Analytica Chimica Acta 506 (2004) 127–132

               Direct immobilization in poly(dimethylsiloxane) for DNA,
128                                    C.A. Marquette, L.J. Blum / Analytica Chimica Acta 506 (2004) 127–132

C.A. Marquette, L.J. Blum / Analytica Chimica Acta 506 (2004) 127–132                            129

the same general pro...
130                                     C.A. Marquette, L.J. Blum / Analytica Chimica Acta 506 (2004) 127–132

Fig. 2. ...
C.A. Marquette, L.J. Blum / Analytica Chimica Acta 506 (2004) 127–132                                131

132                                     C.A. Marquette, L.J. Blum / Analytica Chimica Acta 506 (2004) 127–132

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Direct Immobilization In Poly(Dimethylsiloxane)


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Direct Immobilization In Poly(Dimethylsiloxane)

  1. 1. Analytica Chimica Acta 506 (2004) 127–132 Direct immobilization in poly(dimethylsiloxane) for DNA, protein and enzyme fluidic biochips Christophe A. Marquette∗ , Lo¨c J. Blum ı Laboratoire de Génie Enzymatique et Biomoléculaire, UMR 5013-CNRS, Université Claude Bernard Lyon 1, Bˆ t. CPE, a 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, Cedex, France Received 20 January 2003; received in revised form 23 October 2003; accepted 7 November 2003 Abstract A new arraying method is presented based on the properties of poly(dimethylsiloxane) (PDMS) polymer to entrap beads bearing biologically active compounds. It is shown that such beads could be spotted and dried at the surface of a poly(vinyl chloride) master and subsequently transferred at the PDMS interface by direct moulding of the polymer on the mask. Moreover, the use of the PDMS-assisted-immobilization enables the development of either a low density array (100 spots) or a micro-channel biochip with a direct incorporation of the sensing element in a fluidic system for the quantitative detection of enzyme substrates, antigens and oligonucleotides, depending on the immobilized sensing element. All biochip formats were revealed by a chemiluminescent reaction detected with a charge coupled device camera. As a result, arrays of beads bearing active enzymes, antibodies and oligonucleotides were successfully obtained and enabled the achievement of biochips for the chemiluminescent detection of enzyme substrates, protein antigens and oligonucleotides sequence with detection limit of 1 M, 1.5 × 107 molecules and 108 molecules, respectively. © 2003 Elsevier B.V. All rights reserved. Keywords: Biochip; Chemiluminescence; Enzyme; Fluidic; Low density array; Nucleic acid; PDMS; Protein 1. Introduction are used in conjunction with a detection system, most of the time intimately dependent of the immobilisation procedure. The development of biochips for the detection of nu- The present paper proposed a new approach to the de- cleic acids, proteins or enzyme–substrate interactions has velopment of a general immobilisation procedure useful for experienced a large increase since those tools were found enzymes, proteins and oligonucleotides biochip design. This to provide to researchers and diagnostic companies a rapid technique, based on the entrapment of micrometric beads in sample’s screening [1,2]. Nevertheless, one of the main a poly(dimethylsiloxane) (PDMS) material—a powerful tool handicap for the development in this area appeared to be for designing micro-fluidic systems [14]—open a path to the a lack of generic immobilisation procedure for those bio- development of directly integrated active fluidic systems. logically active compounds; a lack linked in one hand to the obligatory effort to keep active the immobilized biolog- ical molecules and in the other hand to the diversity of de- 2. Materials and methods tection/transduction systems used. The early immobilisation procedure on silicon and glass support based on silane tech- 2.1. Reagents nology, still in use for protein and DNA immobilisation [2–5] is now in competition with thiol-disulfide techniques [6–9] Biotin labelled anti-human IgG ( -chain specific), bi- on gold surface, beads array [10,11], micro-contact printing otin labelled oligonucleotides d(T)22 , glucose oxidase (Gox, [12] and particle lithography [13]. Each of these techniques grade I, EC, from Aspergillus niger), human IgG, luminol (3-aminophtalhydrazide), peroxidase labelled strep- ∗ Corresponding author. Tel.: +33-472-44-8214; tavidin, Sepharose beads bearing human IgG, Sepharose fax: +33-472-44-7970. beads bearing d(A)22 were purchased from Sigma (France). E-mail address: (C.A. Marquette). DEAE (diethylaminoethyl) Sepharose Fast Flow and IDA 0003-2670/$ – see front matter © 2003 Elsevier B.V. All rights reserved. doi:10.1016/j.aca.2003.11.015
