013-7082-z) contains supplementary material, which is available to authorized users.

Preparation Procedure of Liposome-Absorbed Substrate and Tip Shape Correction of Diameters of Liposome Measured by AFM

The procedure to measure liposome in aqueous solution has been examined using atomic force microscope (AFM). We concluded a chemical modified silicon wafer (substrate for AFM observation of liposome) with 3-aminopropyltrieth-oxysilane (APTES) which enabled us to scan anionic liposome softly in water because they were keeping structures as vesicles and stably adsorbed on the substrate by electrostatic force. From captured AFM topographic images, we counted the amount of liposome and analyzed the distribution of mean diameters, which were corrected by an approximated curve of the tip shape. We discussed the method of effective evaluation as practical analysis and its problems for robust analysis.

Preparation of antibacterial surfaces by hyperthermal hydrogen induced cross-linking of polymer thin films

The covalent immobilization of polymers on surfaces has the potential to impart new properties and functions to surfaces for a wide range of applications. However, most current methods for the production of these surfaces involve multiple chemical steps or do not impart a high degree of control over the chemical functionalities at the surface. Described here is the preparation of surfaces covalently functionalized with quaternized poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA), a known antibacterial polymer. PDMAEMA was coated onto octadecyltrimethoxysilane modified silicon wafers and was then cross-linked by the selective cleavage of C–H bonds using a hyperthermal hydrogen treatment. The surfaces were then quaternized with ethyl bromide. At each step the surfaces were characterized extensively using techniques including atomic force microscopy, contact angle measurements and X-ray photoelectron spectroscopy. These results demonstrated a high degree of functional group retention throughout the process. The antibacterial properties of the surfaces against Gram-positive S. aureus and Gram-negative E. coli were investigated using a “drop test” assay. Furthermore, the process was successfully applied to produce antibacterial butyl rubber surfaces, demonstrating the versatility of the method for grafting onto unfunctionalized hydrocarbon surfaces.

Chitosan cushioned phospholipid membrane and its application in imaging ellipsometry based-biosensor

Chitosan cushion can support the air stability of phospholipid membrane, but the problem of serum solubility of phospholipid membrane prevents it from use in serum detection applications. Poly (ethylene glycol) (PEG) shielding promises both stability and non-specific adsorption resistance for phospholipid membrane. An air stable phospholipid membrane microarray has been successfully fabricated on chitosan modified silicon wafer. We have demonstrated the potential application of PEGylated phospholipid membrane in imaging ellipsometry-based protein biosensor. Because of the strong resistance against non-specific adsorption of serum, antigens are immobilized onto the membrane surface through chemical activation and further bind their antibodies without using blocking agent. Taking advantage of the multiple and parallel reaction capabilities of microfluidic reactor system, we have assayed the binding by varying both the density of antigen on the membrane surface and the concentration of antibody in solution.

Preparation and Biocompatibility of BSA Monolayer on Silicon Surface

This paper describes a general strategy for grafting protein molecules on silicon surface by using dopamine as adhesive layer. With this method, silicon surface had been successfully modified by BSA monolayer. Fourier transform infrared spectra, X-ray photoelectron spectroscopy, contact angle analysis and atomic force microscopy confirmed the sequential grafting of initiator and protein molecules. Cell adhesion experiments with PC-12 cells showed that the obtained monolayer exhibits good biocompatibility. The corrosion resistance behavior of the polydopamine and BSA modified silicon wafers was investigated by potentiodynamic test, which indicated that the modified surfaces exhibited a better anti-corrosion capability than silicon surface. All these results must be valuable for the application of protein monolayer in biological and biomedical technology.

Fabrication of Highly Uniform Conductive Polypyrrole Nanowires with DNA Template

Deoxyribonucleic acid (DNA) is considered as one of the alternative materials for electronic device applications; however, DNA has critical limitation to electronic device applications due to its low electrical conductivity and unreliability. Therefore, it is required for electronic devices to prepare the well defined conductive polymer nanowires with DNA as a template. Polypyrrole (PPy) is an attractive polymer due to its high conductivity and environmental stability in bulk; although it is well known that ammonium persulfate (APS) used for the polymerization of pyrrole causes the deformation of DNA molecules. We minimized the damage of immobilized DNA strands on (3-aminopropyl) triethoxysilane (APTES) modified silicon wafer during APS polymerization. Atomic force microscopy (AFM) images from different APS treatment times and from using the vortex process obviously showed the effect on the synthesis of individual and continuous polypyrrole nanowires (PPy NWs). The PPy NWs at various pyrrole concentrations had similar height; however, the higher concentration gave more residues. Fourier transform-infrared spectroscopy (FT-IR) spectroscopy provided the strong evidence that PPy NWs were successfully synthesized on the DNA strands.