Carbon 157 (2020) 40e46
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Carbon journal homepage: www.elsevier.com/locate/carbon
Applying AuNPs/SWCNT to fabricate electrical nanogap device for DNA hybridization detection Yi Yu a, QingYi Zhu a, Feifan Xiang a, Yue Hu a, Lijie Zhang a, Xiangju Xu a, Nannan Liu a, *, Shaoming Huang a, b, ** a b
Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry & Materials Engineering, Wenzhou University, Wenzhou, 325027, PR China School of Material and Energy, Guangdong University of Technology, Guangzhou, 510006, PR China
a r t i c l e i n f o
a b s t r a c t
Article history: Received 26 July 2019 Received in revised form 20 September 2019 Accepted 9 October 2019 Available online 11 October 2019
AuNPs/SWCNT, a hybrid nanomaterial which is single-walled carbon nanotube (SWCNT) modified with gold nanoparticles (AuNPs), has great application prospects for chemical and biological sensors. For the innate nanogap between tiny AuNPs deposited on sidewall of SWCNT, AuNPs/SWCNT is suitable for the fabrication of simple and effective electrical signal switching devices. Here, we develop a novel strategy of applying AuNPs/SWCNT to fabricate nanogap device for DNA hybridization detection. The detection strategy is based on the target DNA mediating the catalytic activity of the AuNPs by desorbing the probe DNA from AuNPs. The signal transduction depends on the growth of tiny AuNPs which is closely related to the AuNPs catalytic activity. Sensing occurs at the tiny AuNPs growing and connecting into a continuous nanowire along the SWCNT, leading to a conductimetric response. The biosensing device can detect target DNA with the detection limit of 1 pM and the ability to discriminate triple and quintuple base pair mismatches. © 2019 Elsevier Ltd. All rights reserved.
Keywords: AuNPs SWCNT Nano-micro device Nanogap biosensor DNA detection
1. Introduction To develop sensitive, robust and economically feasible detection methods for the analysis of genetic disorders or the detection of pathogens have a major impact on human health and safety [1e7]. Owing to the high sensitivity, the techniques based on the polymerase chain reaction (PCR) have been viewed as the most widely used technique for sensitive detection of DNA [8]. However, the PCR-based techniques for DNA detection also encounter many problems, such as complicated procedures, easy contamination and high cost. Gap-based electrical biosensing devices can provide a viable alternative route to PCR for the rapid quantification of DNA, attributing that such devices can directly transduce nucleic acid hybridization events into useful electrical signals through pairs of microgap or nanogap electrodes [9]. These unique properties, coupled with their compatibility with advanced semiconductor
* Corresponding author. ** Corresponding author. Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry & Materials Engineering, Wenzhou University, Wenzhou, 325027, PR China. E-mail addresses:
[email protected] (N. Liu),
[email protected] (S. Huang). https://doi.org/10.1016/j.carbon.2019.10.017 0008-6223/© 2019 Elsevier Ltd. All rights reserved.