  2. 2. 128 C.A. Marquette, L.J. Blum / Analytica Chimica Acta 506 (2004) 127–132 (imidodiacetic acid) Sepharose Fast Flow were obtained then washed with 25 ml of equilibrating buffer and stored at from Pharmacia. PDMS precursor and curing agent (Sylgard 4 ◦ C. 184) were supplied by Dow Corning. All buffers and aque- ous solutions were made with distilled demineralized water. 2.3. Biochips preparation 2.2. Bioactive beads preparation The biochips were prepared by arraying spotting solutions as 0.3 l drops. The spotting solutions were prepared by Glucose oxidase supporting beads were prepared by in- mixing 45 l of an aqueous solution composed of glycerol teraction of Ni-charged IDA-Sepharose with Gox modified 2.5%, 0.05 M NaCl with either 5 l of wet beads bearing with histidine. The histidine grafting on the Gox carbo- d(A)22 , 5 l of human IgG bearing beads, or 5 l of glu- hydrate moiety was performed using a method previously cose oxidase bearing beads added of 5 l of luminol bearing described for horseradish peroxidase modification [18]. beads. Briefly, 5 mg of Gox dissolved in 200 l of distilled water To design the low density array, 0.3 l drops were de- and 80 l of a 0.1 M NaIO4 solution were added and mixed posited on a flat poly(vinyl chloride) (PVC) substrate ev- under stirring for 20 min. Then, 40 l of a 0.2 M histidine ery 3 mm and dried under a tungsten lamp during 30 min. solution in 0.1 M carbonate buffer, pH 9, and 480 l of The presence of glycerol in the spotting solution enables the 0.1 M carbonate buffer, pH 9, were added to the activated achievement of homogeneous and smooth dry beads spots. glucose oxidase and incubated 2 h under stirring. At that The dry bead spots were then transferred to the PDMS in- time, the reaction was complete and 20 l of freshly pre- terface by pouring a mixture of precursor and curing agent pared 0.1 M NaBH4 solution in water were added and mixed onto the PVC substrate and cured for 90 min under a tung- for 15 min in order to stabilize the bounding of histidine on sten lamp. The biochip preparation was then terminated by the activated Gox. peeling off the PDMS polymer (Fig. 1). The Gox-His was then separated from non-reacted species In a similar way, the active fluidic biochip was prepared by desalting on a Sephadex G25-M column. Afterwards, by depositing 0.3 l drops of the different spotting solu- 500 l of IDA-Sepharose beads were equilibrated with tions (see above) on a PVC master composed of 12 channels 30 mM Veronal Buffer, 30 mM KCl, pH 8.5, and perfused (w:2.5 mm, h:1 mm, l:15 mm), prepared by sealing differ- with 100 mM NiCl2 solution. On the Ni-IDA-Separose ent PVC parts together with epoxy glue, and following the column thus obtained, 5 mg of the Gox-His desalted as de- same protocol as presented above. Peeling off the PDMS scribed above were deposited. The column was then washed substrate and covering it with a flat PVC surface leads to with 10 ml of equilibrating buffer and stored at 4 ◦ C. the achievement of 12 active macro channels (Fig. 3). Luminol was immobilized on DEAE-Sepharose beads by electrostatic interactions. Five hundred microliters of 2.4. Nucleic acid assay DEAE-Sepharose were packed from ethanol slurry into a plastic column, equilibrated with 10 ml of 30 mM Veronal As a model oligonucleotide hybridization process, a buffer, 30 mM KCl, pH 8.5, and perfused with 1 ml of 10 mM d(T)22 –d(A)22 couple was used. The low density arrays luminol solution in equilibrating buffer. The column was and the active macro-fluidic systems were assayed with Fig. 1. Scheme for the fabrication of the low density array. (A) The Sepharose beads bearing bioactive compounds are arrayed as 0.3 l drop onto a flat PVC master. (B) A PDMS solution is poured onto the spotted array. (C) The PDMS based array is peeled off from the master and ready to use. (D) Micrograph of a typical low density array revealed by chemiluminescence. Each particular spot contains d(A)22 charged beads and were hybridized with biotin labelled d(T)22 at a concentration of 0.5 nM.
  3. 3. C.A. Marquette, L.J. Blum / Analytica Chimica Acta 506 (2004) 127–132 129 the same general protocol. Briefly, the biochip or a partic- solidified PDMS, bead emergence appeared on the surface ular channel were saturated during 30 min by a solution of the polymer corresponding to the spots deposited (Fig. 1). of buffer A (30 mM Veronal (diethylbarbiturate), pH 8.5 No beads residue were observed on the PVC master after the containing 30 mM KCl, 0.2 M NaCl, 0.1% tween and 1% removal of the PDMS layer, demonstrating the high transfer BSA), then incubated for 1 h with biotinylated d(T)22 at efficiency of the beads to the PDMS interface. Those bead a particular concentration in buffer A. The biochip or a islands were then able to anchor active bio-molecules at the particular channel were then washed 10 min with buffer interface, through the Sepharose beads (Fig. 2). B (30 mM Veronal, pH 8.5 containing 30 mM KCl, 0.2 M The low density array format was used to design pro- NaCl), afterwards saturated with buffer A during 20 min tein and oligonucleotide biochips based on Sepharose and then incubated with peroxidase-labelled streptavidin beads bearing human IgG or d(A)22 homo oligonucleotide. at a 1 g/ml concentration during 30 min. The array or a Fig. 1 presents the immobilisation process and a mi- particular channel were then washed 20 min