Dual amplifying fluorescence anisotropy for detection of respiratory syncytial virus DNA fragments with size-control synthesized metal–organic framework MIL-101

Abstract

In order to eliminate the scattered light induced by the signal amplifier in fluorescence anisotropy (FA) assays, a nanosized metal–organic framework MIL-101, ranging from 80–500 nm, has been synthesized through a hydrothermal method with the addition of glycerol. We chose the 100 nm MIL-101 to enhance FA for label-free detection of the respiratory syncytial virus (RSV) gene sequence and the DNA-intercalating dye SYBR Green I (SGI) as the fluorophore, based on the different affinities of MIL-101 toward ssDNA and dsDNA. The nanosized MIL-101 has a negligible scattering effect owing to its smaller particle size, so all of the experimental data of FA values were smaller than the maximum initial anisotropy of 0.4. As a specific advantage, a dual amplification result of not only an increase in the FA value of SGI/ssDNA (r₁) but also a decrease in the FA value of SGI/dsDNA (r₂) was presented at the same time. Consequently, a larger FA value change Δr (Δr, Δr = r₁ − r₂) was obtained and contributed to improve the sensitivity. In addition, the quantitative detection of the target DNA (T) was achieved according to the relationship between Δr and the concentration of T. In the presence of MIL-101, the Δr is 7-fold higher than that without MIL-101 and achieved the sensitive and selective detection of RSV DNA.

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1. Introduction

Fluorescence anisotropy is the measurement of rotational motion-related factors of a fluorophore or fluorophore-labeled complex. In general, molecular volume and mass increases of the fluorophore often lead to a larger FA value.¹ To expand the applications of FA and improve its sensitivity, various materials of large mass including proteins,² gold nanoparticles,³ graphene oxide (GO)⁴ and metal–organic frameworks (MOFs)⁵ have been employed as mass amplifiers. But, a high anisotropy signal cannot always be obtained by simply enlarging the molecular volume and mass, because this increase may not be able to efficiently retard the rotational movement of the fluorophore.⁶ Furthermore, overly large material is prone to settlement and is not suited for analytical use in aqueous solution. Most importantly, an obvious scattered light will be generated for the big size of the amplifier, thus will interfere with anisotropy measurements.⁷ Generally, if the measured anisotropy for a randomly oriented sample is bigger than 0.4, one can confidently infer the presence of scattered light in addition to fluorescence.^7,8 There are some reports about nanomaterials used as FA amplification platforms for target assays, yet some of the FA values exceed 0.4,⁹ which is unreasonable and not allowed. Furthermore, deduction of scattered light from the measured fluorescence data often leads to demonstrable inaccuracy. So, the application of nanomaterials in enhancing FA needs improvement and standardization. One approach for this problem is to find amplifiers with both an appropriate size and an excellent amplification ability of FA.

MOFs have achieved remarkable progress in a wide range of applications.¹⁰ Despite the more traditional areas of storage,¹¹ separation,¹² and catalysis,¹³ some interesting MOF structures also exhibit great potential in sensing,¹⁴ molecular recognition,¹⁵ and biological applications.¹⁶ In our previous study, we utilized chromium-benzenedicarboxylates (MIL-101) as the FA amplification platform for sensitive detection of DNA,⁵ which is simple and effective. Yet, an obvious scattered light exists for the large size of MIL-101, thus interfering with the FA measurement. So far, the synthesis of MOF-type materials has been studied extensively.¹⁷ However, the morphology control of MOFs, especially to get nanosized MOFs, has not been investigated enough even though it is very important because the nanoscale MOFs have potential applications like drug delivery,¹⁸ imaging¹⁹ and other analytical application in aqueous solution. Therefore, it is necessary to pay more attention to the investigation and synthesis of nanosized MOFs.

Herein, in order to facilitate MOFs to have a better performance in FA assays, the nanosized metal organic framework MIL-101, ranging from 80–500 nm, has been synthesized through a traditional hydrothermal method²⁰ with the addition of glycerol. The obtained smaller size MIL-101 possess better monodispersity and produce weaker scattered light. Furthermore, the zeta potential of the MIL-101 increased with the decreasing size (Fig. 2(a)). So, if this developed MIL-101 is performing as the FA amplifier for DNA detection, the electrostatic interaction between MIL-101 and DNA would be strengthened. And the FA amplification effect will still be obvious or even greater than before.

