The intelligent sensors of lead based on a reconfigurable DNA

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The intelligent sensors of lead based on a reconfigurable DNA-supramolecule logic platform Chunrong Yang, Shu Yang, Jicheng Li, Yuanyuan Du, Lingbo Song, Dan Huang, Jianchi Chen, Qiuju Zhou, Qianfan Yang, and Yalin Tang Anal. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.analchem.8b02782 • Publication Date (Web): 07 Aug 2018 Downloaded from http://pubs.acs.org on August 8, 2018

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Analytical Chemistry

The intelligent sensors of lead based on a reconfigurable DNAsupramolecule logic platform Yang Chunrong, a‡ Yang Shu, b‡ Li Jicheng, a Du Yuanyuan, Jianchi, a Zhou Qiuju, d Yang Qianfan, a* Tang Yalin e

c

Song Lingbo,

b

Huang Dan,

a

Chen

a. College of Chemistry, Sichuan University, Chengdu, 610064, China b. Key Laboratory of Drug Targeting and Drug Delivery Systems, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China c. West China School of Public Health, No.4 West Teaching Hospital, Sichuan University, Chengdu, 610041, China d. Analysis & Testing Center, Xinyang Normal University, Xinyang, 464000, China e. National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China * Corresponding Author: E-mail: [email protected]. Tel: +86-17780501019 (Yang Q. F.) ABSTRACT: The lead (Pb) hazard is not only in connection with the concentration of Pb2+ but also closely related to the ambience which affects its mobility and the synergistic toxicity with other ions. However, most of the existent methods focus highly on detecting Pb2+ concentration accurately but can seldom reflect the pollution-related information in actual samples, thereby limiting their pragmatic applications. In this work, a DNA-supramolecule logic platform was established, which can be configurated to implement three information process functions and act as three unique intelligent sensors of Pb. The demultiplexer that can split signal flow was used to determine Pb2+ in different pH conditions; the multiplexer that can alternate signal channels was applied to detect Pb2+ or Ag+ selectively; and the decoder that can extract information was utilized to test Pb2+ and the coexisted Ni2+ simultaneously. All the three intelligent sensors based on the logic prototypes present practicable sensitivities and specificities. Considering its flexibility, scalability and reconfigurability, we believe the logic platform may provide new solutions to process sophisticated information and implement intelligent analysis in environmental monitoring, biochemical detecting and medical diagnosis. Lead (Pb) has been widely used in building materials, alloy industry and battery manufacturing, and consequently has been increasingly emitted into surroundings as an environmental pollutant.1 It is well-known that Pb is a highly toxic heavy metal, and its intoxication can lead to many dysfunctions, like neurodevelopmental defect, cardiovascular diseases and impaired fertility.2-5 Thus, the monitoring of Pb is of vital importance for both ecosystem and public health. Nowadays, numerous methods, from large-scale instruments (like inductively coupled plasma atomic emission spectroscopy) to portable biosensors (such as immunosensors, enzyme6-8 and aptamer sensors9,10), have provided Pb2+ detection approaches with high specificity and sensitivity. However, unlike the ideal conditions in lab, the sources of real samples are varied and the influences are sophisticated. For example, the impact of soil Pb pollution is not only determined by Pb2+ concentration, but also closely related to its transportation rate, which depends heavily on the pH condition and possible chelation. Another issue is the synergetic toxicity of Pb2+ with other coexisting ions, Ag+, Hg2+, Ni2+ and so on, which commonly enrich in soil, industrial waste and domestic water.11,12 Therefore, the ability of processing pollutionrelated information is becoming one important and imperative requirement in novel Pb analysis methods. In nature, many physical, chemical and biological processes occur with information manipulation similar to the silicon-based circuits, and some of which have been utilized in molecular computation.13-16 Thereinto, DNA computation has attracted much attention, due to the strict base complementarity and controllable structural transitions.17-19 A series of DNA-based logic devices, such as INHIBIT gates (filtering signal under certain conditions),20 multiplexer/demultiplexer (selecting/splitting signal flows)21,22 and parity checker (verifying and correcting data),23

have been developed to implement information process functions. In the virtue of the multi-input capacity and selectivity, these devices not only contribute to the development of molecular computer, but also play important roles in multi-target analysis.24,25 Tan and coworkers20 designed a DNA-based logic platform which can analyze multiple cancer cell-surface markers and produce diagnostic signals. Willner et al.26 employed nucleic acid functionalized CdSe/ZnS quantum dots to construct AND and OR gates and realized the simultaneous analysis of Hg2+ and Ag+. These efforts open a new avenue for analyzing multi-target systems in an intelligent and automated way. In this work, we succeed in constructing a DNA-supramolecule logic platform which can implement three unique information process functions and employing them as Pb2+ intelligent sensors.

