Fabrication of Honeycomb Films Based on Aptamer and Binding

Article pubs.acs.org/JPCC

Fabrication of Honeycomb Films Based on Aptamer and Binding Behavior Studies with Fluorophore-Labeled Complementary Base Sequences Dawei Fan,† Xiulong Xia,† Hongmin Ma, Yanfang Zhao, Guobao Li, Yan Li, Picheng Gao, Bin Du, and Qin Wei* Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong (University of Jinan), School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China ABSTRACT: A novel honeycomb film was successfully fabricated by self-assembly of polystyrene (PS)/polyethylene glycol (PEG)/nucleic acid aptamer with the assistance of dioctyl sodium sulfosuccinate (AOT) using the breath figure method. The nucleic acid aptamer embedded in the composite film remained bioactive and the film presented excellent fluorescent behaviors after binding with fluorophore-labeled complementary base sequences. The distribution of aptamer strands in the composite film was inferred from the fluorescence images and fluorescence spectra. The 3′ end and 5′ end of aptamer strands changed from being embedded to stretching out in the single pore of the composite film. The corresponding fluorescence images shifted from fluorescent spots to semicircular and annular fluorescent structures. This strategy can improve applications of honeycomb films in biosensors and microreactors.

boronic acid pendants.24 They also hybridized enzymes into breath figure arrays to obtain honeycomb-patterned porous biocatalytic films with high activity.25 Fish testes DNA molecules were successfully assembled in honeycomb films in the form of DNA−surfactant complexes.26 Compared with nucleic acids originating from biological sources which are optimized with respect to multiple aspects of their cellular functions, aptamers are artificially synthetic nucleic acid sequences without trading specificity in ligand binding for additional functions.2 In our previous study, we reported honeycomb-patterned fluorescent films fabricated by self-assembly of dioctyl sodium sulfosuccinate (AOT) surfactant-assisted porphyrin/polymer composites.27 In this study, aptamers were introduced in a polystyrene/polyethylene glycol (PS/PEG) polymer blend system with the assistance of AOT to form a novel bioactive film for the first time. The structure of the composite porous films can be confirmed by the change in fluorescence images of the films before and after binding between aptamers (S-Apt) and fluorophore 6-carboxyfluorescein (FAM) labeled strands (oligonucleotide sequences are shown in Table 1). The complementary binding reaction between fluorophore-labeled strands and S-Apt occurs based on the principle of complementary base pairing.

1. INTRODUCTION Aptamers are DNA or RNA oligonucleotides chemically synthesized via an in vitro selection method termed SELEX (systematic evolution of ligands by exponential enrichment), which optimize the nucleic acids for high-affinity binding to given targets.1 The recognition capability of aptamers to targets depends mainly on a variety of key molecular interactions, including specific hydrogen bonding, precise stacking of flat moieties, molecular shape complementarity, etc.2 Aptamers as synthetic nucleic acid molecules have many advantages such as stable secondary structure, high specificity and affinity, ease of production and storage, great reproducibility, and versatility for different applications. To date, aptamers have been extensively researched in chemistry, biology, nanomaterials, analytical sciences, physics, and mathematics. Especially in the field of analytical sciences, aptamers as a recognition module have made special contributions in antigen detection,3,4 tumor marker detection,5−7 heavy metal ion detection,8 protein in blood detection,9 cell imaging,10−14 small molecule detection,15,16 and so forth. Since the successful preparation of ordered honeycombpatterned films by the breath figure method in 1994, there has been great progress in the technology and theory of porous film fabrication.17−21 The structure and pore size of the porous films can be controlled by humidity, temperature, solvent, and filmforming material. Honeycomb film materials have shown many excellent properties in promising applications.19,20 Protein breath figure arrays were prepared by selectively grafting protein recognition moieties on the surface of the pores.22,23 Wan et al. produced glucose-sensing films based on phenyl© 2014 American Chemical Society

Received: August 2, 2014 Revised: October 2, 2014 Published: November 6, 2014 27366

dx.doi.org/10.1021/jp507798j | J. Phys. Chem. C 2014, 118, 27366−27371

The Journal of Physical Chemistry C

Article

Table 1. Oligonucleotide Sequences Used in This Work

* The underlined base sequences (S1, S2, S3) are the complementary base strands of fluorophore-labeled strands (FAM1, FAM2, FAM3); FAM represents the fluorophore 6-carboxyfluorescein.