In this contribution, we chose the 100 nm MIL-101 to amplify the FA for label free detection of the respiratory syncytial virus (RSV) DNA sequence based on the different affinities of MIL-101 toward ssDNA and dsDNA. As shown in Scheme 1, without MIL-101, only a small FA change occurred for the little molecular mass variation before and after the hybridization of (probe DNA) P with T. Conversely, in the presence of ML-101, the FA of SGI/ssDNA sharply increased and the FA value of SGI/dsDNA became smaller than that of SGI/dsDNA without MIL-101. So, a dual FA amplification effect was presented and a larger Δr value was obtained, which is beneficial to the FA assay. Furthermore, in the whole experiment, all of the measured FA values were smaller than 0.4, indicating that the scattered light of MIL-101 is negligible.

Scheme 1 The concept and principle of the MIL-101 amplified fluorescence anisotropy strategy for label-free detection of RSV DNA.

2. Experimental section

2.1 Materials

Cr(NO₃)₃·9H₂O (99%), hydrofluoric acid (HF) (48%) and terephthalic acid (H₂BDC) (99%) were purchased from Aladdin chemistry Co., Ltd. (Shanghai, China). Herein, we used oligonucleotides of a specific sequence (5′-AAA AAT GGG GCA AAT A-3′) as the probe for recognition of the RSV DNA sequence (target DNA). All of the ssDNAs were synthesized and purified by Sangon Biotech Co. Ltd (Shanghai, China), and were used without further purification. The sequence of the complementary target DNA (T) was 5′-TAT TTG CCC CAT TTT T-3′. One-base-mismatched oligomer (MT1), 5′-TAT TTG CCC CAT TTT T-3′; two-base-mismatched oligomer (MT2), 5′-TAT TTG CCC CAT TTT T-3′; and three-base-mismatched oligomer (MT3), 5′-TAT TTG CCC CAT TTT T-3′. SG (10 000×) was purchased from Invitrogen Inc, which was diluted to 1.25× with water to make a stock solution. The concentration of 125× SG is 0.245 mM, according to the research of Liu et al. in 2008.²¹

2.2 Apparatus

An S-4800 scanning electron microscope (SEM) (Hitachi, Japan) was used to record the SEM images. A Model JASCO-810 spectropolarimeter (JASCO, Japan) was employed to measure circular dichroism (CD) spectra. An XD-3 X-ray diffractometer with Cu K_α radiation (λ = 1.5406 Å) was used to collect powder X-ray diffraction (PXRD) patterns at a scan rate of 2.00 min⁻¹ (Purkinje, China). Fluorescence anisotropy was measured with an F-2500 fluorescence spectrophotometer equipped with a polarization filter (Hitachi, Tokyo, Japan). An Oakton pH 510 meter (Singapore) was employed to adjust the pH values. A vortex mixer QL-901 (Haimen, China) was employed to blend the solution. Millipore water from a Milli-Q filtration system (Millipore, USA) was employed to prepare all of the solutions.

2.3 Preparation of MIL-101

Nanosized MIL-101 ranging from 80–500 nm was synthesized according to the published procedure with some modifications.²⁰ Briefly, Cr(NO₃)₃·9H₂O (2.00 g, 5.0 mM), HF (48 wt%, 5.0 mM), terephthalic acid (0.82 g, 5.0 mM) and 24 mL of deionized water and a certain amount of glycerol were added into a hydrothermal bomb and then put into an autoclave held at 220 °C for 20 h. After that, the mixture was naturally cooled to room temperature, followed by filtering the mixture with a large pore fritted glass filter to remove the significant amount of recrystallised terephthalic acid. Then, the product of MIL-101 was separated from the solution using a small pore filter and washed with deionized water and ethanol to remove the glycerol. After being soaked in ethanol (95% ethanol with 5% water) at 80 °C for 24 h, it was washed with hot ethanol. Furthermore, MIL-101 powder was refluxed for 24 h in 1 M NH₄F aqueous solution and washed with hot water. To obtain good dispersion conditions, we did not dry the product into a powder but kept it as a solution for further use. However, we dried 10 mL of the reserved solution into a powder, knowing that its concentration was 40 mg mL⁻¹. The structure of MIL-101 is shown in Fig. 1.

Fig. 1 (a)–(e): SEM images of the synthesized MIL-101s to show the effect of the amount of glycerol on particle size ((a–e), the volume of glycerol was 0, 30, 50, 80 and 100 μL, respectively); (f): powder X-ray diffraction (XRD) spectra of MIL-101 (a)–(e) (f, 1–5, respectively) and simulated XRD of MIL-101 (f6).