technology and large-scale reproducible fabrication and miniaturization, make them very promising in the development of highperformance DNA detection [10]. AuNPs/SWCNT is suitable potential candidate hybrid nanomaterial for the sensitive electrical transduction of different biomolecular recognition events due to its high surface area, favorable electronic properties, ease of biomolecule attachment, and electrocatalytic effects. Many studies have been reported about applying AuNPs/SWCNT to electrochemical biosensor [11e16]. For example, Seong et al. presented the application of electrochemical patterning of gold nanostructures on SWCNT in the development of chemical sensors for hydroxylamine detection [11]. Luong et al. reported a strategy for the detection of HIV-1 protease (HIV-1 PR) by utilizing an AuNPs-SWCNT-modified electrode to attain unprecedented detection sensitivity below the picomolar (pM) level [12]. Wang et al. investigated the electrochemical detection of longer DNAs, specifically hepatitis B (HBV) and papilloma virus (HPV), using both aligned and random SWCNTs arrays coated with AuNPs [13]. However, the applications of the AuNPs/SWCNT in these work were only to apply it into modified electrodes by cyclic voltammetry and impedance analyze for detection. There has been rare research about the application of the AuNPs/SWCNT in nano-micro device. Therefore, it remains great possibility that AuNPs/SWCNT can be
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shining in nano-micro device for biological detections. In this work, we develop a strategy of applying AuNPs/SWCNT to fabricate nano-micro device for DNA hybridization detection by exploiting the innate nanogap between tiny AuNPs deposited on SWCNT. The detection mechanism of the device is based on mediating the catalytic activity of the AuNPs by adsorption and desorption. The AuNPs can catalyze the redox reaction between 0 glucose and AuCl 4 to produce Au which will be deposited on the surface of AuNPs, resulting in the size of AuNPs obviously increasing [17]. This catalytic activity can be inhibited when the surface of AuNPs is wrapped by single-stranded (ss)-DNA [18]. Attributing to the attractive van der Waals force between the uncoiling bases of ss-DNA and the AuNPs, the ss-DNA can adsorb on the AuNPs, leading to the inhibition of catalytic activity. But the same mechanism is not operative with the double-stranded (ds)DNA for the duplex structure not permitting the uncoiling needed to expose the bases [19]. Based on these chemical mechanisms (the middle part of Fig. 1), we develop a strategy to detect lower concentration of DNA. And the detection process can be seen from Fig. 1. The device consists of the single SWCNT modified with tiny AuNPs, and the two gold electrodes fixed on both sides of the SWCNT with the spacing of 30 mm. Attributing to the mentioned mechanisms, the AuNPs will be wrapped by ss-DNA (the probe in our experiment) in high concentration of the probe. Subsequently, we can deal the AuNPs (together with the whole device) with different sample solutions. If the target (complementary strand of the probe) exists in the sample, the probe will hybridize with it to form ds-DNA and depart from AuNPs, resulting in the recovery of AuNPs catalytic activity. Inversely, if no target exists, the catalytic activity will not recover. The catalytic activity of AuNPs will directly affect the growth of AuNPs when the AuNPs dealt with the growth solution containing HAuCl4 and glucose. As can be seen from Fig. 1, the increase of AuNPs size will lead to the connection of the nanogap between the AuNPs along SWCNT, resulting in an obvious alteration for the conductance of the gold electrodes. The variation
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in conductance of the device depends on the target. Therefore, if the conductance increases obviously in the detection, it reveals that the target exists in the sample. If inversely, it does not. The detailed manufacturing process of the AuNPs/SWCNT device is shown in Fig. S1. 2. Experimental section 2.1. Materials Glucose and chloroauric acid (HAuCl4) were provided from Aladdin and used as received. Other reagents and chemicals were all of analytical reagent grade. Ultrapure water with an electrical resistance of >18.2 MU was supplied through a Millipore Milli-Q water purification system (Billerica, MA,U.S.A.). The DNA oligonucleotides and fetal bovine serum (FBS) were purchased from Sangon Biotech. Co. Ltd. (Shanghai, China), and their sequences are as follows. Probe DNA: 5’ -CCACATCATCCATATAGCT-30 Match and mismatch oligonucleotide sequences: Match (Target): 50 -AGCTATATGGATGATGTGG-30 1-base mismatch: 50 -AGCTATGTGGATGATGTGG-30 3-base mismatch: 50 -AGCTACGCGGATGATGTGG-30 5-base mismatch: 50 -AGCTACGCTTATGATGTGG-30 Non-match (control): 50 -ATACAGACTCCGAGACGAAAACAGACTCCGAGACGGAA-30 Buffer: 10 mM TrisHCl, 500 mM NaCl, 1 mM MgCl2, pH
7.4
Fig. 1. In our biosensing device, the AuNPs on SWCNT are wrapped by the probe (ss-DNA). In the presence of target (complementary ss-DNA), the target will hybridize with the probe, resulting in the probe desorption from the surface of AuNPs. After dealt with the glucose and HAuCl4 solution, the conductance between gold electrodes will increase obviously with the connection of AuNPs. (A colour version of this figure can be viewed online.)
