BY-NC-ND 3.0 license Open Access Published by De Gruyter August 26, 2016

Electrochemical aptasensors for detection of small molecules, macromolecules, and cells

Kun Han, Tao Liu, Yuanhong Wang and Peng Miao

Abstract

Aptamers are a kind of special nucleic acids that have the ability to bind various targets (e.g. small molecules, macromolecules, and cells) with high affinity and specificity. As a type of efficient recognition component in analytical designs and applications, aptamers have gained intense achievements in the designs of biosensors. Especially, the past few years have witnessed the fast development of electrochemical aptasensors. In this mini-review, we summarize recent progresses in electrochemical biosensors based on aptamers. Different targets and the corresponding detection principles are introduced. The methods to enhance detectable signals are mentioned including the employment of nanomaterials. Also, some possible limitations and future perspectives are discussed.

Introduction

Nucleic acids belong to biological polymers that possess the functions of genetic information propagation and storage (de Jong et al. 2001). Besides acting as hereditary materials, artificial nucleic acids named as aptamers have been selected and synthesized as bio-elements for recognition purposes (Hermann and Patel 2000). Usually, aptamers are short, single-stranded DNA/RNA oligonucleotides that can fold into certain three-dimensional conformations for recognition, which are selected by an in vitro selection and amplification technique (systematic evolution of ligands by exponential enrichment, SELEX) (Li et al. 2014, Wu et al. 2015, Zhu et al. 2015b). Table 1 lists some examples of targets and corresponding aptamer sequences. So far, many techniques have been developed to select aptamers such as capillary electrophoresis (Yunusov et al. 2009), magnetic bead-assisted SELEX (Tok and Fischer 2008), whole-cell SELEX (Cerchia et al. 2005), capture SELEX coupled with surface plasmon resonance (SPR) (Spiga et al. 2015), microfluidic-based SELEX (Lin et al. 2014), and so on. Detailed information about binding sites and preferences for the targets can be obtained by performing high-throughput sequencing of SELEX pools (Dupont et al. 2015).

Table 1:

Examples of various targets and corresponding aptamers.

TargetAptamer sequence (5′-3′)Ref.
Small molecules
 Zn2+GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC(Ciesiolka et al. 1995)
 As3+GGTAATACGACTCACTATAGGGAGATACCAGCTTATTCAATTTTACAGAACAACCAACGTCGCTCCGGGTACTTCTTCATCGAGATAGTAAGTGCAATCT(Song et al. 2016)
 Pb2+GGTTGGTGTGGTTGG(Lei et al. 2015)
 Cholic acidAGCGCCGATTGACCCAAATCGTTTTGTATGCAAAAGCGCT(Kato et al. 2000)
 ATPACCTTCCTGGGGGAGTATTGCGGAGGAAGGT(He et al. 2011)
 Ochratoxin ACGGGTGTGGGTGCCTTGATCCAGGGAGTCTCTAATC(Soh et al. 2015)
 CocaineGGGAGACAAGGAAAATCCTTCAATGAAGTGGGTCGACA(Soh et al. 2015)
 EstradiolGCTTCCAGCTTATTGAATTACACGCAGAGGGTAGCGGCTCTGCGCATTCAATTGCTGCGCGCTGAAGCGCGGAAGC(Soh et al. 2015)
 ChloramphenicolACTTCAGTGAGTTGTCCCACGGTCGGCGAGTCGGTGGTAG(Mehta et al. 2011)
Macromolecules
 TNF-αTGGTGGATGGCGCAGTCGGCGACAA(Orava et al. 2013)
 CRPGCCUGUAAGGUGGUCGGUGUGGCGAGUGUGUUAGGAGAGAUUGC(Wang et al. 2011)
 ThrombinAGTCCGTGGTAGGGCAGGTTGGGGTGACT(Jung et al. 2013)
 p53 Protein mutantATTAGCGCATTTTAACATAGGGTGC(Chen et al. 2015)
 PDGFCAGGCTACGGCACGTAGAGCATCACCATGATCCTG(Ruslinda et al. 2012)
 VEGFATACCAGTCTATTCAATTGGGCCCGTCCGTATGGTGGGTGTGCTGGCCAGATAGTATGTGCAATCA(Kaur and Yung 2012)
Cells
 CCRF-CEM cellsATCTAACTGCTGCGCCGCCGGGAAAATACTGTACGGTTAGA(Shangguan et al. 2006)
 CD44+ cellsGGGAUGGAUCCAAGCUUACUGGCAUCUGGAUUUGCGCGUGCCAGAAUAAAGAGUAUAACGUGUGAAUGGGAAGCUUCGAUAGGAAUUCGG(Ababneh et al. 2013)
 CD133+ cellsCAGAACGUAUACUAUUCUG(Shigdar et al. 2013)
 MEAR cellsACAGCATCCCCATGTGAACAATCGCATTGTGATTGTTACGGTTTCCGCCTCATGGACGTGCTG(Shangguan et al. 2008)
 HL60 cellsATCCAGAGTGACGCAGCATGCCCTAGTTACTACTACTCTTTTTAGCAAACGCCCTCGCTTTGGACACGGTGGCTTAGT(Sefah et al. 2009)
 PL45 cellsCGCTCGGATGCCACTACAGTGCTAATCTCAAGGGTCGTTCCCGATCACCGAGTCTGAGGCTGG(Champanhac et al. 2015)