7.4) spiked with 20 μL of fluorophore-labeled-strand solution (10 μmol L−1). The fluorescence emission of the solutions was recorded after incubation in the dark for about 30 min.

2. EXPERIMENTAL METHODS 2.1. Materials. All of the oligonucleotide sequences shown in Table 1, including S-Apt, FAM1, FAM2, FAM3, and FAM4, were synthesized by TaKaRa Biotechnology Co. Ltd. (Dalian, China). Polystyrene (average MW 250 000) was commercially obtained from Acros Organics (USA). Polyethylene glycol 400 (PEG 400) was purchased from Sinopharm Chemical Reagent Co. Dioctyl sodium sulfosuccinate (AOT) was purchased from Sigma-Aldrich Co. (USA). Water used in all experiments was deionized to 18.25 MΩ cm. All other reagents were of analytical grade. All the experiments were performed at room temperature. 2.2. Film Preparation. PS/PEG (70/30, w/w) toluene solution (5 wt %) was prepared as the stock solution. The concentrations of AOT and S-Apt in colorless toluene solution of PS/PEG/AOT/S-Apt were 60 mmol L−1 and 10 μmol L−1, respectively. Other sequences (FAM1, FAM2, FAM3, and FAM4) were each dissolved in deionized water to obtain a 10 μmol L−1 solution. The films were fabricated through casting PS/PEG/AOT/SApt toluene solution onto the cleaned substrates using a microinjector. Sample solution (6 μL) was dropped onto cleaned glass slides under about 60% humidity in the atmosphere at room temperature. About 5 min later, solvent and water evaporated completely and a flat PS/PEG/AOT/SApt thin film was obtained by the breath figure method. 2.3. Characterization. Scanning electron microscopy (SEM) images were collected using a Hitachi S-2500 field emission scanning electron microscope (Japan). Atomic force microscopy (AFM) measurements of the honeycomb films were performed with a Nanoscope IIIa Multimode AFM (Digital Instruments Inc., USA) at room temperature. The relative humidity (RH) was measured by a hygrothermograph, CEM DT-321S (China). Fluorescence images of porous films were recorded on an inverted fluorescence microscope (Olympus IX51, Japan). A 10 μmol L−1 solution of fluorophore-labeled strands (6 μL) was dropped onto the PS/PEG/AOT/S-Apt films prepared in the previous step. After incubation in the dark for about 30 min, the films were washed three times with deionized water in order to eliminate the unlinked FAM probe molecules. Finally, the films were examined under the inverted fluorescence microscope with excitation wavelengths (λex) of 450−480 nm. Fluorescence spectra were collected on a PerkinElmer LS 55 specrofluorometer (USA). The prepared PS/PEG/AOT/S-Apt films were removed from glass substrates and incubated in 4 mL of phosphate buffered saline (PBS, 1/15 mmol L−1, pH

