Label-Free Colorimetric Protein Assay and Logic Gates Design Based

Feb 21, 2014 - Department of Chemistry, East China Normal University, Shanghai ... using proteins as inputs, the “OR” and “INHIBIT” logic gate...
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Label-Free Colorimetric Protein Assay and Logic Gates Design Based on the Self-assembly of Hemin-Graphene Hybrid Nanosheet Bin Lin, Qianqian Sun, Kai Liu, Danqin Lu, Ying Fu, Zhiai Xu,* and Wen Zhang* Department of Chemistry, East China Normal University, Shanghai 200062, People’s Republic of China S Supporting Information *

ABSTRACT: Here we report a label-free colorimetric method for protein assay based on the intrinsic peroxidase-like catalytic activity of DNA-hemin-graphene (DNA-GH) composite. By using aptamers as protein recognition elements, protein-mediated aggregation of the DNA-GH composite leads to the decrease or increase of the colorimetric signal depending on the sandwich or competitive design strategy. Thrombin and PDGF-BB were chosen as model analytes and the detection limits (LOD) by this method were estimated to be 0.5 nM and 5 nM, respectively. Compared to traditional ELISA method for protein detection, this method possesses the advantages of high sensitivity, simplicity, and low cost. In addition, by designing different DNA-modified hemin-graphene (GH) constructs, using proteins as inputs, the “OR” and “INHIBIT” logic gates were built. This procedure does not require chemical modification on the aptamer probes or analytes and circumvents the limitation associated with the number of target binding sites. Given the attractive analytical characteristics and distinct advantages of DNA-GH composite, the universal approach can be widely applied for the detection of diverse proteins and for the design of versatile logic gates.

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induced by probe-target recognition.13−18 However, the modification steps such as immobilizing biomolecules onto the gold nanoparticles and separating the modified AuNPs from surplus aptamers should be elaborately controlled. These steps not only lead to complicated operation and relatively high cost of the experiments, but also could weaken the affinity between the target and the aptamer.12,19 Therefore, developing sensitive and label-free colorimetric aptameric assays to simplify the detection process would be important and attractive. On the other hand, the research on artificial enzyme mimetics has been pursued to avoid the limitations of natural enzymes. Among these, Fe3O4 magnetic nanoparticles,20,21 metal nanoparticles,22 Prussian blue nanoparticles,23 hemin-related DNAzymes,24−26 and hemin-graphene hybrids,27−29 have been reported to show peroxidase-like catalytic ability for biochemical assays since these artificial enzymes could effectively catalyze the oxidation of the substrate 3,3,5,5-tetramethylbenzidine (TMB) or 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS2−) in the presence of H2O2 to develop a blue or green color change, which was used as a transduction reporter. Most notably, the advantages of high catalytic activity, good stability, and easy synthesis make artificial enzyme mimetics suitable for a broad range of applications. The emerging research field of DNA logic gates, which is based on the application of DNA molecules for mimicking the logic operations, has offered a promising paradigm for future

INTRODUCTION The recognition and quantification of disease-marker proteins, especially those associated with cancers, are of particular significance in fundamental research and clinical applications.1 Nowadays, the most popular method for protein detection is enzyme-linked immunosorbent assay (ELISA) which involves an antibody and an enzyme.2 Although ELISA is a versatile and powerful tool providing quantification information, it still faces some challenges including stringent environmental requirements for maintaining activity, complicated labeling process, and high cost of production, due to the protein nature of antibody and enzyme.3 Compared with antibodies acting as recognition elements, aptamers can retain high binding affinity to their targets under a wide range of conditions4−6 while possessing significant advantages such as easy synthesis, design flexibility, and desirable stability.7 These superiorities make aptamers appear as promising alternatives to traditional antibodies in protein recognition, sensing, and profiling.8 However, compared with the well-established antibody technology, aptamer research is still in its developmental stage.7,9 To improve the performance of aptameric protein systems, researchers should overcome or alleviate effects originating from the low association constants of some aptamers to their ligands10 or chemical modification-induced loss of binding activity.11 Therefore, development of aptameric tools for applications still remains a considerable challenge. Among the various aptameric methods, colorimetric assay has attracted significant interest for its simplicity, low cost, and especially the macroscopically observable features.12−18 Many strategies take advantage of the absorbance changes of gold nanoparticle (AuNPs) on the basis of AuNPs aggregation © 2014 American Chemical Society

Received: December 23, 2013 Revised: February 11, 2014 Published: February 21, 2014 2144

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Figure 1. (A) UV−vis spectra of GO suspension, hemin solution, and GH suspension. (B) Cyclic voltammograms of bare GCE, GNs/GCE, and GH/GCE in 0.1 M PBS (pH = 7.4) saturated with N2 at a scan rate of 0.05 V/s. GNs: chemically reduced graphene oxide.