with buffer B crograph of a 100 d(A)22 spots array revealed with a and was then ready to be measured. streptavidine–peroxidase conjugate after an hybridization of the entire biochip with a biotin labelled d(T)22 . A 8% 2.5. Protein biochip assay standard deviation of the chemiluminescent signal was found within the array. Similar results were obtained when In a way similar to that used for the nucleic acid biochip, incubating the protein array, composed of immobilized hu- the protein biochip was saturated during 30 min by a solu- man IgG, with biotin labelled anti-human IgG antibodies. tion of buffer A, then incubated for 1 h with biotinylated The present biochip preparation procedure appeared then anti-IgG antibody at a particular concentration in buffer A. to enable the achievement of homogenous array of the two The biochip was then washed 10 min with buffer B, saturated most studied types of bio-molecules. Moreover, changing with buffer A during 20 min and then incubated with perox- the properties of the beads used could lead to a larger scale idase labelled streptavidin at a 1 g/ml concentration during of immobilized bio-molecule. Thus, oligosaccharide [15] or 30 min. The array was then washed 20 min with buffer B kinase [9] substrate could be easily immobilized and used and was then ready to be measured. as analytical tools. The non-specific signal generated by the non-specific ad- 2.6. Biochips measurement sorption on either the PDMS or the Sepharose material were evaluated by preparing a biochip with unmodified beads The ready-to-measure nucleic acid and protein biochips (not bearing any bioactive compound) and running the pro- were bring into contact with a buffered solution (30 mM tein or nucleic assay in the presence of a maximum amount Veronal, 30 mM KCl, pH 8.5) containing in addition of labelled antibody or labelled nucleic acid (100 g and 200 M luminol, 500 M hydrogen peroxide and 20 M 7 pmol, respectively). An extraordinary low non-specific sig- p-iodophenol. At that time, the arrays were introduced in nal, close to the limit of the instrumentation sensitivity, was the charge coupled device (CCD) light measurement system found. (Intelligent Dark Box II, Fuji Film) and the emitted light The PDMS assisted biochip demonstrates here its great integrated during 3 min. potential capabilities in array technology, since a low stan- The enzyme substrate biochip was used in a similar way; dard deviation and an almost non-existing background were a buffered solution (30 mM Veronal, 30 mM KCl, pH 8.5) observed. containing a particular concentration of glucose and 200 M of the triggering agent (1,3-dichloro-5,5-dimethylhydantoin) 3.2. Quantitative measurement with the active fluidic was injected in each channel just before the introduction biochip of the biochip in the measurement system, and the signal integrated during 3 min. The macro-fluidic biochips were prepared by spotting The biochip pictures obtained were quantified with a Fuji the bioactive bead solution on a three-dimensional master film image analysis program (Image Gauge 3.12). leading to the achievement of 2.5/1/15 mm (w/h/l) channels (Fig. 3). The different solutions used in each assay formats were manually introduced in the channels under vacuum 3. Results pressure, and stand to react during a stop flow duration (as described in the Section 2). 3.1. Low density arrays A first study was performed to evaluate the ability of the biochip to quantitatively detect nucleic acid. Samples Low density arrays were prepared by spotting aqueous so- with different biotin labelled d(T)22 concentrations were in- lution composed of glycerol 2.5%, NaCl 0.05 M containing jected in each particular channel, hybridized and revealed. 1:10 (v/v) of wet modified Sepharose beads at the surface Fig. 4A presents the evolution of the chemiluminescent sig- of a PVC substrate, drying the spots under a tungsten lamp nal obtained as a function of the oligonucleotide amount in- and pouring a PDMS solution on it. After the removal of the troduced in each channel. As a matter of fact, the nucleic
  4. 4. 130 C.A. Marquette, L.J. Blum / Analytica Chimica Acta 506 (2004) 127–132 Fig. 2. The different possibilities of the active PDMS biochips. (A) A Sepharose bead bearing oligonucleotide emerges from the PDMS surface. A biotinylated tracer is hybridized to the immobilized nucleic acid and revealed with a peroxidase labelled streptavidin. (B) A protein modified Sepharose bead is included in the PDMS polymer. A biotin labelled antibody reacts with the immobilized antigen and is revealed with a peroxidase labelled streptavidin. (C) An IDA-Sepharose bead bearing glucose oxidase (Gox) and a luminol-charged bead emerge from the PDMS surface. The Gox oxidizes the glucose present in the reaction medium, generating H2 O2 which in turn, reacts with the immobilized luminol to produce light. acid biochip enables the quantitative detection of biotiny- format, a 3 l sample volume could be used, lowering the lated oligonucleotide amounts in the range 58 pM–23 nM. number of nucleic acid molecules