EXPERIMENTAL SECTION Chemicals and Apparatus. DNA oligonucleotides D1 and D2 were synthesized from Sangon Biotechnology Co. Ltd. (Shanghai, China). The cyanine dye MTC was synthesized according to the methods of Hamer27 and Ficken,28 and the purity was determined by MS, elemental analysis, NMR and absorption spectroscopy (shown in Figure S1-S4 and Table S1-S2). All the metal salts (analytical reagent grade) were purchased from Sigma-Aldrich Ltd. (Shanghai, China) and used as received without further purification. Ultrapure water was prepared by an ULUPURE (Chengdu, China) ultrapure water system and was used throughout the experiments. The stock solution of MTC was prepared by dissolving its powder in methanol and was stored in darkness. The D1D2 complex was prepared by mixing D1 and D2 in equimolar amounts and annealing in a thermocycler (heated at 90 °C for 5 min and

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then cooled slowly to room temperature). The DNA concentra-

tions

Figure 1. Scheme of the DNA-supramolecule logic platform. (A) The changes of DNA conformation and MTC assembly behaviour triggered by various inputs. (B) The molecular structure and various assembly states of MTC. (C) The possible conformations of D1 and D2.

were determined by measuring the absorbance at 260 nm. The spectroscopy measurements. The fluorescence spectra were collected with a F-4600 spectrophotometer (HITACHI, Japan) in a 10 mm quartz cell. Xenon arc lamp was used as the excitation light source. Both the excitation and emission slits were 5 nm, and the excitation wavelength was 530 nm. The absorption spectra were acquired with an EVOLUTION 201 spectrophotometer (Thermo SCIENTIFIC, USA) at room temperature in a 10 mm quartz cell. The logic operation of the DEMUX, MUX and DC. To better execute the logic functions, optimized input conditions were selected for both devices. All samples were incubated in the dark at room temperature for 5 min before the measurement. For the DEMUX, 2 µM D1D2 and 4 µM MTC in 10 mM Tris-HCl buffer solution (pH 7.0) were used as the initial state. 2 µM PbCl2 was employed as the data input and H+ (pH 4.0, 10 mM Tris-HCl buffer solution) was employed as the address input. For the MUX, 4 µM D1 and 4 µM MTC in 10 mM Tris-Ac buffer solution (pH 6.5, with 5 mM NaNO3) were used as the initial state; 0.1 µM PbCl2 and 5.5 µM AgNO3 were employed as the data inputs; and 4 µM D2 with 10 mM KNO3 was employed as the address input. For the DC, 7 µM D1 and 4 µM MTC in ultrapure water were used as the initial state; 50 µM PbCl2 and 100 µM NiSO4 were employed as the inputs.

RESULTS AND DISCUSSION The changes of DNA conformation and MTC assembly behaviour. Apart from the traditional double helix, DNA can

self-assemble to various multi-stranded structures, such as triplex, G-quadruplex, i-motif and DNA junction.29,30 In this work, we designed a G (guanine)-rich D1 (5′GGTGGTGGTGGT-3′) and a complementary C (cytosine)rich D2 (5′-CCACCACCACCACAACCACCACCACCAAA-3′) as the building blocks of the logic platform (Figure 1). It has been observed that either Pb2+ or K+ can induce single-stranded D1 to form G-quadruplex while Ni2+ presents an opposite function, suppressing the formation of G-quadruplex. Meanwhile, Ag+ or H+ can fold D2 into i-motif structure (Figure 1A and S5). To execute the desired functions properly, D1 and D2 are designed to content the stability order of D2 i-motif > D1D2 complex > D1 G-quadruplex. The stabilities are exemplified by melting experiment, polyacrylamide gel electrophoresis (PAGE) and circular dichroism (CD) (Figure S6-S8). To produce detectable signals, MTC [3,3'-di(3sulfopropyl)-4,5,4’,5’-dibenzo-9-methyl-thiacarbocyanine triethylammonium salt] (Figure 1B) was introduced into the platform. Our previous work showed that MTC is an excellent fluorescence probe for DNA G-quadruplex.31,32 Normal singlestranded or double-stranded DNA can hardly enhance MTC fluorescence while certain G-quadruplex can disassemble MTC aggregates and dramatically enhance its monomeric fluorescence emission (typically at 610 nm, termed M-FI) (Figure S9A). Besides the interaction with specific DNA structures, MTC can also self-assemble into various supramolecular aggregates, providing extra signal types.33-35 For example, in aqueous solution, MTC is primarily in the form of dimer (typical absorption peak near 532 nm, termed D-band), while in neutral Tris-HCl buffer solution it is in J-aggregates