computing technology.30,31 Being different from the traditional biosensors, logic gate biosensors are smart, and able to intelligently analyze the relationship between different targets in complex samples according to the Boolean logic operations.32 To date, various DNA logic gates that transduce specific inputs to output signals have been devised by using the sequence-specific recognition property of DNA.33−46 Most of the logic gates reported to date employ DNA,33−37 or small molecules, such as metal ions,38−41 ATP,35,42 cysteine,43−45 or cocaine33,42,46 as their inputs, and fluorescent, electrochemical, colorimetric, or luminescent signals as their outputs. Few logic gates using protein as inputs have been established. To the best of our knowledge, the application of protein-as-inputs colorimetric logic gates has not been reported. In the present report, we designed a colorimetric method for protein assay based on protein-mediated aggregation of DNAhemin-graphene (DNA-GH) composite and the peroxidase-like catalytic reaction of hemin-graphene (GH). With the use of thrombin and platelet-derived growth factor (PDGF-BB) as proofof-principle analytes, this sensing platform exhibited good sensitivity and specificity toward targets. To broaden the scope of applications, a universal protein detection scheme was presented in the aid of a complementary sequence based on competitive binding. In addition, by designing different DNA-GH constructs, using thrombin and PDGF-BB as inputs, the “OR” and “INHIBIT” logic gates were built. This method does not need any complex chemical modification of DNA probe, and the target molecules can be simply detected by the naked eye or with UV−vis spectroscopy, which is observable, rapid, and low-cost. Moreover, this detection system which could be expanded easily to other targets by simply changing the aptamer sequence appears to be a universal sensing approach for the detection of target protein.

DNA 2: 5′-GAA AAG AGG AAA GAG TAT ATG GTT GGT GTG GTT GG-3′ DNA 3: 5′-GAA AAG AGG AAA GAG TAT ATA GTC ACC CCA ACC-3′ DNA 4: 5′-GAA AAG AGG AAA GAG TAT ATC AGG CTA CGG CAC GTA AGA CAT CAC CAT GAT CCT G-3′ Water used through all experiments was purified with the Millipore system. Instruments and Measurements. Scanning kinetics were carried out by monitoring the absorbance change at 652 nm on a Cary 60 UV−vis spectrophotometer (Agilent Technologies, USA). Electrochemical measurements were carried out on CHI electrochemical workstation (ChenHua Instruments Co., Shanghai, China). A three-electrode system was used in the experiment with bare or modified glassy carbon electrode (3 mm in diameter) as the working electrode, respectively. An Ag/AgCl electrode (Saturated KCl) and a Pt wire electrode were used as reference and counter-electrode, respectively. AFM images were taken using a multimode 8 atomic force microscope (Bruker Corporation, Germany). Size distributions were measured by dynamic light scattering (DLS) using Nanosizer ZS equipped with a 4 mW He−Ne laser at wavelength of 633 nm (Malvern Instruments, Worcestershire, U.K.). Synthesis of Hemin-Functionalized Graphene Nanosheets (GH). GH were synthesized by following the procedure as previously described. 27−29 Briefly, 20.0 mL of the homogeneous graphene oxide dispersion (0.5 mg/mL) was mixed with 20.0 mL of 0.5 mg/mL hemin aqueous solution and 200.0 μL of ammonia solution, followed by the addition of 30 μL of hydrazine solution. After being vigorously shaken or stirred for a few minutes, the vial was put in a water bath (60 °C) for 3.5 h. The stable black dispersion was obtained. The solution was centrifuged at 13 000 rpm for 30 min to remove free hemin, and the precipitated conjugates were then redispersed in water and these processes were repeated two times. Finally, GH was redispersed in Tris-HCl (10 mM TrisHCl, pH = 8.0) for further use. Synthesis of DNA-GH Conjugates. According to the literature,27,29 the self-assembly of GH and DNA was easily obtained through the π−π stacking interactions. Generally, 500 μL GH and DNA (4 μM) were mixed by sonicating for 10 min and then incubated at room temperature for 24 h, and the concentration of NaCl was slowly increased to 10 mM during the incubation. The pure DNA-GH conjugates were obtained by centrifuging at 13 000 rpm for 30 min. Target Detection. In sandwich assay, GH-DNA1 and GH-DNA2 were mixed together in 100 μL Tris buffer, then adding different concentration of target solutions respectively.