Aptamers endowed with functional groups that mimic amino acid side chains can expand the chemical diversity (Gold et al. 2010, Rohloff et al. 2014). The resulting modified aptamers create unique intramolecular motifs and can contact with proteins directly. Nucleic acid-based ligands and protein-based ligands can then be substantially bridged. Aptamers have high affinity towards a variety of target analytes, including small molecules (Huizenga and Szostak 1995, Radi and O’Sullivan 2006), macromolecules like proteins (Pavlov et al. 2004, Centi et al. 2007), and even whole cells (Farokhzad et al. 2004, Smith et al. 2007). The binding affinity of aptamers and targets rivals that of antibodies and antigens. One of the most remarkable structural characteristics of nucleic acids is the specific base pairing, which helps the design of various aptamer sensors. Additionally, many other favorable characteristics, such as ease of synthesis and isolation, low cost, high resistance against denaturation, small size, and low immunogenicity (Cansiz et al. 2015, Lao et al. 2015, Roy et al. 2015), make aptamers promising candidates for further applications, which are developing rapidly (Han et al. 2010, Zhu et al. 2015a, Kim et al. 2016).

Considering the antibody-like affinity to biomolecules, aptamers are taken into several promising researches. Aptamers can be employed for delivery and then controlled release of targets like small interfering RNAs to improve corresponding therapeutic efficacy and safety (McNamara et al. 2006, Zhang et al. 2015). Wang et al. (2015a) designed a closed-loop aptamer to inhibit thrombin activity, which can be restored with near-infrared light to increase solution temperature and then disrupt the closed-loop structures using gold nanorods as photothermal agents. This aptamer-based strategy for protein activity regulation may have broad applications in biological mechanisms study.

Aptamers, taken as recognition elements, are playing important roles in the design of colorimetric, fluorescent, quartz crystal microbalance, SPR, and electrochemical biosensors (Vance and Sandros 2014, Kavosi et al. 2015, Osypova et al. 2015, Qiu et al. 2015, Wang et al. 2015b, Zhao et al. 2015). Among all these techniques, electrochemical methods are widely incorporated with aptamers-based target recognition due to their advantages such as well-developed theory, facile design, low cost, high sensitivity, easy operation, and so on (Miao et al. 2015a, Dixit et al. 2016). So far, different kinds of electrochemical aptasensors have been developed, which have wide applications for various analytical purposes. Additionally, the employment of nanomaterials like graphene oxide may further assist or improve the analysis (Erdem et al. 2015, Gao et al. 2015).

Herein, in this mini-review, we mainly focus on recent advances in aptamer-based electrochemical biosensors for the detection of small molecules, macromolecules, and cells. Their analytical performances and unique features are introduced. The limitations and future development are also discussed.

Electrochemical aptasensors for small molecules analysis

Small molecules such as ions (Nguyen et al. 2014), ATP (Jia et al. 2015), and hydrogen peroxide (H2O2) (Miao et al. 2015b) have a diversity of physiological and pathological effects, and their aberrant levels have been found to be significantly indicative in various clinical diagnoses.

Miao et al. (2014) developed a K+ aptasensor utilizing the digestion reaction of RecJf exonuclease. A single DNA probe with stem-loop structure was designed and located on the gold electrode through covalent thiol-gold bonds. The probe contained an anti-K+ aptamer sequence, which formed a G-quadruplex structure in the presence of K+. As shown in Figure 1, the destruction of stem-loop facilitated the release of free 5′ end of the DNA probe, which can be further recognized and digested by RecJf exonuclease (Wu et al. 2014). As the reaction proceeded, K+ was returned back to the solution and could bind to another DNA probe with stem-loop structure on the electrode, initiating a new cycle of cleavage. Due to the loss of the electrochemical species (methylene blue, MB), which were labeled on the DNA probe, the signal declined sharply, which could be used to evaluate the concentration of K+. This aptasensor achieved linear detection range from 50 nm to 1 mm and a detection limit of 50 nm. Moreover, other interfering cations such as Na+, Ag+, Ca2+, Fe2+, Fe3+, Zn2+, and Al3+ could be successfully distinguished with little change of the current peak. The limitation was that the aptasensor could not be reused since the DNA probe was digested by exonuclease.