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Analytical Chemistry (typical absorption peak around 655 nm, termed J-band),the typical emission for which is around 660 nm.32,33,36 Moreover,

metal ions Ni2+ and Pb2+ can facilitate actual detectability. As shown in Figure 3, in the pH 7.0 condition (A=0), the MTC H-band is the detecting signal. A good

Figure 2. (A) Schematic illustration of the implementation of the 1-to-2 DEMUX. (B) The normalized MTC H-band and M-FI as the outputs of the 1to-2 DEMUX. (C) The truth table of the 1-to-2 DEMUX logic operation.

MTC assembling into J- and H-aggregates (typical absorption peaks around 475 nm and 440 nm, termed H-band), respectively. In short, MTC can present at least four different assembly states under certain conditions, and correspondingly, provides four distinguishable output channels, i.e., M-FI, Dband, J-band and H-band. These unique assembly and spectral properties make MTC an excellent signal transducer in our system. The DEMUX: detecting Pb2+ in neutral/acid conditions. A demultiplexer (DEMUX) consists of a couple of input and output data channels, as well as address (A) inputs that act as rotary switches. It implements data splitting function and plays a central role in electronics, telecommunication and signal processing systems.21,37 In this work, we constructed a simplest DEMUX (termed 1-to-2) which can split the input data (Pb2+) into two output channels according to the “state” of A (pH value) (Figure 2). According to the expected logic function, Pb2+ and H+ (pH) are regarded as the data input and A input, respectively. As shown in Figure 2A, MTC and D1D2 complex are designed as the initial state. MTC H-band (448 nm) and M-FI (616 nm) signals are considered as the two outputs (O1 and O2). The normalized H-band and M-FI of 0.3 is defined as the threshold value. In the case of A=0 (pH 7.0), since D1D2 is more stable than D1 G-quadruplex, Pb2+ cannot unwind D1D2 complex but convert MTC from J-aggregates to H-aggregates, presenting O1 = 1 and O2 = 0. In contrast, when A=1 (pH 4.0), H+ would induce D2 to fold into i-motif structure and unwind D1D2 complex. Consequently, Pb2+ induces the released D1 to Gquadruplex, resulting in the disassembly of MTC aggregates, as well as its strong fluorescence emission. In this case, O1 = 0 and O2 = 1. The absorption and fluorescence spectra in all input situations were shown in Figure S10 and the normalized H-band and M-FI were plotted as bar charts in Figure 2B, which satisfy the logic requirement of 1-to-2 DEMUX (the truth table was shown in Figure 2C). The DEMUX is a sensor prototype that can split Pb2+ detecting signal in various pH conditions. We further tested its

Figure 3. (A) The absorption spectra of different concentration of Pb2+ and (B) the titration curve of Pb2+ in pH 7.0, 10 mM Tris-HCl buffer solutions. (C) The fluorescence spectra of different concentration of Pb2+ and (D) the titration curve of Pb2+ in pH 4.0, 10 mM Tris-HCl buffer solutions. The red and black lines are the fitting curves.

linear correlation between the H-band and [Pb2+] ranging from 0.5 to 1.75 µM is obtained (Figure 3B, red line). The

linear coefficient R2 = 0.99963. When pH=4.0 (A=1), the MFI is the detecting signal and it is in direct proportion to [Pb2+] in the range of 0-1.5 µM (R2 > 0.998) (Figure 3D, black line). By comparison, it can be seen that the M-FI signals in pH 7.0 are no more than that of the zero point in pH 4.0 (Figure 3D, red dots), and the H-band signal in pH 4.0 is invariably less than 0.02 (Figure 3B, black dots), indicating an excellent signal splitting ability of the DEMUX. Following the 3σ criteria, the detection limit of Pb2+ in neutral condition is about 40 nM and in acid conditions is about 29 nM, both of them are lower than the permitted maximum level of Pb in drinking water (72 nM) regulated by the U.S. Environmental Protection Agency (USEPA). The MUX: selective detecting Pb2+ or Ag+. Multiplexer (MUX) executes an opposite function to DEMUX, which can receive different input flows selectively, depending on the state of the address (A) input(s).38 Here, by changing the initial state of DNA, we reconfigured the DEMUX to a 2-to-1 MUX. The MUX is designed to pick out one of the specific data from the two input channels (Pb2+ and Ag+) and used as a sensor to selective detect Pb2+ or Ag+ (Figure 4). To meet the detection requirements, Pb2+ and Ag+ are defined as the parallel data inputs. As shown in Figure 4A, MTC and D1 are designed as the initial state, D2 with 10 mM KNO3 as the A input and the MTC M-FI signal as the output (O). Same as the DEMUX, the normalized M-FI of 0.3 is defined as the threshold value.