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EXPERIMENTAL SECTION Reagents. Graphene oxide was purchased from J. C. Nano Co. (Nanjing, China). Hemin was purchased from Sinopharm Chemical Reagent Co. (Shanghai, China). 3,3′,5,5′-Tetramethylbenzidine (TMB) was obtained from j&k Chemical Reagent Co. (Pforzheim, Germany). Human thrombin was from Sigma (St. Louis, MO, USA). Recombinant Human PDGF-BB was bought from Peprotech (Rocky Hill, NJ, USA). All other reagents were of analytical reagent grade and were obtained from Sinopharm Chemical Reagent Co. (Shanghai, China). DNA oligonucleotides were obtained from Sangon Biotechnology Co. (Shanghai, China). The DNA sequences used in this study were as follows: DNA 1: 5′-GAA AAG AGG AAA GAG TAT ATA GTC CGT GGT AGG GCA GGT TGG GGT GACT-3′ 2145

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localized at opposite sides of thrombin. In the absence of thrombin, DNA-GH hybrids remain stable without distinct aggregation, because DNA1 and DNA2 are not capable of hybridization. However, when adding thrombin, aptamers specifically combine with thrombin to form a sandwich structure with the 20-base fragment still adsorbing on grapheme, which leads to the cross-linking aggregation of DNA-GH. As a result, after centrifugation, the absorbance signal of supernatant is expected to be lower than that without thrombin and the degree of aggregation depends on thrombin concentration. We then investigated the color signal produced by GH-catalyzed TMB oxidation in the absence and presence of thrombin (Figure 2A). The DNA-GH exhibit high catalytic ability toward TMB oxidation as monitored by the absorbance change at 652 nm. As thrombin concentration increases, the absorbance at 652 nm correspondingly decreases in their intensities. It resulted from the different degrees of aggregation directly related to thrombin concentration. In order to improve the sensitivity of protein assay, the volume of GH was optimized in advance (Figure S1A). As can be seen in Figure 2B, a good linearity between the absorption intensity and the concentrations of thrombin from 0.5 nM to 10 nM is obtained. The regression equation is A = −0.0112C + 0.3528 with a correlation coefficient of 0.99868, where A and C represent the absorption intensity and thrombin concentration, respectively. The observed detection limit (LOD) is estimated to be 0.5 nM, which compares well with the value obtained from colorimetric analytical techniques based on gold nanoparticle.15−18 A control experiment was carried out to test the selectivity using 100 nM bovine serum albumin (BSA). As shown in Figure 2C and D, BSA exhibits a much deeper color signal than the same concentration of thrombin, which can be discriminated with the naked eye, indicating that our assay possesses a great selectivity. The results suggested that specific recognitioninduced aggregation should be responsible for the reduction of color signal. AFM was used to study the typical morphology of monolayer DNA-GH and the aggregates. Figure 3A shows the AFM image of monolayer DNA-GH nanosheets, and the thickness is around 2 nm (Figure 3C). As observed in AFM images of Figure 3B, after adding 20 nM thrombin to DNA-GH hybrids, large aggregates could be obtained owing to the specific combination between aptamers and thrombin with the formation of a sandwich structure. The height of section extracted from the AFM image indicates that the DNA-GH aggregates increase to 7− 18.5 nm in apparent thickness (Figure 3B,D). It is obvious that such aggregate height data are consistent with the thickness of multilayer of DNA-GH nanosheets. Besides, it can be clearly observed that the diameter of DNA-GH hybrids increases upon addition of 20 nM thrombin. To demonstrate the generality of this strategy, PDGF-BB was also employed to demonstrate the sandwich mechanism which was based on the ability of PDGF to bind with aptamers at its two available binding sites. The DNA sequence adsorbed on GH was changed to DNA4, which was composed of a 20-base tail and PDGF-BB aptamer. In the presence of PDGF-BB, the aptamer sequence in DNA4 folds into a hairpin structure,47 coupling to PDGF-BB, and GH aggregation will occur. By the same measuring method as thrombin, the relationship between the absorbance at 652 nm and the PDGF-BB concentration was constructed in Figure 4A. A linear relationship is observed in the concentration range from 0 to 20 nM with a LOD around

The samples were incubated for 12 h at room temperature with gentle shaking. The samples were centrifuged at 3000 rpm for 10 min, and supernatants were collected. Scanning kinetic measurements were carried out with 10 μL supernatants in 500 μL 25 mM phosphate buffer solution (pH = 4.0) in the presence of 10 mM H2O2, using 0.1 mM TMB as the substrate. Error bars in all figures indicate the relative standard deviation of three repeated experiments. In competitive assay, 10 μL GH-DNA1 and different concentration target solutions were first incubated in Tris buffer for 12 h at room temperature. Ten microliters GH-DNA3 was added in the mixture, and then the samples were shaken slowly for 12 h. The samples were centrifuged at 4000 rpm for 10 min, and the supernatants were collected. The test process was the same as the method mentioned above.