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2.2. Device manufacture 2.2.1. Growth of SWCNTs on the substrate The superlong SWCNTs were generated by ethanol-CVD method [20,21]. The metallic Fe catalysts were loaded on one side of the SiOx/Si substrate by dipping the edge of wafer into a catalystcontaining solution. Then, the wafer was placed in the middle of a quartz tube in order to acquire laminar flow. The furnace was first heated to 950 C under the atmosphere of H2 (300 sccm). Ethanol vapor was delivered by bubbling H2 (300 sccm) into ethanol at ambient temperature. The SEM image of the superlong SWCNT was shown in Fig. S2. 2.2.2. Decorating gold nanoparticles onto SWCNT The SWCNT samples were immersed into a 5 mM HAuCl4 ethanol/water (1/1, v/v) solution for 15 min to deposit gold seeds [22], then rinsed with ethanol and water. 2.2.3. Manufacture and selection of electrodes Firstly, the AuNPs/SWCNT substrate was covered with a special metallic mask. And then the gold film was deposited on Surface by vacuum coating (Fig. S3). For the metallic wire of the mask being 30 mm, the spacings of the electrodes could be 30 mm as same (Fig. S4). By SEM, the electrodes with single AuNPs/SWCNT were selected to apply for following experiments. And the conductance of each AuNPs/SWCNT device should be tested before detection.
500 mM NaCl and 1 mM MgCl2 at room temperature for 30 min. After adequately adsorbed with the probe, the electrodes were washed with ultrapure water. Subsequently, the devices were immersed in sample solutions containing target with different concentrations for 30 min at room temperature to desorb the probe DNA. After washed with ultrapure water again, the growth solution containing 250 mM glucose and 500 mM HAuCl4 was applied onto the surface of the devices at room temperature for 15 min to make the AuNPs grow. The devices then were rinsed with ultrapure water and dried under mild nitrogen flow. Finally, the conductance of each AuNPs/SWCNT device was tested again to be compared with the conductance before the AuNPs growing. 2.4. Apparatus All of the electrical measurements were performed under ambient conditions in the air with a Keithley 6487 picoammeter/ voltage source (Keithley Instruments, OH). The electrode was placed in air, one pole connected to the working electrode and the other pole connected to the reference and counter electrodes. According to Ohm’s law, the current through two poles of microelectrodes is proportional to the voltage applied on microelectrode arrays, with a slope equal to the electrical conductance. Thus, the conductance of electrodes can be calculated. SEM images are taken from FEI NanoSEM. AFM images were recorded at NanoScope III in tapping mode. 3. Results and discussion
2.3. DNA detection assay Firstly, the AuNPs/SWCNT devices were immersed in the mixture containing 1 mM ss-DNA probe in 10 mM TrisHCl,
Fig. 2a shows the SEM image of the device with the gold electrodes fixed in the both side of single SWCNT. The AFM image of the SWCNT was taken and shown in Fig. 2b. The height measurement
Fig. 2. (a) SEM image of the SWCNT between the gold electrodes with the 30 mm spacing. (b) AFM image and the height measurement of the SWCNT. (c) Raman spectrum of SWCNT with the G band peak at 1588.1 cm1 and the RBM peak at 163.7 cm1. (d) Raman spectra of SWCNT before (black curve) and after (blue curve) gold nanoparticles’ decoration. (A colour version of this figure can be viewed online.)