3. RESULTS AND DISCUSSION 3.1. Morphology of Composite Films before and after Incubation. In the toluene solution of PS/PEG, S-Apt and AOT surfactant are hydrophilic and soluble in the hygroscopic portion of PEG. The cationic amino groups of S-Apt attract the anionic AOT molecules forming ion pairs, while the carboxyl groups of S-Apt repel them. In the porous films of PS/PEG/ AOT/S-Apt prepared by the breath figure method, the hygroscopic PEG portion containing AOT and S-Apt ion pairs appears in the inner wall of the pores formed by water droplets.28 Fluorophore 6-carboxyfluorescein (FAM) is one of the most stable fluorochromes which is generally used for cell staining, DNA molecular labeling, and preparation of nucleic acid aptamer probe.29−31 The complement binding reaction between fluorophore-labeled strands with fluorescence properties and S-Apt occurs based on the principle of complementary base pairing of DNA. First, the structure of the PS/PEG/AOT/S-Apt film was characterized by SEM and AFM. As a typical example, Figure 1a,b shows the film morphologies before incubation with FAM1 and Figure 1c,d shows the film morphologies after incubation with FAM1. Figure 1a shows the general view of the porous film fabricated using the breath figure method, which presents longrange order arrangement. AFM images show that the thickness of the porous film is about 1 μm (Figure 1d). The diameters of the pores of the honeycomb PS/PEG/AOT/S-Apt films do not change obviously before (Figure 1b) and after (Figure 1c) incubation with FAM1, which suggests that the morphology of the composite films was not destroyed after incubation and washing. 3.2. Effect of AOT on the Fluorescence Intensity of Self-Assembled Films. Free AOT molecules on the surface of self-assembled films may have a certain effect on the fluorescence intensity as suggested by our results. In Figure 2a (λex 440 nm), the fluorescence intensity of solution containing composite film and FAM1 strands (curve II) was higher than that of solution containing only FAM1 strands (curve III), but lower than that of mixed solution of AOT and FAM1 labeled chains (curve I). The concentration of the AOT solution is equal to that of AOT used to make the composite films. The binding of S-Apt embedded in the composite film to the FAM1 led to the concentration decrease of FAM1 strands in the solution shown as the reduction of fluorescence intensity. 27367



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ascribed to the absence of the complementary base sequence of FAM4 in S-Apt aptamer embedded in the composite film. In other words, FAM4 strands cannot be captured by the composite film. 3.3. Fluorescence Images of Composite Films before and after Incubation. The structure of the composite porous films also can be confirmed by the change in fluorescence images of the films before and after binding between S-Apt and fluorophore-labeled strands. According to the principle of complementary base pairing of DNA, the stronger the fluorescence intensity of the incubated film, the more captured probe strands. An inverted fluorescence microscope was employed to study the fluorescence change of the films. Figure 3 shows the

Figure 1. SEM images of PS/PEG/AOT/S-Apt film (a, b) before and (c) after incubation with FAM1. Scale bar = 10 μm. (d) AFM images of PS/PEG/AOT/S-Apt film incubation with FAM1.

Figure 2. Effect of AOT on fluorescence spectra. (a) (I) 20 μL of FAM1 + 6.0 μL of 6.0 mmol L−1 AOT solution; (II) 20 μL of FAM1 + composite film; (III) 20 μL of FAM1. (b) (I′) 20 μL of FAM4 + composite film; (II′) 20 μL of FAM4 + composite film cleaned by deionized water five times; (III′) 20 μL of FAM4.

Figure 3. Fluorescence images of (a) PS/PEG/AOT/S-Apt porous film, (b) PS/PEG/AOT/S-Apt/FAM1, (c) PS/PEG/AOT/S-Apt/ FAM2, and (d) PS/PEG/AOT/S-Apt/FAM3. λex = 450−480 nm; scale bar = 20 μm.

