Abstract
Herein, a rapid and sensitive current–volt measurement was developed for identifying the IS6110 DNA sequence to diagnose Mycobacterium tuberculosis (TB). An aminated capture probe was immobilized on a 1,1′-carbonyldiimidazole-functionalized interdigitated electrode (IDE) silica substrate, and the target sequence was detected by complementation. It was found that all tested concentrations displayed a higher response in current changes than the control, and the limit of detection was 10 fM. The sensitivity ranged from 1 to 10 fM. The control sequences with single-, triple-mismatch and noncomplementary sequences showed great discrimination. This rapid and easy DNA detection method helps to identify M. tuberculosis for early-stage diagnosis of TB.
Keywords: Tuberculosis, Surface chemistry, DNA sensor, Interdigitated electrode
Introduction
Tuberculosis (TB) is a widely found life-threatening disease caused by Mycobacterium tuberculosis, mainly attacking the human lungs and further spreading to the brain, kidney and spine (Russell et al. 2008; Brites and Gagneux 2015). Since TB spreads easily through airborne droplets, it is difficult to control its spread, and people with a lower immune response are easily affected by TB (Koch and Mizrahi 2018). This situation makes it mandatory to identify TB at its latent period (earlier stages of TB) (Dorman 2010). Active TB is generally identified by microscopic analysis, chest X-ray and radiological analyses and culture methods (Chan et al. 2000; Russell et al. 2008). These methods are not sensitive enough and consume a relatively long procedure time period, especially with the culturing method. Usually, the latent stage of TB is diagnosed by blood and skin tests (Brock et al. 2004). These tests are expensive and have complicated procedures; moreover, treating TB is difficult due to the necessity of multiple antibiotics when the infection has reached the mature stage. Studies have been finding ways to control TB, and one of the ways is to develop an efficient early diagnostic system before reaching the mature stage of the disease (Shams et al. 2005; Ryu 2015; Lakshmipriya et al. 2016). Different biomarkers such as ESAT and CFB-10 proteins have been used to identify and analyze the condition of TB, but the growth of M. tuberculosis is slow and difficult to identify at the earlier stage (Brock et al. 2001; Hashim 2016). Compared to using protein biomarkers, identifying diseases with nucleic acids brings more advantages, including higher specificity, high sensitivity and selective detection at an early stage (Jolly et al. 2016; Lin et al. 2019; Lv et al. 2019a). In this research, a high-affinity DNA biosensor is shown to detect IS6100 M. tuberculosis insertion gene sequences on an interdigitated electrode (IDE) by complementation analysis on a chemically functionalized surface.
IS6110 is an M. tuberculosis insertion gene sequence belonging to the family IS3 and was first described in 1990 (Millan-Lou et al. 2013). It has been proven that M. tuberculosis strains are characterized by very high copy numbers and repetitive sequences of IS6110, suggesting that IS6110 is a potential biomarker for TB (Alonso et al. 2013). The capture probe and target sequences were designed for the gene IS6110 to diagnose TB (Liu et al. 2014). This kind of DNA sensing application in the field of medical diagnosis is popular due to its high accuracy, compatibility and rapidity. DNA sensors are widely applied not only for the purpose of identifying diseases but also in mutated gene identification, food technology, drug discovery and forensics (Rasouli et al. 2018). In particular, DNA identification by electrochemical sensors exhibits more positive features than other approaches, such as faster, simple and less expensive methods (Drummond et al. 2003). A subsequent study reported DNA detection on an electrochemical sensor based on oligonucleotide immobilization on the electrode sensing surface and detection via hybridization (Teengam et al. 2018). The viability of the sensing system mainly depends on the linkage between the electronic transducer and the nucleic acid. Various physical and chemical methods were used to efficiently immobilize the nucleic acid sequence on the electrode surface (Letchumanan et al. 2019a, b). An IDE is an electrochemical voltammetry sensor that has been used to identify various blood-based biomarkers such as proteins, antibodies, DNA and RNA (Cheen et al. 2017; Ge et al. 2019; Liang et al. 2019). In this research, the IDE sensing surface was chemically functionalized by 1,1′-carbonyldiimidazole to diagnose TB by complementation analysis. Amine modification was used to immobilize the capture sequence on the IDE electrode surface and detect the target sequence of IS6110.