As shown in Figure S11, MTC is primarily in the form of Jaggregates in Tris-Ac (10 mM, pH 6.5, with 5 mM NaNO3) buffer solution, presenting an emission peak around 660 nm. In the case of A=0, Pb2+ converts D1 into G-quadruplex, and consequently, partly disassembles MTC J-aggregates into



monomer and enhances the M-FI signal significantly, indicating O=1. In contrast, Ag+ causes no interference with the system, leading to O = 0. When A=1, adding D2 would complement D1 to D1D2 complex, thus the induction of Pb2+ to D1 is suppressed, while Ag+ can unwind D1D2 complex and further induce D2 to fold into i-motif. In this situation, inputting Pb2+ would lead to

Figure 4. (A) Schematic illustration of the implementation of the 2-to-1 MUX. (B) The normalized MTC M-FI as the output of the 2-to-1 MUX. (C) The truth table of the 2-to-1 MUX logic operation.

O = 0; while inputting Ag+ can release D1, which can then fold into G-quadruplex under the effect of K+, leading to O =1. In short, Pb2+ takes precedence over Ag+ and is detectable when A=0, but when A=1 only Ag+ can be detected. The normalized M-FI were plotted as bar charts in Figure 4B, which satisfy the logic requirement of MUX (the truth table was shown in Figure 4C). Further, we also use the MUX prototype as a sensor to selective detection of Pb2+ or Ag+. As shown in Figure 5, in the Pb2+ detecting mode (A=0), M-FI signal is gradually enhanced along with the increased [Pb2+] and an excellent linear correlation from 0 to 500 nM (R2 > 0.999) (red line in Figure 5B) is obtained, while Ag+ can hardly cause any M-FI signal. Likewise, in the Ag+ detecting mode (A=1), the M-FI is in direct proportion to [Ag+] in the range of 1 to 8 µM (R2 > 0.988) (black line in Figure 5D), while Pb2+ cannot enhance the M-FI signal. It is noticed that in both situations, the fluorescence of MTC J-aggregates is slightly increased and proportional to neither Pb2+ nor Ag+ equivalent, which may be caused by the side effect of the M-FI signal enhancement. Though the Jaggregates signal exists in the fluorescence spectra, the M-FI signals were not affected. And the results show that the constructed MUX performs effectively in data selection. Following the 3σ criteria, the detection limit of Pb2+ and Ag+ are 15 nM and 191 nM, respectively, both of which are lower than the permitted levels of Pb and Ag (72 nM and 460 nM, respectively) in drinking water by USEPA,39 indicating the sensor has potential to be applied in practice. The DC: simultaneous testing Pb2+ and Ni2+. As both the DNA oligos and MTC supramolecule can response to various

targets, the system could also be reconfigured to other advanced logic devices and perform more types of intelligent analyzing modules. Decoder (DC) is an important logic circuit that can exponentially covert correlated data into output signals and has been widely utilized in data storage, information transmission and telecommunication. According to its function, each output of

Figure 5. (A) The fluorescence spectra of different concentration of Pb2+ and (B) the titration curve of Pb2+ in the A=0 context. (C) The fluorescence spectra of different concentration of Ag+ and (D) the titration curve of Ag+ in the A=1 context. The red and black lines are the fitting curves.