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RESULTS AND DISCUSSION Initially, the hemin-graphene hybrid nanosheets (GH) were synthesized by a simple wet-chemical strategy according to the previously established method.27−29 The as-prepared GH has intrinsic peroxidase-like activity which can catalyze the oxidization of 3,3,5,5-tetramethylbenzidine (TMB) to produce a blue color reaction. The formation of GH was characterized by UV−vis spectra and electrochemistry (Figure 1A and B). The GH exhibit two characteristic absorption peaks at 266 and 416 nm, which respectively correspond to reduced graphene oxide (GO) and the Soret band of hemin with a large bathochromic shift, clearly confirming that hemin molecules were attached to graphene nanosheets (GNs) successfully through π−π interactions between GO and hemin. In addition, compared with GNs/GCE, a pair of well-defined redox peaks is obviously observed at the potential range of −0.4 to −0.5 V when the GH were modified on the electrode surface, indicating that hemin-functionalized graphene nanosheets were obtained. We first designed a colorimetric assay for thrombin detection using sandwich aptamer recognition mechanism (Scheme 1). Scheme 1. Schematic Representation of Colorimetric Assay for Protein Detection Using Sandwich Aptamer Recognition Mechanism

Taking advantage of π−π stacking and hydrophobic interactions, GH still possess strong affinities to single-stranded DNA. DNA1 contains a 20-base tail and a 29-base thrombin aptamer sequence, and DNA2 has the same 20-base tail and a 15-base aptamer sequence corresponding to the different binding sites of thrombin. These two binding sites are spatially 2146

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Figure 2. (A) Time-dependent absorbance changes upon analyzing different concentrations of thrombin (top to down: 0−250 nM) in 25 mM PBS (pH 4.0) solution containing 0.1 mM TMB and 10 mM H2O2. (B) Dependence of absorbance at 652 nm on thrombin concentration. Inset shows a linear calibration curve from 0 to 10 nM. (C) Time-dependent absorbance changes at 652 nm of the supernatant solution after reaction with 100 nM BSA, 100 nM thrombin, PBS. (D) The absorbance ratio A0/A histograms, where A0 and A are the absorbance in the absence and presence of the proteins. Inset shows the typical photographs of specificity experiments with the colorimetric method developed using GH, (a) 100 nM thrombin, (b) 100 nM BSA, (c) PBS.

Figure 3. AFM images and height profiles of DNA-GH complex (A, C), DNA-GH aggregate formed by DNA1-GH and DNA2-GH mixing with 20 nM thrombin (B, D).

as outputs. As shown in Figure 5A, in the presence of either thrombin or PDGF-BB, or both inputs of thrombin and PDGF-BB, cross-linked aggregation of DNA-GH will occur respectively, ascribing to the formation of sandwich structure which results from aptamers specifically combining with corresponding protein toward different binding sites, leading to the reduction of colorimetric absorbance of centrifugal

5 nM (Figure 4B). Therefore, the GH-based colorimetric sensor is of sufficient sensitivity for protein detection, which has great potential to be a quantitative detection tool for diverse application. By means of designing two aptamer-modified GH conjugates, DNA1/DNA4/GH and DNA2/DNA4/GH, an “OR” logic gate has been successfully constructed by employing thrombin and PDGF-BB as inputs and the change in colorimetric absorbance 2147

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Figure 4. (A) Time-dependent absorbance changes in the presence of different amounts of PDGF-BB ranging from 0 to 200 nM in 25 mM PBS (pH 4.0) solution containing 0.1 mM TMB and 10 mM H2O2. (B) Dependence of absorbance at 652 nm on PDGF-BB concentration. Inset shows a linear calibration curve from 0 to 20 nM.

Figure 5. (A) Schematic illustration of the “OR” logic-gate. (B) Truth table for this two-input logic gate. (C) Absorbance changes of the “OR” logic gate system in the form of a bar presentation. A0 is the absorbance of the system without any input, and A corresponds to the resulting absorbance of the system after adding the respective inputs.

supernatant (Figure S2). The aggregation of GH was also confirmed by dynamic light scattering (DLS) experiment (Figure 6). The hydrodynamic diameter of DNA-GH hybrids increases from 192 to 335.5 or 1869 nm upon the addition of 50 nM PDGF-BB or 20 nM thrombin, indicating that the large aggregates of GH should be induced by either thrombin or PDGF-BB. Moreover, in the presence of both thrombin and PDGF-BB, the hydrodynamic diameter of DNA-GH hybrids further increases to 2003 nm, resulting from the combined effects of two kinds of proteins. Figure 5C summarizes the changes of the absorbance of the system subjected to the different inputs in the form of a bar configuration. By defining a high absorbance change (A0 − A) as an output “1”, whereas no absorbance changes corresponds to an output “0”, Figure 5B provides the derived truth table. Evidently, the system operates as an “OR” logic gate. The strategy of sandwich protein assay is limited to proteins which have two binding sites toward their aptamer sequences. In order to expand the scope of applications, we sought to develop a universal sensing platform based on competitive strategy for label-free colorimetric detection of a broad range of proteins. The strategy chiefly relies on the competition for binding the aptamer-GH between target protein and the complementary single-stranded DNA (DNA3) (Scheme 2). The signal of centrifugal supernatant increases linearly in response to concentration changes of protein, because the formation of the target/aptamer complex inhibits the hybrid-