fluorescence images of PS/PEG/AOT/S-Apt film (Figure 3a) and incubated films by fluorophore-labeled strands (Figure 3b− d). Figure 3a shows the distinct porous structure of the PS/ PEG/AOT/S-Apt composite film with no fluorescence detected due to the lack of fluorophore-labeled strands. In Figure 3b obtained from FAM1 incubated films, some bright fluorescent spots unevenly scattered around the inner rings can be observed. For FAM2 incubated films (Figure 3c), the fluorescent spots increased distinctly with the appearance of a few semicircular and annular fluorescent structures. Finally, in Figure 3d obtained from FAM3 incubated films, further enhanced fluorescence activity can be seen with growing numbers of semicircular or annular fluorescence structures. Figure 3 shows the progression of the distribution architecture of the fluorophore-labeled strands in a single pore from fluorescent spots to semicircular fluorescent structures, and then to annular fluorescent structures. This observation can be ascribed to the increase of bound fluorophore-labeled strands on the films (FAM3 > FAM2 > FAM1). This trend can be explained by the accessibility of the base sequences (S1, S2, S3) on S-Apt. As stated before, the ion pairs formed by AOT molecules and the amino groups at the 3′ end of S-Apt can be embedded in the PEG inner ring,28 while carboxyl groups at the 5′ end of S-Apt extend out into the open space of the pores due to electrostatic repulsion by negatively

Meanwhile, physically adsorbed AOT molecules on the surface of the composite films may leach from the films into the solution, enhancing the sensitivity of fluorophore,32 which led to enhanced fluorescence intensity. In the solution, both fluorescence reduction by S-Apt capturing and fluorescence enhancement by AOT played important roles in this system. The former effect may be less significant than the latter, leading to higher fluorescence intensity of curve II than curve III. To study the effect on fluorescence intensity caused by physically adsorbed AOT molecules on the surface of the composite film, FAM4, which contains part of the S1 base sequence in S-Apt, was used for comparison. Figure 2b shows the fluorescence spectra (λex 440 nm) of the FAM4 solution containing composite film (I′), FAM4 solution containing cleaned composite film (II′), and FAM4 solution (III′). The fluorescence intensity of FAM4 solution with washed composite film (curve II′) is distinctly lower than that with unwashed composite film (curve I′), suggesting that physically adsorbed AOT can be cleared with deionized water and the cleaned film can maintain its intact structure (see Figure 1). The fluorescent intensities of II′ and III′ are almost identical, which indicates that cleaned composite film added in FAM4 solution has no effect on the fluorescence intensity. Meanwhile, the decrease of fluorescence intensity was not observed, which should be 27368



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charged AOT molecules. Since the base sequence S1 is located closest to the 3′ end, it is the least accessible for FAM1 resulting in the fewest captured fluorescent strands (Figure 3b). Similarly, the base sequence S3 is located closest to the 5′ end, and it is the most accessible for FAM3 resulting in the most captured fluorescent strands (Figure 3d). Therefore, medium fluorescence activity from FAM2 incubated films can be explained by the location of the base sequence S2 in between S1 and S3. Notably, S-Apt still maintained its biological activity after being assembled into the porous films as implied by the fluorescence images. 3.4. Binding Behavior Study of Composite Film to Different Fluorophore-Labeled Strands. The fluorescence intensity of solution containing composite film and FAM1 strands (Figure 4a) is stronger than that without composite

Figure 5. (a) Mechanism of porous film formation. (b) Illustration of PS/PEG/AOT/S-Apt honeycomb film formed at suitable humidity. (c) Illustration of distribution of AOT and S-Apt in a part of a single pore of the PS/PEG/AOT/S-Apt composite film.

formation by the breath figure method is shown. Condensed water droplets caused by evaporation of toluene solvent dipped into the sample solution and dense hexagonal packing occurs when humidity reaches a suitable value.20,22,33 After complete evaporation of the water droplets and solvent, the ordered PS/ PEG/AOT/S-Apt honeycomb film is formed as shown in Figure 5b, which is consistent with the SEM images in Figure 1a. Hydrophobic PS acted as the matrix of the porous film, and the hygroscopic PEG part containing AOT and S-Apt aptamer appears in the inner wall of the pores that stabilized the water droplets.28 Figure 5c shows the distribution of AOT and S-Apt in a section of a single pore of the composite film. AOT anions attract the 3′ end (−NH2) and repulse the 5′ end (−COOH) of S-Apt due to electrostatic interactions. Many S1 base sequences of S-Apt are embedded in the films, which hinders the base pairing with FAM1 complementary strands, resulting in some fluorescent spots in the fluorescence images (Figure 3b). A small number of S2 base sequences of S-Apt are embedded in the film, which is beneficial for the base pairing with FAM2 complementary strands, leading to more fluorescent spots and a few semicircular and annular fluorescent structures (Figure 3c). S3 base sequences of S-Apt tend to stretch further from the interface; many semicircular and annular fluorescent structures are obtained after binding with FAM3 probe strands (Figure 3d).