detected to 108 , which is Compared to the detection limits obtained with fluorescence close to the best results obtained in previous works [3,8,11]. [8,11] or radiolabeled-based [3] systems, involving gener- In a next study, the performance of the protein array to ally highly complex micro array designs, the present method detect free antigen in a competition format was evaluated. exhibits a slightly lower sensitivity but a larger detection Samples containing human IgG at different concentrations range. The present detection limit of 58 pM corresponds to were incubated in a particular channel, together with biotin an amount of 1010 molecules in a 300 l assay volume. labelled anti-IgG antibodies. The chemiluminescent reading Nevertheless, when using the biochip in a low density array of the biochip leads to the obtaining of the competition curve, Fig. 3. Scheme for the fabrication of the active fluidic biochip. Sepharose beads bearing bioactive compounds are arrayed as 0.3 l drop onto a PVC master. (B) A PDMS solution is poured onto the spotted array. (C) The PDMS based array is peeled off from the master and ready to use. (D) Micrograph of a typical active fluidic biochip revealed by chemiluminescence. Each particular channel is incubated with biotin labelled d(T)22 at a concentration of (a) 20 nM, (b) 10 nM, (c) 5 nM, (d) 1 nM, (e) 0.5 nM, (f) 0.1 nM, (g) 0.05 nM.
  5. 5. C.A. Marquette, L.J. Blum / Analytica Chimica Acta 506 (2004) 127–132 131 molecules in the active fluidic format and could be lowered, as above, in the macro array format to 1.5 × 107 molecules. To demonstrate all the potentialities of the active macro fluidic biochip, an enzyme-based system was designed (Fig. 1), in which chelating beads bearing glucose oxidase [15] were co-entrapped at the PDMS interface with luminol charged beads. In the reaction sequence, the glucose oxi- dase catalyses the oxidation of glucose and the production of hydrogen peroxide which reacts in the presence of a trig- gering agent [17] with the immobilized luminol to generate light. It has been previously shown that this configuration, with a different immobilisation system [16], enabled the re- alization of sensitive biosensor array without contamination problem between the different spots. Samples containing glucose at different concentrations were injected in the biochip and the light intensity produced was measured con- comitantly on the entire biochip. The obtained calibration curve is presented in Fig. 4C. Again, the performances of the PDMS biochip appeared to be competitive with regard to the sensitivity and the linear range presented in previous reports dealing with chemiluminescent detection of enzyme substrate [16,18–21]. Moreover, we demonstrated in a pre- vious study that six different oxidase enzymes could be used at the same time under the same experimental conditions, allowing to obtain a six-parameter biosensor. The present technology could then be transferred in a close future to the design of PDMS based enzyme substrate biochip for the detection of multiple parameters. 4. Conclusion PDMS as an immobilisation matrix has been successfully used to design multi-purpose biochips i.e. for either nu- cleic acids, proteins or enzymes. It is shown that the ability of the PDMS-assisted immobilisation to generate homoge- neous spot arrays exhibiting very low non-specific adsorp- tion of biological compounds is one of the key path for a Fig. 4. Performances of the PDMS-based biochip. Dose–response and generic biochip production. Indeed, the present spotting pro- micrograph of (A) the nucleic acid biochip (B) the protein biochip and (C) cedure enables the use of a large scale of immobilization the enzyme biochip. The biochips were measured during 3 min and the image quantified with a Fuji film quantification program. B0 represents procedures and chemistries, and of chemical synthesis on the light intensity obtained in the absence of free IgG and B the light beads, prior to the spotting. intensity obtained in the presence of a particular IgG concentration. Moreover, the use of PDMS material allows to consider the design of micro-fluidic systems integrating some sens- ing elements directly trapped at the macro-channel/flowing which a linearization by the “logit” function is presented on solution interface. A first step to those systems has been Fig. 4B. passed with the presented macro-fluidic systems integrating B nucleic acids, proteins or enzymes. The performances of the logit = ln present analytical systems are competitive with previously B0 − B described methods [3,8,11,16,18–21]. where B is the signal obtained at a fixed free antigen con- centration and B0 the signal obtained in the absence of free antigen. References The protein biochip allows the detection of free antigen with a detection limit of 12 ng/ml and a detection range over [1] P.S. Lee, K.H. Lee, Curr. Opin. Biotech. 11 (2000) 171. four decades at least. This amount corresponds to 1.5 × 109 [2] H. Zhu, M. Snyder, Curr. Opin. Chem. Biol. 5 (2001) 40.
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