ization of the DNA3 with the aptamer probe that can initiate the aggregation of DNA-GH. Significantly, the competitive mechanism sensor does not require the ability to bind aptamer at different sites of protein, and this strategy gives a turn-on signal response. Therefore, this versatility allows the technology to be widely applied to detect many protein targets. Thrombin was used as proof-of-principle analyte to demonstrate the general applicability of the strategy. Figure 7A depicts the timedependent absorbance changes upon analyzing different concentrations of thrombin under the optimized conditions. Obviously, without the disturbance of target protein, more GH aggregates resulting from DNA hybridization will occur. The absorbance values increase as higher concentrations of thrombin were added, which is consistent with the fact that the lower aggregation was generated by thrombin-assisted hindering the formation of aptamer/DNA duplex. A linear correlation is obtained in the concentration ranging from 0 nM to 20 nM with a limit of detection (LOD) for this system of 2.5 nM (Figure 7B). The regression equation is A = 0.002C + 0.04415, where A and C denote the absorbance intensity and target concentration, respectively. The corresponding correlation coefficient of the calibration curve is 0.99605. In the specificity analysis of competitive assay for thrombin detection, it is clear that the specific target thrombin leads to an increase in the absorbance value, while BSA of the same concentration does not cause obvious variation of absorption intensity, easily distinguished by the naked eye, demonstrating 2148

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Scheme 2. Schematic Representation of Colorimetric Assay for Protein Detection Based on Competitive Binding Mechanism

promising platform for the analyses of a wide range of protein analytes. To further confirm the usefulness of DNA-GH in the construction of protein logic gates, an “INHIBIT” logic gate was fabricated based on protein-mediated aggregation. As shown in Figure 8A, the construction of the “INHIBIT” system is realized by replacing the DNA2 sequences in the “OR” logic gate design with DNA3. Figure S3 showed the absorbance changes of the system. It was found that only introduction of input thrombin led to the high absorbance owing to the inhibition of the hybridization of DNA1 with DNA3, whereas the other three situations that initiate aggregation to varying degrees lead to the low absorbance (Figure 8C). These results demonstrate that the system indeed performs the

Figure 6. Size distribution (in diameter, nm) of DNA-GH assay solutions in the absence and presence of 20 nM thrombin or 50 nM PDGF-BB determined by DLS experiment. (A) GH: 192.5 nm, PDI 0.222; (B) PDGF-BB/GH: 335.5 nm PDI 0.587; (C) Thrombin/GH: 1869 nm, PDI 0.335; (D) Thrombin/PDGF-BB/GH: 2003 nm, PDI 0.389.

that the assay exhibited high specificity toward thrombin (Figure 7C,D). Given the excellent analytical properties and distinct advantages, the proposed strategy performed as a

Figure 7. (A) Time-dependent absorbance changes upon analyzing different concentrations of thrombin (bottom to up: 0−100 nM) based on competitive mechanism in 25 mM PBS (pH = 4.0) solution containing 0.1 mM TMB and 10 mM H2O2. (B) Dependence of absorbance at 652 nm on thrombin concentration. Inset shows a calibration curve of absorption intensity changes at 652 nm versus the concentration of thrombin. Error bars indicate the relative standard deviation of three repeated experiments. (C)Time-dependent absorbance changes upon incubating with PBS, 100 nM BSA, and 100 nM thrombin in 25 mM PBS (pH = 4.0) solution containing 0.1 mM TMB and 10 mM H2O2. (D) The absorbance ratio A/A0 histograms, where A0 represents the absorbance of sample with PBS and A stands for the absorbance of samples with proteins after an interval of 10 min. Error bars indicated the relative standard deviation of three repeated experiments. Inset shows the typical color changes with incubation by (a) PBS, (b) 100 nM BSA, (c) 100 nM thrombin. 2149

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Figure 8. (A) Schematic illustration of the “INHIBIT” logic gate. (B) Truth table for this two-input logic gate. (C) Absorbance changes of the “INHIBIT” logic gate system in the form of a bar presentation. A0 is the absorbance of the system without any input, and A corresponds to the resulting absorbance of the system after adding the respective inputs.

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“INHIBIT” gate operation with a characteristic truth table (Figure 8B).

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CONCLUSION

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ASSOCIATED CONTENT

In summary, we have developed a universal, label-free, and sensitive colorimetric sensing system for protein detection by taking advantage of protein-mediated aggregation of DNAhemin-graphene composite and peroxidase-like catalytic activity of the hemin-graphene. Under the optimum conditions, this procedure displayed excellent analytical characteristics (low detection limit, and high specificity). Also, this simple and versatile approach does not require any chemical modification on the aptamer probe or analytes, and circumvents the limitation associated with the number of target binding sites. Above all, this detection system appears to be a universal approach which can be widely applied for the detection of diverse proteins. Moreover, by rational design, diverse logic gates using proteins as inputs can be successfully designed.