2.4 Detection of RSV DNA

Briefly, 50 μL of PB buffer (pH 7.2), 100 μL of probe DNA (0.1 μM) and a certain volume of target DNA (0.1 μM) were sequentially added into a 1.5 mL tube, and kept at 30 °C for 40 min. Then 50 μL of SG (2.45 μM) was added and incubated at room temperature for 5 min. Lastly, 35 μL of MIL-101 solution (0.05 mg mL⁻¹) was added into the mixture and further diluted with ultrapure water to 500 μL. After 20 min incubation, fluorescence anisotropy measurements were carried out on a F-2500 fluorescence spectrophotometer with an excitation wavelength of 490 nm and the emission intensity at 529 nm was recorded. Then the FA value was calculated according to the Perrin equation.^4,22

3. Results and discussion

3.1 Characterization of the synthesised MIL-101 and the effect of the volume of glycerol on the particle size

Fig. 1 displays SEM images and XRD spectra of the synthesized MIL-101s, synthesized with the addition of different amounts of glycerol. As we can see, the particle size of MIL-101 decreased with the increasing amount of glycerol. The particle size of MIL-101 was about 500 nm in the absence of glycerol Fig. 1(a). In the presence of 30 μL glycerol, the particle size has no obvious change compared with that without glycerol Fig. 1(b). With the addition of 50 μL, 80 μL and 100 μL of glycerol, the particle size was about 300 nm, 100 nm and 80 nm Fig. 1(c–e), respectively. Besides, the synthesized MIL-101 was a regular octahedron and all the PXRD spectra of the different sizes of MIL-101 were consistent with that of previously reported literature,²⁰ suggesting that the glycerol has not participated in coordination.

The decreased size of MIL-101 for the addition of glycerol may be explained by the slowed rate of crystal growth than before.²³ As one of the methods for miniaturization of MOF crystals, some organic additives can regulate the crystal size and morphology.²⁴ Glycerol has been reported as an additive for size-control synthesis of zeolite A²⁵ and silver nanoparticles.²⁶ Similar to these reports, in our experiments, glycerol may also perform as a capping agent to suppress the crystal growth, resulting in a decrease of the crystal size.²⁴ At the same time, the addition of glycerol increased the monodispersity of MIL-101 owing to the hydroxyl groups.

As we can see from Fig. 2, the 100 nm MIL-101 (the addition volume of glycerol was 80 μL) has the largest zeta potential among the different sizes of MIL-101 (Fig. 2(a) and (d)). But the zeta potential had no obvious change if we added a different amount of glycerol after the MIL-101 was synthesized (Fig. 2(b)). Besides, when the same FA value was induced by different sizes of MIL-101 (Fig. 2(c)) the scattering light intensity of the 100 nm MIL-101 was the lowest (Fig. 2(d)). So, 100 nm MIL-101 was chosen for further experiments.

Fig. 2 (a) Zeta potentials of different size MIL-101s synthesized with different amounts of glycerol (a–e, 0, 30, 50, 80 and 100 μL, respectively). (b) Zeta potential of already synthesized MIL-101 with the addition of different amounts of glycerol (1–5, 0, 30, 50, 80 and 100 μL, respectively). (c) Similar fluorescence anisotropy values induced by certain amounts of different sizes of MIL-101 and (d) the scattered light intensity they produced (a–e represent the obtained different sizes of MIL-101 when the volumes of glycerol were 0, 30, 50, 80 and 100 μL, respectively). Conditions: P, 20 nM; SG, 0.245 μM; Tris–HCl buffer; pH 7.2.

3.2 The interaction between SG/DNA complex and MIL-101

As shown in Fig. 3, in the absence of MIL-101, the FA value changed from 0.14 to 0.1 with a small Δr₁ of 0.04 before and after hybridization. However, with the addition of MIL-101, ssDNA can be adsorbed onto the surface of MIL-101 mainly through electrostatic and π–π stacking interactions.⁵ The rotation of SGI/ssDNA was confined by MIL-101, thus the FA value sharply increased to 0.38. Once P was hybridized with T at first, the formed dsDNA has a stable conformation that stays away from MIL-101 and the obtained FA was only about 0.09. So, in the presence of MIL-101 the FA value change (Δr₂) was 0.29, which is 7-fold higher than that of without MIL-101 (Δr₁ = 0.04). The amplified Δr resulted from the remarkably larger mass change induced by MIL-101, according to the Perrin equation.²² Specifically, in the presence of MIL-101, the FA of P (r₁) increased and the FA of P + T (r₂) decreased conversely. In other words, herein the MIL-101 had a dual amplification effect of amplifying the FA value of P and reducing the FA value of P + T, thus obtaining a larger Δr. This is one of the advantages of employing MIL-101 as an amplifier in this label-free DNA detection strategy compared with other amplification platforms and labeled fluorophores.