Figure 1: Scheme of the K+ aptasensor based on RecJf exonuclease cleavage.Reproduced by permission of The Royal Society of Chemistry.

Figure 1:

Scheme of the K+ aptasensor based on RecJf exonuclease cleavage.

Reproduced by permission of The Royal Society of Chemistry.

Ochratoxin A (OTA) is one of the most abundant food-contaminating mycotoxins, which is potentially carcinogenic to humans (Giovannoli et al. 2015, Lee and Ryu 2015). Marty’s group realized sensitive analysis of OTA by an aptasensor using differential pulse voltammetry (Mishra et al. 2016). A competition strategy was employed. Free OTA to be detected competed with biotin-labeled OTA to bind with aptamer which was previously modified on the screen-printed carbon electrode. After adding avidin-ALP to generate signals, the percentage of free OTA binding event could be calculated. This aptasensor showed a good linear range from 0.15 to 5 ng/ml with the detection limit of 0.07 ng/ml. It could be further integrated into portable systems for wider applications.

Mao et al. (2015) fabricated an electrochemical biosensing method for ATP analysis based on triple helix forming strategy. Three DNA probes were involved: a signal transduction probe (STP) with the modification of 5′ end MB and 3′ end SH; an aptamer for ATP; and a triplex-forming oligonucleotide probe (Wang et al. 2015d). The three probes contained partial complementary sequences self-assembled on the electrode. MB molecules were distal to the electrode surface; thus, electron transfer (eT) OFF state was exhibited. After the introduction of ATP, the aptamer binded to ATP, and the MB end of STP was liberated and folded back to form a triplex-helix structure. In this case, MB molecules were very close to the electrode surface, and eT ON state was achieved. This simple strategy allowed the detection of ATP with the concentration as low as 7.2 nm and can be extended to detect other targets like thrombin.

Feng et al. (2015) split aptamers and applied sandwich structure to detect ATP. First, ATP aptamer was divided into two parts, and the electrode was modified with only a 14-mer split aptamer. Another 13-mer split aptamer strand was modified with a ferrocene (Fc) tag. It could be localized onto the electrode surface in the presence of ATP, which helped the formation of the sandwich structure. However, this split strategy depended on the aptamer sequence, which could not be extended to detect other targets directly. Due to the fact that ATP-aptamer complex could be dissociated by adenosine deaminase, which efficiently catalyzed the deamination of adenosine (deoxyadenosine) into inosine (deoxyinosine), an inhibit logic gate was operated.

Electrochemical aptasensors for macromolecule analysis

The need for the development of macromolecule biosensors is continuously increasing since macromolecule analysis such as C-reactive protein (CRP) (Eid et al. 2015), matrix metalloproteinase (Lee et al. 2015), and endotoxin (Miao 2013) are important in aspects of public health and food safety. However, selective recognition elements for macromolecules are always difficult to develop. The most commonly used antibodies or enzymes may be restricted to certain targets. Therefore, the development of aptasensors brings new sight for macromolecule analysis.

Thrombin is the critical enzyme in the process of hemostasis and blood coagulation, which have great clinical significance (Koo et al. 2010). Zhao et al. (2014) developed an electrochemical aptasensor for thrombin using a ligase-assisted exonuclease III (Exo III)-catalyzed reaction for signal amplification. As depicted in Figure 2, probe DNA, thrombin-binding aptamer (TBA), and extension strand (E-strand) formed double strands with a ligatable nick between TBA and E-strand, which could be ligated by the catalysis of DNA ligase. Exo III could further recognize the thermostable duplex and degrade DNA probe, releasing the ligated TBA and E-strand to hybridize with other DNA probes, triggering the next round of degradation reaction. Therefore, numerous signal outputs of MBs could be released from DNA probe that were captured by cucurbit[7]uril (CB[7])/gold nanoparticles (AuNPs)/PDDA-modified electrode.

Figure 2: Schematic diagram for the preparation of the thrombin aptasensor based on ligase-assisted Exo III-catalyzed degradation reaction. CB [7], cucurbit[7]uril.Reprinted with permission from (Zhao et al. 2014). Copyright (2014) American Chemical Society.