S Supporting Information *

Optimization on the volume of GH used for incubation, and time-dependent absorbance changes in the absence or presence of proteins in “OR” Logic gate. This material is available free of charge via the Internet at http://pubs.acs.org.

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REFERENCES

(1) Hartwell, L.; Mankoff, D.; Paulovich, A.; Ramsey, S.; Swisher, E. Cancer Biomarkers: A Systems Approach. Nat. Biotechnol. 2006, 24, 905−908. (2) Zhu, H.; Klemic, J. F.; Chang, S.; Bertone, P.; Casamayor, A.; Klemic, K. G.; Smith, D.; Gerstein, M.; Reed, M. A.; Snyder, M. Analysis of Yeast Protein Kinases Using Protein Chips. Nat. Genet. 2000, 26, 283−289. (3) Schweitzer, B.; Wiltshire, S.; Lambert, J.; O’ Malley, S.; Kukanskis, K.; Zhu, Z.; Kingsmore, S. F.; Lizardi, P. M.; Ward, D. C. Immunoassays with Rolling Circle DNA Amplification: A Versatile Platform for Ultrasensitive Antigen Detection. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 10113−10119. (4) Liu, L.; Lu, Y. Fast Colorimetric Sensing of Adenosine and Cocaine Based on a General Sensor Design Involving Aptamers and Nanoparticles. Angew. Chem. 2006, 118, 96−100. (5) Farokhzad, O. C.; Cheng, J.; Teply, B. A.; Sherifi, I.; Jon, S.; Kantoff, P. W.; Richie, J. P.; Langer, R. Targeted NanoparticleAptamer Bioconjugates for Cancer Chemotherapy in Vivo. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 6315−6320. (6) Potyrailo, R. A.; Conrad, R. C.; Ellington, A. D.; Hieftje, G. M. Adapting Selected Nucleic Acid Ligands (Aptamers) to Biosensors. Anal. Chem. 1998, 70, 3419−3425. (7) Song, S. P.; Wang, L. H.; Li, J.; Zhao, J.; Fan, C. H. AptamerBased Biosensors. TRAC-Trends Anal. Chem. 2008, 27, 108−117. (8) Baldrich, E.; Restrepo, A.; O’ Sullivan, C. K. Aptasensor Development: Elucidation of Critical Parameters for Optimal Aptamer Performance. Anal. Chem. 2004, 76, 7053−7063. (9) Wang, X. L.; Li, F.; Su, Y. H.; Sun, X.; Li, X. B.; Schluesener, H. J.; Tang, F.; Xu, S. Q. Ultrasensitive Detection of Protein Using An Aptamer-based Exonuclease Protection Assay. Anal. Chem. 2004, 76, 5605−5610. (10) Shlyahovsky, B.; Li, D.; Weizmann, Y.; Nowarski, R.; Kotler, M.; Willner, I. Spotlighting of Cocaine by an Autonomous Aptamer-Based Machine. J. Am. Chem. Soc. 2007, 129, 3814−3815. (11) Hagihara, M.; Fukuda, M.; Hasegawa, T.; Morii, T. A Modular Strategy for Tailoring Fluorescent Biosensors from Ribonucleopeptide Complexes. J. Am. Chem. Soc. 2006, 128, 12932−12940. (12) Huang, Y.; Chen, J.; Zhao, S. L.; Shi, M.; Chen, Z. F.; Liang, H. Label-Free Colorimetric Aptasensor Based on Nicking Enzyme Assisted Signal Amplification and DNAzyme Amplification for Highly Sensitive Detection of Protein. Anal. Chem. 2013, 85, 4423−4430. (13) Li, J.; Fu, H. E.; Wu, L. J.; Zheng, A. X.; Chen, G. N.; Yang, H. H. General Colorimetric Detection of Proteins and Small Molecules Based on Cyclic Enzymatic Signal Amplification and Hairpin Aptamer Probe. Anal. Chem. 2012, 84, 5309−5315.