Materials and methods
Reagents and biomolecules
Phosphate-buffered saline (PBS) at pH 7.4, 1,1′-carbonyldiimidazole (CDI) and ethanolamine were purchased from Sigma-Aldrich (USA). A silica wafer was received from Mallinckrodt Baker (USA). The resist developer and positive photoresist were purchased from Futurrex Inc. (USA). The amine probe and target sequences were synthesized and received from a local supplier in Malaysia. The target (5′-AGACCTCACCTATGTGTCGA-3′) and capture sequences (capture probe: 5′-NH2-C6-TCGACACATAGGTGAGGTCT-3′) were adapted from the report by Liu et al. (Liu et al. 2014). Three-dimensional nanoprofiling images were captured as stated by Letchumanan et al. (2019a, b).
IDE sensing surface fabrication by the wet-etching process
The IDE sensing surface was fabricated by the traditional wet-etching process (Ramanathan et al. 2019a). Initially, the silica wafer was cleaned by RCA2 and RCA1 solutions to remove unwanted deposits on the surface. Next, thermal oxidation at 500 °C was carried out for 1 h to oxidize the wafer and form a layer of silicon dioxide (SiO2). Al was deposited on these oxidized layers using an Al-coil in a thermal evaporator. On the Al substrate, the electrode pattern was deposited by the conventional photolithography technique. For this process, positive photoresist was coated on the Al-modified substrate using a spin coater and then soft-baked for 1 min at 90 °C to remove the moisture on the SiO2 surface. The substrate was exposed to ultraviolet (UV) light to transfer the IDE pattern onto the photoresist. The removal of the unexposed area was carried out by dipping the wafer in the photoresist developer. The developed IDE electrode was then hard-baked for 1 min at 110 °C to remove the moisture content and to strengthen the adhesion force between the SiO2 and Al layers. Finally, the unexposed Al layer on the IDE was etched by immersing the substrate in etchant solution containing Al. The fabricated IDE was washed with acetone and distilled water and kept in a dry cabinet for further use.
Probe immobilization on the IDE surface through a chemical linker
The probe for desired target sequence complementation from M. tuberculosis was immobilized on the fabricated IDE surface through a chemical linker. CDI was used as the linker to attach the aminated probe to the surface. Initially, 0.5 M CDI was diluted in 30% hexane, added to the IDE sensing surface and kept for 2 h at room temperature (RT). Then, the surface was washed with distilled water three times to remove the unbound CDI. Next, 1 µM amine probe was dropped on the CDI-modified surface and maintained for 1 h at RT. The excess probe was removed by washing the surface with 10 mM PBS (pH 7.4). All the experimental conditions remained wet, and washing was performed in between each step before the electrical measurements.
Complementation of the target sequence on the probe-modified IDE surface
The target sequence for M. tuberculosis was detected by complementation on the aminated-probe-immobilized IDE surface. Before detection, the probe-modified surface was blocked by 1 µM ethanolamine to cover the unoccupied CDI surfaces. After each washing step, 10 nM target sequence was used to interact with the surface. Changes in the current were noted before and after immobilization of the target sequence.
Limit of detection with the target sequence on the probe-modified IDE surface
The detection limit of the target sequence was analyzed by titrating from the lowest femtomolar to nanomolar level by separately interacting each concentration with the probe-modified IDE surface. The highest concentration of the target sequence was chosen to be 10 nM, which was decreased by ten-fold dilutions until reaching 10 fM. These diluted solutions containing the target sequences were dropped individually on the probe immobilized IDE surface and maintained for 15 min at RT. After the washing steps, the current reading was recorded to find the detection limit. The difference in the current before and after immobilization was plotted by Excel to find the limit of detection. A linear regression analysis was performed on the plotted data.