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indicates that the diameter of the SWCNT is ~1.2 nm. Fig. 2c shows the full Raman Spectrum of SWCNT. The G band peak at 1588.1 cm1 corresponds to graphitic structure and the radial breathing model (RBM) at 163.7 cm1 can be used to further identify the structure and the diameter (d) of the SWCNT. According to the equation of d ¼ 223.75 cm1/u, the diameter of the SWCNT is calculated to be about 1.3 nm which is consistent with AFM measuring result. AuNPs/SWCNT which the tiny AuNPs are deposited on the sidewall of SWCNT, can be gotten by dealing the SWCNT samples with 5 mM HAuCl4 ethanol/water (1/1, v/v) solution [22]. For the redox reaction between Au3þ and SWCNT, the Au3þ will be reduced into Au0 between the interface of SWCNT and HAuCl4 solution, resulting in the tiny AuNPs generated on the surface of SWCNT. It can be observed from Fig. 3a that there are obvious tiny AuNPs selectively and densely deposited along the SWCNT with uniform size. For the surface-enhancement effect of the metal (normally gold or silver) nanoparticles, the Raman signal of SWCNT will increase after the deposition of AuNPs. From Fig. 2d, it can be found that the signal of G band peak indeed gets enhancement. These characterizations indicate that the SWCNT have been successfully decorated with tiny AuNPs. After modifying SWCNT with tiny AuNPs, it needs to be confirmed that the tiny AuNPs can grow into a gold nanowire in growth solution and further significantly affect the conductance of
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the AuNPs/SWCNT device. It can be known from Fig. 3a that the height of AuNPs/SWCNT is about 2.4 ± 0.3 nm. The tiny AuNPs can keep mutual isolated and the size of which will not increase before dealt with growth solution. Upon the addition of the growth solution, it can be found that the AuNPs no longer remain isolated but form into a continuous nanowire, from which it is hard to discover the obvious interparticle nanogap between AuNPs (Fig. 3b). It can be known from AFM image that the diameter of the gold nanowire is about 9 nm which is evidently bigger than the tiny AuNPs diameter of 2.4 ± 0.3 nm. As shown in Fig. 3c, the Raman signal of SWCNT (G band peak) has got distinct enhancement after the AuNPs/SWCNT dealt with growth solution. It certainly fits with the experimental theory that the increase of gold nanoparticles diameter and the decrease of interparticle distance both will be benefit to the surface-enhancement effect of AuNPs [23]. It further reveals that the AuNPs can be wired along the SWCNT after the growth of tiny AuNPs. Fixed with the two gold electrodes on both sides, AuNPs/SWCNT can be manufactured into the AuNPs/SWCNT device with spacing of electrodes about 30 mm. To confirm that the growth of tiny AuNPs can significantly affect the conductance of the AuNPs/SWCNT device, the conductance of the device can be measured before and after the AuNPs/SWCNT dealt with growth solution. Applying a constant voltage between gold electrodes, it is easy to calculate the
Fig. 3. AFM images and height of the AuNPs/SWCNT before (a) and after (b) the AuNPs growing into a continuous nanowire. (c) Raman spectra of AuNPs/SWCNT before (blue curve) and after (red curve) AuNPs’ growth. (d) The conductance increase of the AuNPs/SWCNT device with the growth time under 250 mM glucose and 500 mM HAuCl4 solution at room temperature. (A colour version of this figure can be viewed online.)
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conductance between the gold microelectrodes. Before AuNPs growing, the conductance of the AuNPs/SWCNT device was about 250 nS. Then, AuNPs/SWCNT device was immersed into 250 mM glucose and 500 mM HAuCl4 solution (growth solution), and the conductance of which was measured every 3 min. Subtracting the conductance before the gold seeds grew from the obtained conductance every time, the conductance increment at the corresponding time point can be obtained. It can be seen from Fig. 3d that the conductance of the AuNPs/SWCNT device is constantly increasing with the growth time. It spends 15 min that the conductance increment reaches the top (about 650 nS) and no longer alters. Given that SWCNT may catalyze the reaction of glucose and AuCl 4 resulting in significant effect for the conductance between electrodes, a control experiment is needed to ascertain the effect of SWCNT. In the control experiment, the SWCNT device which was not modified with AuNPs, was fabricated and immersed in the growth solution for 15 min. Compared with the conductance increment of AuNPs/SWCNT device in Fig. S5, the conductance of SWCNT device hardly increases. Moreover, it shows from Fig. S6 that there are only little particles deposited on SWCNT after SWCNT dealt with