AUTHOR INFORMATION

Corresponding Authors

*Phone: +86-21-62232801. E-mail: [email protected]. *E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We greatly appreciate the financial support of the National Natural Science Foundation of China (21075041, 21305047, 21375040), Science and Technology Commission of Shanghai Municipality (No. 12ZR1408600), and The Research Fund for the Doctoral Program of Higher Education (No. 20110076110003). 2150

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(14) Zhao, W.; Chiuman, W.; Lam, J. C. F.; McManus, S. A.; Chen, W.; Cui, Y.; Pelton, R.; Brook, M. A.; Li, Y. DNA Aptamer Folding on Gold Nanoparticles: From Colloid Chemistry to Biosensors. J. Am. Chem. Soc. 2008, 130, 3610−3618. (15) Wei, H.; Li, B. L.; Li, J.; Wang, E. K.; Dong, S. J. Simple and Sensitive Aptamer-based Colorimetric Sensing of Protein Using Unmodified Gold Nanoparticle Probes. Chem. Commun. 2007, 36, 3735−3737. (16) Ou, L. J.; Jin, P. Y.; Chu, X.; Jiang, J. H.; Yu, R. Q. Sensitive and Visual Detection of Sequence-Specific DNA-Binding Protein via A Gold Nanoparticle-Based Colorimetric Biosensor. Anal. Chem. 2010, 82, 6015−6024. (17) Huang, C. C.; Huang, Y. F.; Cao, Z. H.; Tan, W. H.; Chang, H. T. Aptamer-Modified Gold Nanoparticles for Colorimetric Determination of Platelet-Derived Growth Factors and Their Receptors. Anal. Chem. 2005, 77, 5735−5741. (18) Yi, Y. H.; Huang., Y.; Zhu, G. B.; Lin, F. B.; Zhang, L. L.; Li, H. T.; Zhang, Y. Y.; Yao, S. Z. A Colorimetric and Fluorescence Sensing Platform for Two Analytes in Homogenous Solution Based on Aptamer-Modified Gold Nanoparticles. Anal. Methods 2013, 5, 2477− 2484. (19) Jiang, Y. X.; Fang, X. H.; Bai, C. L. Signaling Aptamer/Protein Binding by A Molecular Light Switch Complex. Anal. Chem. 2004, 76, 5230−5235. (20) Gao, L.; Zhuang, J.; Nie, L.; et al. Intrinsic Peroxidase-Like Activity of Ferromagnetic Nanoparticles. Nat. Nanotechnol. 2007, 2, 577−583. (21) Kim, M. I.; Shim, J.; Li, T.; Lee, J.; Park, H. G. Fabrication of Nanoporous Nanocomposites Entrapping Fe3O4 Magnetic Nanoparticles and Oxidases for Colorimetric Biosensing. Chem.Eur. J. 2011, 17, 10700−10707. (22) He, W. W.; Wu, X. C.; Liu, J. B.; et al. Design of AgM Bimetallic Alloy Nanostructures (M = Au, Pd, Pt) with Tunable Morphology and Peroxidase-like Activity. Chem. Mater. 2010, 22, 2988−2994. (23) Li, J.; Qiu, J. D.; Xu, J. J.; Chen, H. Y.; Xia, X. H. The Synergistic Effect of Prussian-Blue-Grafted Carbon Nanotube/Poly(4-vinylpyridine) Composites for Amperometric Sensing. Adv. Funct. Mater. 2007, 17, 1574−1580. (24) Tang, L. H.; Liu, Y.; Ali, M. M.; Kang, D. K.; Zhao, W. A.; Li, J. H. Colorimetric and Ultrasensitive Bioassay Based on A DualAmplification System Using Aptamer and DNAzyme. Anal. Chem. 2012, 84, 4711−4717. (25) Bi, S.; Li, L.; Zhang, S. S. Triggered Polycatenated DNA Scaffolds for DNA Sensors and Aptasensors by A Combination of Rolling Circle Amplification and DNAzyme Amplification. Anal. Chem. 2010, 82, 9447−9545. (26) Li, T.; Wang, E.; Dong, S. Multifunctional G-Quadruplex Aptamers and Their Application to Protein Detection. Chem.Eur. J. 2009, 15, 1036−1042. (27) Guo, Y. J.; Deng, L.; Li, J.; Guo, S. J.; Wang, E. K.; Dong, S. J. Hemin-Graphene Hybrid Nanosheets with Intrinsic Peroxidase-like Activity for Label-free Colorimetric Detection of Single-Nucleotide Polymorphism. ACS Nano 2011, 5, 1282−1290. (28) Guo, Y. J.; Li, J.; Guo, S. J. Hemin Functionalized Graphene Nanosheets-based Dual Biosensor Platforms for Hydrogen Peroxide and Glucose. Sens. Actuators, B: Chem. 2011, 160, 295−300. (29) Tao, Y.; Lin, Y. H.; Ren, J. S.; Qu, X. G. Self-Assembled, Functionalized Graphene and DNA as A Universal Platform for Colorimetric Assays. Biomaterials 2013, 34, 4810−4817. (30) Benenson, Y.; Gil, B.; Uri Ben-Dor, R. A.; Shapiro, E. An Autonomous Molecular Computer for Logical Control of Gene Expression. Nature 2004, 429, 423−429. (31) Seelig, G.; Soloveichik, D.; Zhang, D. Y.; Winfree, E. EnzymeFree Nucleic Acid Logic Circuits. Science 2006, 314, 1585−1588. (32) Wang, J.; Katz, E. Digital Biosensors with Built-in Logic for Biomedical Applications-Biosensors Based on A Biocomputing Concept. Anal. Bioanal. Chem. 2010, 398, 1591−1603. (33) Xia, F.; Zuo, X. L.; Yang, R. Q.; White, R. J.; Xiao, Y.; Kang, D.; Gong, X.; Lubin, A. A.; Valle’e-Be’lisle, A.; Yuen, J. D.; Hsu, B. Y. B.;