Fig. 3 Fluorescence anisotropy of P and P + T in the absence (navy columns) and presence (purple columns) of MIL-101. Conditions: P, 20 nM; T, 15 nM; MIL-101, 3.5 μg mL⁻¹; pH, 7.2; λ_ex, 490 nm.

The reason for the dual amplification phenomenon may be explained as follows. In the presence of MIL-101, the FA of ssDNA (r₁) sharply increased because the rotation of ssDNA was significantly confined compared with that without MIL-101. The species of metal ion in the MOF, the framework and the BET surface of the MOF may be the factors that cause MIL-101 to combine with ssDNA. Consequently, the FA valve was amplified. After the addition of the target DNA, P hybridized with T, and the positively charged SGI intercalated into the formed dsDNA. So, the electrostatic repulsion between positively charged MIL-101 and SGI interferes with the rotation of dsDNA causing it to be faster and more irregular than that without MIL-101, thus leading to a smaller FA value of dsDNA (r₂). As a result, Δr (Δr = r₁ − r₂) was dually amplified. Furthermore, MIL-101 has a 3D zeotype architecture, which can adhere the flexible ssDNA but it is difficult for the rigid dsDNA to adsorb. This is beneficial for MIL-101 to distinguish between ssDNA and dsDNA. It is expected that further research can be done to make the mechanism more clear.

3.3 Optimization of experimental conditions

Several factors including the dosage of MIL-101, pH value and incubation time were optimized to obtain the best quantitative result. Performing as the amplification platform, the amount of MIL-101 plays a significant role on the target quantification. An insufficient amount of MIL-101 would cause MIL-101 to integrate with only part of P, resulting in a lower background FA value (r₁). However, an overdose of MIL-101 would interact with the formed P/T to some degree and inhibit its release, leading to a bigger recovery FA value (r₂). Thus, bringing about a smaller Δr value (Δr = r₁ − r₂). Additionally, the positively charged MIL-101 can interact with negatively charged DNA through electrostatic interaction. Therefore, the pH of the environment would have a great influence on the FA value. Experiments showed that the optimal conditions were 20 nM of P hybridized with T at 30 °C for 40 min and then incubated with 3.5 μg mL⁻¹ of MIL-101 (Fig. 4(a)) at pH 7.2 for 15 min (Fig. 4(b) and (c)).

Fig. 4 Fluorescence anisotropy of P, P + T and Δr at different concentrations of MIL-101 (a), pH (b) and incubation time (c). Conditions: P, 20 nM; SG, 0.245 μM; pH 7.2.

3.4 High sensitivity and selectivity for RSV DNA detection

Under the optimal conditions, the relationship between the FA value change (Δr) of SGI and the concentration of target DNA was investigated. Fig. 5 shows the dependence of Δr before and after the P/T hybridization on the increasing concentration of T. In the presence of MIL-101, there is a linear relationship between them in the range of 1–20 nM with a linear regression equation of Δr = 0.087 + 0.0088c_T and a detection limit of 1 nM (S/N = 3). Contrastingly, in the absence of MIL-101, the Δr has no obvious change with the increasing concentration of T. Apparently, MIL-101 can remarkably enhance Δr mainly attributable to its FA amplification effect on SGI/ssDNA. The results confirm that this strategy can be successfully applied for quantitative detection of RSV DNA.

Fig. 5 Fluorescence anisotropy changes Δr against the increasing concentration of T from 1 nM to 40 nM with (black data points) and without (red data points) the presence of MIL-101. Conditions: P, 20 nM; MIL-101, 3.5 μg mL⁻¹; pH, 7.2; λ_ex: 490 nm.

In this study, to evaluate the feasibility and sequence specificity, control experiments were carried out by comparing the Δr of target DNA with that of different mismatched target DNA. As shown in Fig. 6, in the presence of MIL-101, the specificity of the assay is excellent. Based on the different hybridization efficiency of targets with P, the addition of T produces a significant Δr increment, while the mismatched targets M1, M2 and M3 give relatively lower Δr and T can be easily distinguished from M1, M2 and M3. However, in the absence of MIL-101, there is a negligible difference among the Δr values of T, M1, M2 and M3. Besides, all of the values are very small. Therefore, the proposed method using MIL-101 as a FA amplification platform provides high sensitivity and selectivity in RSV DNA detection.