Figure 2:

Schematic diagram for the preparation of the thrombin aptasensor based on ligase-assisted Exo III-catalyzed degradation reaction. CB [7], cucurbit[7]uril.

Reprinted with permission from (Zhao et al. 2014). Copyright (2014) American Chemical Society.

Platelet-derived growth factor (PDGF-BB) is a cancer-related protein, which is involved in many cell transformation processes including tumor growth and progression (Xie et al. 2014). Recently, Song et al. (2014a) fabricated a disposable electrochemical aptasensor for protein assay. As shown in Figure 3A, they first immobilized the aptamer for PDGF-BB on AuNPs-modified screen-printed electrode (SPE). Second, a sandwich-type reaction occurred on the SPE surface employing in situ hybridization of two kinds of DNA-modified silver nanoparticles (AgNPs), which leads to AgNPs aggregate. Through stripping detection of silver after peroxidation, amplified signals could be obtained to reveal the PDGF-BB level. Moreover, SPE assay chips were tested for logic gate operation of multiple target detection. PDGF-BB and thrombin were applied as the models to demonstrate the successful fabrication of multiplexed protein measurements (Figure 3B).

Figure 3: Scheme of the (A) electrochemical detection and (B) multiplexed electrochemical detection of proteins.Reprinted with permission from (Song et al. 2014a). Copyright (2014) American Chemical Society.

Figure 3:

Scheme of the (A) electrochemical detection and (B) multiplexed electrochemical detection of proteins.

Reprinted with permission from (Song et al. 2014a). Copyright (2014) American Chemical Society.

Tumor necrosis factor-α (TNF-α) is a type of cell-signaling protein, which plays an important role in the regulation of immune cells (Locksley et al. 2001). Dysregulation of TNF-α is implicated in a range of human diseases including cancer, Alzheimer’s disease, and so on (de Oliveira et al. 2015, Hsu et al. 2016). Mazloum-Ardakani et al. (2015) fabricated a simple label-free aptasensor for TNF-α based on the Ag@Pt core-shell nanoparticles/reduced graphene oxide (rGO). AgNPs were firstly loaded on rGO, and Pt shells were further loaded on AgNPs. The nanocomposites were demonstrated to be electrochemically enhanced materials, which were modified on gold screen printed electrodes, electrocatalyzing catechol for signal output in the aptasensor for TNF-α. Good linear range of 0–60 pg ml–1 and low detection limit (2.07 pg ml–1) were achieved.

Endotoxin, also named as lipopolysaccharide, is the major component of the outer membrane of gram-negative bacteria, which can cause a strong immune response (Raetz and Whitfield 2002). To avoid further symptoms of organ failure, shock, or even death, effective endotoxin contamination monitoring methods should be carried out (Inoue et al. 2012, Miao et al. 2013). Kim et al. (2012) tried to harness aptamers for endotoxin detection using electrochemical impedance spectroscopy. They first employed a nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM)-based non-SELEX method to identify aptamers with nanomolar level dissociation constants. Then, they immobilized aptamer self-assembled monolayer on the electrode surface, which was used to interact with endotoxin to be detected. The sensitivity was high with femtomolar level detection limit. This developed aptasensor also had advantages of little cross-interaction reactivity to other molecules such as DNA, RNA, proteins, saccharides, and so on, which showed excellent selectivity.

Electrochemical aptasensors for cell analysis

Recently, fast analysis of cells especially cancer cells can be a critical step in disease diagnosis. To achieve the goal of early diagnosis, it is essential to apply a sensitive method for the detection of certain lesion cells (Zheng et al. 2014).

Wang et al. constructed a label-free electrochemical aptasensor for cancer cell detection with layer-by-layer assembly technology (LAL) (Wang et al. 2015c). Fc-appended poly(allylamine hydrochloride) (Fc-PAH) was a positively charged reversible redox-active probe, which was modified on the surface of graphene matrix through electrostatic interaction, forming Fc-PAH-G composites. Fc-PAH-G not only carried a number of signal probes but also promoted eT; thus, the obtained electrochemical signal could be significantly enhanced. Poly(sodium-p-styrenesulfonate) is a negatively charged polymer and functions as the linker of Fc-PAH-G through LAL (Noh et al. 2015). Aptamer was then assembled on the outmost layer of the electrode via electrostatic interaction, which formed stable G-quardruplex structure afterbound to cancer cells. The attached cells could hinder eT, and the detected current response had direct relationship with the number of adsorbed cells. This aptasensor showed good stability and high sensitivity and selectivity towards the detection of cancer cells.