Figure 4. Fluorescence spectra of different solutions: (a) 20 μL of FAM1 + composite film, (b) 20 μL of FAM1, (c) 20 μL of FAM2 + composite film, and (d) 20 μL of FAM3 + composite film.

film (Figure 4b). This can be explained by the enhanced sensitivity by loose AOT as described before. On the other hand, the fluorescence intensity of solution containing composite film and FAM2 strands (Figure 4c) or FAM3 strands (Figure 4d) is lower than that of the FAM1 solution (Figure 4b) with the same concentration. These results indicate that the decrease of fluorescence intensity induced by capturing of fluorophore strands is larger than the increase of fluorescence intensity induced by the enhancing effect of loose AOT. The fluorescence intensity of solution containing composite film and FAM1 strands is much higher than that of solution containing composite film and FAM2 strands. It should be concluded that the amount of FAM1 strands binding to the composite films was less than the amount of FAM2 strands. Therefore, FAM2 strands could be captured more easily by SApt in the composite film than FAM1 strands. The fluorescence intensity of solution containing composite film and FAM3 strands is lower slightly than that of solution containing composite film and FAM2 strands, indicating that the concentration of FAM3 probe strands was slightly lower than that of FAM2 probe chains in solution. The difference of binding ability of the composite film to fluorophore-labeled strands can be explained by the accessibility of the base sequences as detailed before. The S1 base sequence is least accessible, leading to the highest concentration of probe-labeled strands in the solution shown as the highest fluorescence intensity FAM1. Similarly, S3 base sequence is the most accessible, resulting in lowest fluorescence intensity of the solution. 3.5. Mechanism of Honeycomb-Patterned Film Formation Based on Aptamers and Fluorescent Behaviors. Figure 5 illustrates the proposed formation mechanism of the porous films. In Figure 5a, the classic mechanism of porous film

4. CONCLUSIONS A honeycomb film based on aptamer was successfully fabricated, and its binding behaviors with different fluorophore-labeled strands were studied. Physically adsorbed AOT molecules on the surface of the composite film may leach into the solution and enhance the sensitivity of fluorophore, leading to increased fluorescence intensity. Meanwhile, the fluorescence intensity of the solution was reduced through binding of S-Apt and FAM molecules. S-Apt strands stretched gradually away from the film from S1 to S3 parts by repulsion between AOT anions and carboxyl groups of S-Apt, which was beneficial for the association with FAM2, and FAM3 complementary base strands. Therefore, more fluorescent spots and semicircular and annular fluorescent structures were observed. This paper presented a unique honeycomb film containing bioactive 27369



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aptamers. Moreover, we are working on the application of the aptamer-based honeycomb film as a fluorescent biosensor. The mechanism studies of fabrication and binding behaviors may have significance in the making of biosensors, capture and detection of protein, tumor markers, and other bioactive materials.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Tel.: +86-0531-82767872. Author Contributions

† D.F. and X.X. contributed equally to the work and share first authorship.

Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS This research was supported by the Natural Science Foundation of China (Nos. 21103071, 21375047), the Natural Science Foundation of Shandong Province (ZR2011BQ016), and Doctor Foundation of University of Jinan (XBS1311). Q.W. thanks the Special Foundation for Taishan Scholar Professorship of Shandong Province and UJN (No. ts20130937). All of the authors express their deepest thanks.

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Fabrication of Honeycomb Films Based on Aptamer and Binding

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