DC can present one specific input combination mode, making it has great potential in correlate-targets analysis.21,40 However, it is so difficult to screen multiple independent outputs that only a few DC systems have been reported till now33 and none of them have been used in practical. Hence, we further reconfigured the DEMUX to a 2-to-4 DC and employed it to simultaneous analyze Pb2+ and Ni2+. As shown in Figure 6A, Pb2+ and Ni2+ are designed as the input data, MTC and D1 are designed as the initial state, and the four unique spectral signals of MTC, i.e., D-band (517 nm), J-band (643 nm), H-band (453 nm) and M-FI (616 nm), are exploited as the four parallel outputs. In the initial state, MTC is primarily in the form of dimer in aqueous solution. After inputting Pb2+, as described above, MTC dimer is totally disassembled to monomer by D1 Gquadruplex. In the presence of Ni2+, the D1 G-quadruplex cannot be formed and MTC assembles into J-aggregates under the effect of Ni2+. In the case of inputting Pb2+ and Ni2+ together, since the formation of D1 G-quadruplex is suppressed by Ni2+, the assembly behaviour of MTC is dominated by Pb2+, presenting H-aggregates. The absorption and fluorescence spectra in all input situations were shown in Figure S12 and the normalized outputs were plotted as bar charts in Figure 6B. Setting the threshold at 0.3, the outputs satisfy the logic requirement of 2-to-4 DC (the truth table was shown in Figure 6C). In brief, in the 2-to-4 DC sensor, the M-FI signal shows the existence of Pb2+, the J-band shows the existence of Ni2+ and the H-band indicates the coexistence of both ions. Although the features of the sensor make it more suitable for qualitative analysing multiple targets, its quantitative detectability was also verified preliminarily. Based on our design, Pb2+ detection


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Analytical Chemistry channel in the DC system is the same as that in the MUX and the detectability has been shown in Figure 5B. For Ni2+ channel, the ratio of J-band/D-band is utilized as the detecting index of Ni2+ and the detection limit is about 370 nM (Figure S13). In our effort to construct the three advanced DNA logic circuits, i.e. the DEMUX, MUX and DC, their information processing capability and multi-target detectability have been demonstrated. Through the delicate design of DNA, both the

platform for the realization of intelligent sensors of Pb in different contexts. Benefiting from the data flow splitting function of DEMUX, the developed sensor can detect Pb2+ in different pH conditions. By utilizing the data flow selecting function of MUX, the selective sensor for Pb2+ and Ag+ has been realized. Further, the logic system can also be reconfigured to implement DC function and used to simultaneous analyze Pb2+ and Ni2+. All the three sensors based on the logic prototypes present practicable sensitivities and specificities, indicating their excellent potential in environmental monitoring, biochemical analysis and medical diagnosis. Moreover, owning to its reconfigurability, flexibility and scalability, the DNAsupramolecule logic platform could also be expanded to developing sensors with more analyzing targets and more intelligent functions.

ASSOCIATED CONTENT Supporting Information. The identification of MTC, stability order of the DNA oligos, the spectra of the DNA logic devices and the sensitivity and specificity of the sensors.

AUTHOR INFORMATION Corresponding Author Figure 6. (A) Schematic illustration of the implementation of the 2-to-4 DC. (B) The normalized MTC D-band, M-FI, J-band and H-band as the outputs of the 2-to-4 DC. (C) The truth table of the 2-to-4 DC logic operation.

rotary switch functions of DEMUX and MUX and the decompress function of DC were finely performed, endowing the sensors good selectivity to detect the corresponding metal ions. As shown in Figure S14, a variety of environmentally relevant metal ions and their mixture with Pb2+/ Ni2+ were tested as interferents, and the results indicate that all the sensors present excellent anti-interference features. By introducing supramolecular reporter, the interference among multiple reporters can be avoided, and the signal differentiation process is simplified. This feature is of importance in constructing advanced multi-output logic circuits, especially in the DC construction. For example, Wang et al.21 succeed in constructing a DNA-based 2-to-4 DC utilizing four different fluorescent groups/probes, including FAM (6carboxyfluorescein), NMM (N-methyl mesoporphyrin IX), HEX (hexachlorofluorescein) and Excimer. However, due to the partially overlapped signals of FAM and HEX, the operation performance and further practical application of the DC are limited. In our work, the MTC assembly states present unique and well-separated spectra bands that ensures excellent performance of the DC and the sensor for analysing Pb2+ and Ni2+. In addition, for the flexibility and reconfigurability of DNAsupramolecule platform, it is expected that through altering the inputs and nucleotide sequence, the platform can be further extended not only to targeting more chemical and biochemical analytes, but also to implementing other advanced logic functions with intelligent analysing modules.

CONCLUSIONS In summary, we have designed a DNA-supramolecule logic

* E-mail: [email protected]. Tel: +86-17780501019

Author Contributions ‡These authors contributed equally.

Notes The authors declare no competing financial interest.

ACKNOWLEDGMENT This work is supported by the National Natural Science Foundation of China (31400702), the Henan Key Scientific Research Project (18A150049), the Fundamental Research Funds for the Central Universities and the Graduate Student's Research and Innovation Fund of Sichuan University (2018YJSY051). The kind assistance of Prof. Peng Wu from the Analytical & Testing Center at Sichuan University with the CD measurements was greatly appreciated.

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