A multivalent recognition strategy for electrochemical cytosensing by combining concanavalin A (Con A) and aptamer was developed (Chen et al. 2014b). Multivalent strategy has many merits over monovalent interaction, which was proved to possess enhanced affinity by a factor as large as 104–105 (Barboiu et al. 2014, Chen et al. 2014a). Con A was a mannose binding protein, which could interact with mannose or trimannoside, the core oligosaccharide of N-glycan on the cell surface (Dong et al. 2015, Idil et al. 2015). As shown in Figure 4, Chen et al. firstly coated poly(amidoamine) (PAMAM) dendrimers-conjugated rGO on a glassy carbon electrode (GCE), which could not only promote eT rate but also provide multiple groups for further Con A immobilization (Han et al. 2014, Song et al. 2014b). After cell capture by Con A, aptamer and horseradish peroxidase (HRP) dual modified AuNPs could bind to the cells, forming a sandwich structure. Electrochemical catalysis signals of hydroquinone could be largely enhanced by the huge amount of HRP on AuNPs (Rogozhin and Verkhoturov 1999). Moreover, the multivalent recognition strategy promised high selectivity and sensitivity. As low as 10 cells/ml could be detected by this aptasensor.

Figure 4: Schematic illustration of the cytosensor based on multivalent recognition and dual signal amplification.Reprinted with permission from (Chen et al. 2014b). Copyright (2014) American Chemical Society.

Figure 4:

Schematic illustration of the cytosensor based on multivalent recognition and dual signal amplification.

Reprinted with permission from (Chen et al. 2014b). Copyright (2014) American Chemical Society.

Qu et al. also used dual-recognition elements for highly sensitive and selective detection of circulating tumor cells (CTCs) (Qu et al. 2014). CTCs shed from a primary tumor and circulate in the bloodstream. CTCs are responsible for metastases of cancer to distant organs via hematogenous dissemination (Fehm et al. 2002). They are used as clinical biomarkers for the diagnosis and prognosis of various cancers (Myung and Hong 2015, Sugimoto et al. 2015). As shown in Figure 5, two cell-specific aptamers were chosen and modified on GCE via the amide bonds. However, the links between GCE and the two aptamers were different. One was flexible using a single-stranded DNA, and the other was rigid using a double-stranded DNA. The rigid linker might have low binding to graphite and thus kept the aptamer away from GCE surface. Moreover, the linker could also help the upright stature of another linker, which had flexible structure and larger binding efficiency to cells. Additionally, cells could be recognized on the site away from GCE surface, minimizing the steric hindrance. Experimental results confirmed that the dual-aptamer modification strategy had improved sensitivity in comparison with single-aptamer modification strategy. Moreover, other advanced signal probes could be exploited. A single cell in 109 whole blood cells could be detected, making this strategy a promising potential for CTC-related clinical studies and applications.

Figure 5: Scheme of the dual-aptamer modified electrode interface for specific and sensitive detection of MEAR tumor cells.Reprinted with permission from (Qu et al. 2014). Copyright (2014) American Chemical Society.

Figure 5:

Scheme of the dual-aptamer modified electrode interface for specific and sensitive detection of MEAR tumor cells.

Reprinted with permission from (Qu et al. 2014). Copyright (2014) American Chemical Society.

Conclusions and perspectives

This mini-review primarily focuses on recent developments in electrochemical aptasensors for the detection of small molecules, macromolecules, and cells, in which the applications of aptamers are the key points. The targets are mainly of clinical importance. Despite the attractive advantages of aptamers, more work should be done. For example, more aptamers for different targets can be selected and optimized; the mechanisms of aptamer interaction and immobilization should be studied further; novel strategy of the combination of nanomaterials and aptasensors may improve current performances; development of aptamer-based electrochemical biochip is the one option to meet the requirement of point of care test in clinical scenario; more multi-target-sensing strategies are needed; and the future development of high-throughput platform may influence the analytical performance and efficiency significantly.

Funding source: Youth Innovation Promotion Association of the Chinese Academy of Sciences

Award Identifier / Grant number: 2015261

Funding source: National Natural Science Foundation of China

Award Identifier / Grant number: 31400847

Award Identifier / Grant number: 31500805

Funding statement: This work was supported by Youth Innovation Promotion Association CAS (Grant no. 2015261) and the National Natural Science Foundation of China (Grant nos. 31400847 and 31500805).

Acknowledgments

This work was supported by Youth Innovation Promotion Association CAS (Grant no. 2015261) and the National Natural Science Foundation of China (Grant nos. 31400847 and 31500805).

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Received: 2016-3-11
Accepted: 2016-7-1
Published Online: 2016-8-26
Published in Print: 2016-12-1

©2016 Walter de Gruyter GmbH, Berlin/Boston

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