Plaxco, K. W. Label-Free, Dual-Analyte Electrochemical Biosensors: A New Class of Molecular-Electronic Logic Gates. J. Am. Chem. Soc. 2010, 132, 8557−8559. (34) Liu, X. Q.; Aizen, R.; Freeman, R.; Yehezkeli, O.; Willner, I. Multiplexed Aptasensors and Amplified DNA Sensors Using Functionalized Graphene Oxide: Application for Logic Gate Operations. ACS Nano 2012, 6, 3553−3563. (35) Zhu, J. B.; Zhang, L. B.; Dong, S. J.; Wang, E. K. Four-Way Junction-Driven DNA Strand Displacement and Its Application in Building Majority Logic Circuit. ACS Nano 2013, 7, 10211−10217. (36) Huang, Z. Z.; Tao, Y.; Pu, F.; Ren, J. S.; Qu, X. G. Versatile Logic Devices Based on Programmable DNA-Regulated SilverNanocluster Signal Transducers. Chem.Eur. J. 2012, 18, 6663−6669. (37) Xiang, Y.; Qian, X.; Chen, Y.; Zhang, Y.; Chai, Y.; Yuan, R. A Reagentless and Disposable Electronic Genosensor: from Multiplexed Analysis to Molecular Logic Gates. Chem. Commun. 2011, 47, 2080− 2082. (38) Zhang, L.; Wang, Z. X.; Liang, R. P.; Qiu, J. D. Easy Design of Colorimetric Logic Gates Based on Nonnatural Base Pairing and Controlled Assembly of Gold Nanoparticles. Langmuir 2013, 29, 8929−8935. (39) Zhang, Y. M.; Zhang, L.; Liang, R. P.; Qiu, J. D. DNA Electronic Logic Gates Based on Metal-Ion-Dependent Induction of Oligonucleotide Structural Motifs. Chem.Eur. J. 2013, 19, 6961−6965. (40) Kanayama, N.; Takarada, T.; Fujita, M.; Maeda, M. DNA Terminal Breathing Regulated by Metal Ions for Colloidal Logic Gates. Chem.Eur. J. 2013, 19, 10794−10798. (41) Zhang, L.; Zhang, Y. M.; Liang, R. P.; Qiu, J. D. Colorimetric Logic Gates Based on Ion-Dependent DNAzymes. J. Phys. Chem. C 2013, 117, 12352−12357. (42) Xu, X.; Zhang, J.; Yang, F.; Yang, X. Colorimetric Logic gates for Small Molecules Using Split/Integrated Aptamers and Unmodified Gold Nanoparticles. Chem. Commun. 2011, 47, 9435−9437. (43) Xie, W. Y.; Huang, W. T.; Li, N. B.; Luo, H. Q. Design of A Dual-Output Fluorescent DNA Logic Gate and Detection of Silver Ions and Cysteine Based on Graphene Oxide. Chem. Commun. 2012, 48, 82−84. (44) Lin, Y.; Tao, Y.; Pu, F.; Ren, J.; Qu, X. Combination of Graphene Oxide and Thiol-Activated DNA Metallization for Sensitive Fluorescence Turn-On Detection of Cysteine and Their Use for Logic Gate Operations. Adv. Funct. Mater. 2011, 21, 4565−4572. (45) Zhu, X.; Xu, H.; Gao, X.; Li, X.; Liu, Q.; Lin, Z.; Qiu, B.; Chen, G. Design of A DNA Electronic Logic Gate (Inhibit Gate) with An Assaying Application for Ag+ and Cysteine. Chem. Commun. 2011, 47, 9080−9082. (46) Shlyahovsky, B.; Li, Y.; Lioubashevski, O.; Elbaz, J.; Willner, I. Logic Gates and Antisense DNA Devices Operating on A Translator Nucleic Acid Scaffold. ACS Nano 2009, 3, 1831−1843. (47) Green, L. S.; Jellinek, D.; Jenison, R.; Ö stman, A.; Heldin, C. H.; Janjic, N. Inhibitory DNA Ligands to Platelet-Derived Growth Factor B-Chain. Biochemistry 1996, 35, 14413−14424.

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dx.doi.org/10.1021/la4048769 | Langmuir 2014, 30, 2144−2151