Selective detection by control experiments
Selective detection of the targeted sequence was evaluated by the control sequences, namely, single-mismatch, triple-mismatch and noncomplementary target sequences. These sequences (10 nM) were diluted in PBS and dropped individually on the aminated-probe surfaces, which were blocked by 1 M ethanolamine. The current changes of the specific target sequences were compared.
Results and discussion
In this research, a method for TB diagnosis was demonstrated by complementing the target sequence of IS6110, which was found to have a very high copy number in the causative microbe, Mycobacterium tuberculosis. The capture probe was immobilized on the IDE sensing surface through chemical modification and detected its target sequences (Fig. 1). As shown in Fig. 2, the amine-ended capture probe was immobilized on the IDE surface through the CDI chemical linker. The carbamate linkage in CDI can interact with the amine-ended capture probe; at the same time, CDI can link to the silica surface without any intermediate steps. Through this chemistry, compared to the coverage in other systems, a larger number of capture probes have been immobilized on the IDE surface, improving the detection of targets (Lv et al. 2019b; Zheng et al. 2019). As shown in the figure, the molecular attachment via surface chemistry was confirmed by 3D nanoprofiling.
Fig. 1.
Schematic representation for detection of the target sequence from the IS6110 gene. The capture probe was immobilized on the IDE surface through a CDI chemical linker and was used to detect the target sequence. The dipole moment mechanism involved on the surface is shown. The IDE sensor is shown with molecular interactions and surface changes
Fig. 2.
Representation of the chemical linker and complementation on IDE. The insets display the molecule immobilization on the bare device by 3D nanoprofiling. Further differences have been shown by surface images with molecular attachment
Efficient immobilization of the aminated probe on the IDE surface by a chemical linker
The aminated probe was immobilized on an IDE sensing substrate through a chemical linker to complement the target sequence for M. tuberculosis. CDI was used as the linker between the IDE surface and the aminated probe. Figure 3a displays the voltammetry changes with the step-by-step process of aminated-probe immobilization on the IDE surface. As shown in the figure, only the bare IDE surface shows a current level of 3.20E−09 A. After the surface was modified by CDI, the current level was increased to 3.48E−08 A. This change in current confirmed that the surface of IDE was modified by CDI. Then, 1 µM aminated probe was dropped on the CDI-modified surfaces, and the current level reached 6.89E−08. This change happened due to the interaction of the aminated probe with CDI. After each immobilization process, the current level was gradually increased, indicating the proper immobilization of the probe sequence on the IDE sensing surface (Fig. 3b).
Fig. 3.
Capture probe immobilization on the IDE surface. a Current changes for each immobilization. b Difference in current change with each immobilization step. Differences are based on the charges on the molecules. Averaged data from triplicate experiments (n = 3) are shown
Complementation of the capture probe and specific target of the M. tuberculosis sequence
The model for TB diagnosis was shown by identifying the interaction between the probe and target sequence of M. tuberculosis. A 10 nM target sequence was dropped on the aminated-probe-immobilized IDE surface followed by blocking with ethanolamine. As shown in Fig. 4a, the ethanolamine-modified surface shows a current level of 7.47E−08. A small current change after ethanolamine addition was noted due to the high coverage of the aminated probe on the CDI surface. When this ethanolamine-modified surface interacted with 1 nM target sequence, the current level was 1.56E−07. The difference in the current was 7.23E−08, clearly indicating the complementation of the target with the probe sequence.
Fig. 4.