growth solution. These results can indicate that it is only AuNPs instead of SWCNT that can tremendously catalyze the reaction between glucose and AuCl 4 , leading to the obvious conductance variation. Therefore, in the following experiments, the AuNPs/SWCNT device can be applied to the study of DNA hybridization detection for the growth time of 15 min. It was known that ss-DNA adsorbed on AuNPs could the block catalytic activity of AuNPs, resulting in the inhibition of the redox reaction between glucose and AuCl 4 [18]. But, the concentration of ss-DNA (the probe DNA in our detection system), which can absolutely inhibit the catalytic activity of AuNPs, is necessary to be known for the following DNA detection. To affirm optimum probe concentration, the AuNPs/SWCNT devices were dealt with the probe DNA solution of different concentrations separately and then immersed in the growth solution for 15 min. The result was shown in Fig. 4a. With the concentration of probe DNA increasing, the observed conductance gradually decreased and reached the equilibrium at 1 mM. It illustrates that the surface of AuNPs can be gradually wrapped with the increment of ss-DNA concentration. The ss-DNA of 1 mM concentration is adequate to perfectly adsorb on the AuNPs, leading to the absolute inhibition of AuNPs catalytic activity. Raman characterization result, which AuNPs/SWCNT was dealt with 1 mM ss-DNA solution, was shown in Fig. 4b. The G band peak at 1581.6 cm1 was corresponding to graphitic structure of
SWCNT. And the presence of ss-DNA adsorbed on AuNPs can be mainly judged by the rather stronger PO 2 signal, since the number of PO 2 is the same as the total number of all bases. According to the assignment of DNA principal peaks [24] listed in Table 1, it can be found from Fig. 4b that the band peaks at 785.6 cm1 and 1087.8 cm1 perfectly correspond to the skeleton stretching and symmetric stretching of PO 2 . The result of Raman characterization can further indicate that probe DNA can be well adsorbed on the surface of AuNPs. In control experiment, the AuNPs/device was dealt with 1 mM ds-DNA solution and then immersed in the growth solution for 15 min to demonstrate whether the potential DNA nonspecific adsorption on SWCNT will affect device performance. And it can be found from Fig. S7 that there’s no significant difference of conductance increment for the AuNPs/SWCNT device whether dealt with 1 mM ds-DNA under growth solution for 15 min. The result further reveals that ds-DNA will not adsorb on AuNPs and also demonstrates that the potential DNA nonspecific adsorption on SWCNT will not affect device performance. Therefore, after dealt with 1 mM probe solution to absolutely inhibit catalytic activity of AuNPs, AuNPs/SWCNT device can be taken for the detection of various samples. In the DNA detection experiment, the AuNPs/SWCNT devices were applied to detect various sample solutions (some of which contained target with different concentrations). And the detection process was as follows. The AuNPs/SWCNT devices after dealt with 1 mM probe solution, were first dealt with various samples to desorb the probe DNA from AuNPs, and subsequently dealt with the growth solution for 15 min. The result of detection was presented in Fig. 5. It can be observed that the conductance dynamically increases with the concentration of the target DNA increasing within the concentration ranging from 1 pM to 1 nM (samples 4 to 7). Fig. S8 shows the AFM images of the devices corresponding to target DNA of different concentrations (from low to high). And it
Table 1 Raman frequencies of typical vibrational modes of DNA. Raman bands (cm1)
assignments
675 723 739 776 786 1087
G, ring breathing A, ring breathing T, ring breathing C, ring breathing PO 2 , skeleton stretching PO 2 , symmetric stretching
Fig. 4. (a) Effect of the concentration of the probe DNA on conductance increment of the AuNPs/SWCNT device, under growth solution at room temperature for 15 min. In the concentration of 1 mM, the growth of AuNPs were restrained absolutely. (b) Raman spectra of AuNPs/SWCNT after dealt with 1 mM probe DNA solution. The strong broad band of 900e1000 cm1 belongs to the characteristic peak of SiOx/Si substrate. (A colour version of this figure can be viewed online.)
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Fig. 5. The conductance responses to various samples for the biosensing device. DNA concentrations for samples 3e8 (cyan bar graphs), 100 fM, 1pM, 10 pM, 100 pM, 1 nM, and 10 nM, respectively. Blank sample 1 without DNA (gray bar graph). Control sample with 1 nM complete mismatch DNA (yellow bar graph). No significant difference was found between samples 1e3. Error bars show the standard deviation of six samples. (A colour version of this figure can be viewed online.)