Fig. 6 Specificity of target DNA assay over mismatched DNA in the absence (light gray) and presence (dark gray) of 3.5 μg mL⁻¹ MIL-101. Conditions: P, 20 nM; T, M1, M2 and M3 are all 15 nM; pH, 7.2; λ_ex: 490 nm.

3.5 Mechanism of the interaction between DNA and MIL-101

Electrostatics play an important role in the interaction between MIL-101 and DNA. Therefore, the zeta potential variation measurement of MIL-101 throughout the reaction process can illustrate the mechanism. Table 1 shows the zeta potential variation of different MIL-101 samples. MIL-101 was positively charged with the zeta potential of +33.2 mV in water. To reflect the real situation during the experiments more accurately, we tested the zeta potential of MIL-101 samples under the experimental conditions. The measured zeta potential of MIL-101 was −17.3 mV in the presence of pH 7.2 buffer solution. But the variation tendency of different samples can also be used for explanation of the mechanism. After the addition of negatively charged ssDNA, the zeta potential decreased to −27.4 mV, suggesting that the ssDNA joined onto the surface of MIL-101 and neutralized part of its potential. After the addition of the target DNA, the formed dsDNA has a more stable conformation that stays away from the surface of MIL-101. So, the zeta potential is larger. In the presence of positively charged SGI, the variation tendency is consistent with that of without SGI. So, the measured results are consistent with the mechanism we proposed.

Table 1 Zeta potential variation of MIL-101 in different samples

Sample name	Zeta potential (mV)
MIL-101	−17.3
MIL-101 + P	−27.4
MIL-101 + P + T	−23.5
MIL-101 + P + SGI	−25.5
MIL-101 + P + T + SGI	−21.3

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To further demonstrate the proposed mechanism, we measured the circular dichroism (CD) of P and P/T in the presence and absence of MIL-101 (Fig. 7). As is known, dsDNA produces a typical DNA spectrum with the positive and negative peak at 275 nm and 246 nm (crossover point, 258 nm),²⁷ respectively. The results we obtained are consistent with that reported. Compared with the spectrum of P, an increase in the amplitude of the negative CD band was observed in the presence of target DNA. So, the DNA helicity increased and the dsDNA structure formed. Furthermore, the peaks’ location has not changed in the presence of MIL-101, suggesting that the introduction of MIL-101 did not damage the structure of DNA.²⁸ The results are not only evidence for the mechanism, but also demonstrated the feasibility of MIL-101 for this application.

Fig. 7 Circular dichroism of P and P/T in the absence and presence of MIL-101. Conditions: P, 1.2 μM; T, 1.2 μM; SG, 0.245 μM; MIL-101, 3.5 μg mL⁻¹; pH 7.2.

3.6 Amplification ability comparison between MIL-101 and GO

There are several reports about graphene oxide performing as the fluorescence anisotropy amplification platform for metal ions²⁹ and detection of other targets,⁹ which also present good performance. Under the same conditions to our experiments, we applied GO to enhance the FA for detection of RSV DNA fragments. As shown in Fig. 8, in the presence of GO, both the FA value of P and P/T are enlarged. So, GO did not show the dual amplification ability, which is inferior to MIL-101. As we mentioned above, it may be just the special structure and chemical properties of MIL-101 which facilitate the dual amplification effect.

Fig. 8 Fluorescence anisotropy of P and P/T in the absence (violet columns) and presence (pink columns) of GO.

4. Conclusion

In conclusion, a good dispersion of the nanosized metal organic framework MIL-101 ranging from 80–500 nm has been synthesized with the organic additive glycerol. The 100 nm sized MIL-101 was successfully used to enhance the FA for label-free detection of RSV DNA with a dual amplification ability. The scattered light produced by the nanosized MIL-101 is negligible, which guaranteed that the measured FA values were smaller than the maximum initial anisotropy of 0.4. The addition of glycerol not only decreased the size of MIL-101 but also increased its monodispersity owing to the hydroxyl groups. We expect that this newly synthesized nanosized MIL-101 will find better use in analytical applications which require MOFs with a small size, such as cell imaging and drug delivery. On this basis, it will be more favorable for FA assays if the fluorescence of the fluorophore is unchanged when the FA is amplified by the amplifier, on which we will do more work in the future.

Acknowledgements

The authors are grateful for financial support from the National Natural Science Foundation of China (NSFC, no. 21175109) and the special fund of Chongqing key laboratory (CSTC).

Notes and references

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