Probe-target complementation analysis. a Target sequence (10 nM) detection by the capture probe. Target-capture complementation was shown by increasing current levels. b Dose-dependent detection of the target sequence. Different concentrations of target were detected on a similar concentration of the capture probe. With increasing target concentrations, the current levels increased. The figure inset is the enlarged profile. The arrow indicates the direction of changes
Detection limit of the complemented target with the probe sequence on the IDE surface
To find the detection limit of the complemented target with the probe sequence on the IDE sensing surface, the target sequence was titrated from 1 fM to 10 nM by testing each concentration independently. Figure 4b shows the complementation of different concentrations of the target sequence on the probe sequences. When 1 fM target was added on the surface, no clear change in current was noticed. After increasing the concentration to 10 fM, the current level started to increase from 7.47E−08 to 9.06E−08. This change in current confirms the detection of 10 fM target sequence by the specific probe. With a further increase in the concentration, the current levels increased concomitantly. The changes in current were noted for 10 fM, 100 fM, 1 pM, 10 pM, 100 pM, 1 nM and 10 nM, which were 0.15, 0.3, 0.42, 0.60, 0.72 and 0.85E−07, respectively. It was clearly noted that with an increase in the target sequence concentration, the current levels and the corresponding differences also gradually increased (Fig. 5a). The differences in the current changes were plotted by linear regression, and the detection limit was 10 fM for the target sequence using the 3σ estimation (Fig. 5b).
Fig. 5.
Sensitivity analysis by complementation. a Current level for each target sequence concentration by complementation with the capture probe. Averaged data from triplicate experiments (n = 3) are shown. The figure inset presents a diagrammatic explanation. b Differences in current changes for each target sequence concentration. A linear regression analysis was performed. The limit of detection is indicated, as determined by 3σ estimation
Selective detection of the target sequence on the IDE surface by complementation
Control experiments were carried out with single- and triple-mismatch sequences and noncomplementary target sequences (Fig. 6a). For that purpose, 1 nM diluted control sequences were independently complemented on the capture probe-modified IDE surfaces, and the changes in current were recorded after the washing steps. As shown in Fig. 6b, the control sequences did not show any significant changes in current; at the same time, the target sequence displayed a clear increase in the current due to its complementation with the capture probe. This result indicates the selective detection of the target sequence from IS6110, which helps to selectively detect M. tuberculosis on the IDE sensing surface.
Fig. 6.
Selective detection of the target sequence. a Diagrammatic representation; b I–V quantitative measurements. Control experiments were performed with single-, triple-mismatch and noncomplementary sequences of the target sequence with a capture probe for comparison. Only the target sequence shows the current change, indicating selective detection. Averaged data from triplicate experiments (n = 3) are shown
In the past, similar sensing strategies have been used for DNA-based probe–target complementation, displaying different levels of sensitivity and selectivity. The levels of discrimination are primarily due to the sequence complementation and involvement of third oligonucleotide sequences to complement the sandwich pattern. The range of sensitivities falls between low-attomolar and low-femtomolar levels (Lv et al. 2019a, b; Lin et al. 2019). On the other hand, comparing these strategies with the ‘gold-standard’ enzyme-linked immunosorbent assay involving proteins, the DNA-based IDE sensors shown in past and current studies displayed a higher performance and reached more than 10,000-fold higher sensitivity (Lakshmipriya et al. 2016; Ramanathan et al. 2019a, b). Even sensing strategies using nanoparticle-mediated signal enhancements for the detection of TB have shown less sensitivity (Wang et al. 2018). Overall, the present work has proven the ideal sensitivity and selectivity for detecting and discriminating TB against other closely related diseases.
Conclusion
In this research, the target sequence designed from IS6110 was found to have the highest copy number and is a highly repetitive sequence in M. tuberculosis. An amine-ended capture probe was immobilized on an interdigitated electrode sensing surface and used to detect the target sequence. The detection limit for the target sequence complementation was found to be 10 fM, with a sensitivity of 1–10 fM. The control experiments with single-, triple-mismatch and noncomplementary sequences did not show significant current changes, indicating the specific detection of the target sequence.
Author contributions
The authors are contributed to the preparation of the manuscript and discussion. All authors read and approved the final manuscript.
Compliance with ethical standards
Conflict of interests
The authors declare that they have no competing interests.
Contributor Information
Shu Xu, Email: xianxiongkexushu@sina.com.
Yu Xue, Email: xueyueglantine@sina.com.
Fengyan Guo, Email: guofengyanzy@sina.com.
Miaomiao Xu, Email: xumiaomiaoky@sina.com.
Subash C. B. Gopinath, Email: subash@unimap.edu.my
Xiaohui Mao, Email: xaxkmxh@sina.com.
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