can be found that the nanogap between AuNPs is gradually diminishing with the target concentration increasing, which is consistent with the result of conductance increasing. These both reveal that the catalytic activity of AuNPs can gradually recover with the target concentration increasing. And the variation of conductance of the device was shown to increase as a function of increasing target concentration from 1 pM to 1 nM. According to the nonsignificant difference for sample 3 with 1 and distinct difference for sample 4 with 3, the concentration of 1 pM can be the detection limit of the device for target. In addition, control experiments in the absence of DNA or in the presence of 1 nM complete mismatch DNA led to negligible conductivity increment (Fig. 5, samples 1 and 2). Table 2 discusses the comparison of the electrical biosensors on DNA hybridization detection with our work. As shown in Table 2, our proposed electrical nanogap device demonstrates a low limit of detection and a well wide range that is comparable to the mentioned biosensors. This is due to the subtle design of detection strategy and the novel application of AuNTs/ SWCNT in nano-micro device for biological detections. In the specificity experiment (Fig. 6a), the biosensing device was challenged with single, triple, and quintuple mismatched target sequences (here at 1 nM). It can be known that 1-, 3- and 5mismatch target sequences could be distinguished separately for the device. But it remains a challenge to distinguish 1-mismatch target from perfect match target. In the experiment of interference immunity (Fig. 6b), we performed the detection for 1 nM perfect match target sequence in 10% fetal bovine serum. It can be known from part b of Fig. 6b that the biosensing device can distinguish target sample from no target sample in 10% fetal bovine serum. It reveals that the detection strategy of our biosensing device is still
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Fig. 6. (a) Conductance responses for perfect matched, 1-, 3- and 5- mismatched DNA. The concentration of all target DNA was 1 nM. (b) The biosensing device was tested with the target DNA in 10% fetal bovine serum. Error bars show the standard deviation of six samples.
feasible in some complex biological fluid. These results indicate that the biosensing device exhibits well specificity in buffer solution for the ability to discriminate triple and quintuple base pair mismatches and it is possible for the biosensing device to detect analytes in some complex biological fluid. 4. Conclusions It is the first attempt of applying AuNPs/SWCNT to fabricate nano-micro device for biosensing. Based on the innate character of tiny AuNPs arranged in SWCNT, we develop a novel strategy to fabricate nanogap device for DNA hybridization detection. The detection strategy is based on the target DNA mediating the AuNPs catalytic activity by desorbing the probe DNA from AuNPs. Subsequently, the variation of catalytic activity can affect the growth of AuNPs, resulting in conductance alteration between electrodes. The device can exhibit dynamic responses to various lower concentrations of target DNA ranging from 1 pM to 1 nM. Moreover, the biosensing device can discriminate triple and quintuple base pair mismatches in buffer solution with well performance in serum sample. Though, it remains the limitations that the biosensing device cannot well distinguish one-based mismatch DNA with perfect match DNA and the sensitivity of detection demands more improvement. However, we believe that these limitations can be well solved in our future work with some new ideas, such as adjusting the affinity between ss-DNA and AuNPs and further shortening the distance between electrodes. And DNA should not be the sole analyte which our biosensing device can detect. Aptamers, a sort of ss-DNA with special sequences, can be well combined with metal ions, small molecules and proteins. These potential analyte (metal ions etc.) may play the role of target to desorb corresponding aptamers from AuNPs resulting in the variation of AuNPs’ catalytic activity, which is matched with the
Table 2 Comparison of the different biosensors for DNA Hybridization Detection. Reference
Materials
Detection Technique
Detection Limit
Linear Range
[10] [7] [3] [6] This Work
AuNPs Polyaniline/MWCNT Carbon nano-onions Au electrode AuNPs/SWCNT
LSV CV and SWV Amperometry CV and DPV conductance responses
100 pM 490 pM 0.5 nM 3.8 nM 1 pM
100 pM - 1 mM 10 nMe50 nM 0e20 nM 2.5 nMe350 nM 1pMe1 nM
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detection mechanism of our biosensing device. Therefore, it is possible to detect these potential analyte as the aptamers are applied as probe for our biosensing device. Additionally, the biosensing device may be fabricated to multiple microelectrodes arrays device to simultaneously measure multiple molecular targets in the same solution. We expect that AuNPs/SWCNT will find more important and widespread applications in nano-micro device for biosensing.
[8]
[9] [10]
Declaration of competing interest [11]
The authors declare no competing financial interest. [12]
Acknowledgment We acknowledge funding from the National Natural Science Foundation of China (21505101, 51672193 and 51920105004), and Zhejiang Provincial Natural Science Foundation of China (LQ16B050003).
[13]
[14]
[15]
Appendix A. Supplementary data Supplementary data to this article can be found online at https://doi.org/10.1016/j.carbon.2019.10.017.
[16]
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