Comparison of the nucleic acid based biosensors.
\r\n\tEqually important are the consequences deriving from the extraordinary nature of the present times. The COVID-19 pandemic and the restrictive measures to contain the infection (lockdown and "physical distancing" in primis) have revolutionized the lives, and a distortion/modification of habits, rhythms, arrangements will continue to be necessary.
\r\n\tGovernments have implemented a series of actions to mitigate the spread of infections and alleviate the consequent pressure on the hospital system. On the other hand, the Covid-19 pandemic has caused a series of other cascading effects that will probably be much more difficult to mitigate and which expose to complex consequences. The past two years have brought many challenges, particularly for healthcare professionals, students, family members of COVID-19 patients, people with mental disorders, the frail, the elderly, and more generally those in disadvantaged socio-economic conditions, and workers whose livelihoods have been threatened. Indeed, the substantial economic impact of the pandemic may hinder progress towards economic growth as well as progress towards social inclusion and mental well-being.
\r\n\t
\r\n\tAlthough in all countries the knowledge on the impact of the pandemic on mental health is still limited and mostly derived from experiences only partially comparable to the current epidemic, such as those referring to the SARS or Ebola epidemics, it is likely that the demand for intervention it will increase significantly in the coming months and years. The extraordinary growth of scientific research in the field of neuroscience now offers the possibility of a new perspective on the relationship between mind and brain and generates new scenarios in understanding the long wave of the pandemic and in the prospects for treatment. Moreover, the pandemic also has led to opportunities to implement remote monitoring and management interventions.
\r\n\t
\r\n\tOverall this volume will address the complex relationship existing between COVID-19, mental health, acquired knowledge, and possible interventions taking a highly multidisciplinary approach; from physiological and psychobiological mechanisms, and neuromodulation through medical treatment, psychosocial interventions, and self-management.
Autophagy is an intracellular process whereby cells break down long-lived proteins and organelles and is morphologically characterized by the formation of many large autophagic vacuoles in cytoplasm [1]. This evolutionary process is conserved across all eukaryotic cells and is fundamentally important in normal and pathological cell physiology and development [2, 3]. Autophagy occurs constitutively at a basal level in quiescent cells but the process may be up-regulated during periods of starvation [4] and in response to other stress stimuli [5]. Many recent studies also suggest the increasing association of autophagy in numerous physiological and pathological conditions such as neurodegeneration, death of cancer cells, tissue formation and host cells response to pathogens [5].
The process of autophagy begins with the formation of isolation membrane or phagophore followed by sequestration of organelles or part of the cytoplasm to form autophagosome. The double-membrane autophagosome subsequently fuses with lysosome to form autolysosome where its content are degraded and released into the cytoplasm [6]. Several important autophagy related genes (
Vegetative
Our study has provided evidence that autophagy was involved in anthrax pathogenesis. These results are briefly described below.
RAW 264.7 murine macrophage cells were transfected with pEGFP-LC3. The transfected cells were treated with anthrax LT. The existence of autophagy was identified by immunoblotting, fluorescent punctuate counting, formation of acidic vacuoles, and viability of the LT treated cells.
Increased in AVO formation is a typical feature observed in cells undergoing autophagy [16]. Hence, we examined the effect of LT on AVO formation in RAW 264.7 cells by using lysosomotropic agent acridine orange (AO). RAW 264.7 cells treated with LT displayed a dose-dependent increase in AVO formation [17].
Atg8 is an ubiquitin-like protein that undergoes conjugation process during autophagy and is determined to be an essential component for autophagy [7]. LC3 is the human orthologue of Atg8 and is also the most widely used protein marker for detecting autophagic organelles. During autophagy, cytosolic LC3-I is linked to phosphatidylethanolamine (PE) to form LC3-II and remain tightly bound to the autophagosomal membranes [8]. This process can be indirectly monitored through the use of reporter protein GFP conjugated to LC3 [18]. In order to determine if LT induces autophagy, we overexpressed GFP-LC3 in cells and observed for fluorescent punctuate distribution of GFP-LC3, which represent autophagosome formation.
Transfection of cells with GFP-LC3 for fluorescence microscopy analysis is widely used to detect autophagosome. Stable GFP-LC3 expressing RAW 264.7 cells were treated with anthrax LT for 2 hours and exhibited increased GFP-LC3 punctuates distribution whereas untreated cells displayed a diffuse GFP-LC3 appearance (Figure 1) [17]. These punctuate fluorescent dots indicate autophagosomes formation. Most of these fluorescent dots were probably autophagosomes as autolysosomes had weaker or no fluorescence signals due to the presence of lower LC3-II proteins [8]. The reduced LC3-II level in autolysosome may be possibly due to degradation or recycling back to cytosolic LC3-I [8]. The punctuate distribution of GFP-LC3 in LT treated cells were similar to those treated with rapamycin which serve as positive control for autophagy induction. Rapamycin binds to and inhibits mammalian target of rapamycin (mTOR), a negative regulator of autophagy [5]. Nutrients starvation is also able to trigger autophagy. Accordingly, cells incubated in nutrient free salt solutions, EBSS, for 2 hours showed punctuate distribution of GFP-LC3. Autophagy induced by nutrients starvation produced more intense fluorescence punctuates compared to rapamycin or LT treated cells [17].
During autophagy, processing of cytosolic LC3-I to LC3-II permits autophagosomal membrane recruitment through an autophagic specific conjugation. As the amount of LC-II correlates with the extent of autophagosome formation [8], immunoblotting of LC3-II can be used to determine autophagy induction. To further corroborate that the GFP-LC3 punctuate observed was indeed autophagy induction by LT, we therefore examined the endogenous LC3-II levels in LT-treated cells.
RAW 264.7 cells were pre-treated with E64d and pepstatin A for 1 hour to inhibit lysosomal proteases followed by incubation with LT for 1 and 3 hours. At both time points, increase of LC3-II level from LT treated cells were detected, although the ratio differs from 1 to 3 hours after incubation (Figure 2A) [17]. It is not unusual to observe fluctuation of LC3-II level across various time point during autophagy induction [20].
We further determined if LT components could also induce autophagy individually. Treatment of cells with PA alone showed moderate increase of LC3-II while LF alone produced similar ratio of LC3-II / actin as control cells (Figure 2B) [17]. RAW 264.7 cells treated with LT for 1 hour showed elevated amount of endogenous LC3-II (Figure 2B). These observations are generally consistent with the fluorescent punctuate count in GFP-LC3 transfected RAW 264.7 cells. It may appear obvious that LF did not induce autophagy simply because it is not able to cross cell membrane in the absence of PA although it was reported that a small fragment of LF can enter into the cell cytoplasm without the assistance from PA [21]. Apparently, this mechanism of PA-independent insertion of LF into cytosol did not have an observable effect on autophagy induction at the concentration tested.
Inhibition of autophagy process can be used to investigate the role of autophagy in cellular response to toxins, bacteria or viruses. Depending on the interaction between autophagy mechanism and stimulus, the induction of autophagy may sometimes be beneficial or detrimental to the cells. Autophagy protects cells against
RAW 264.7 cells were treated with 10mM 3MA for 1 hour to inhibit autophagy followed by 2 and 3 hours of incubation with LT. Cells viability as determined by MTS assay showed no differences in 3MA treated and untreated cells (data not shown). This could be attributed to rapid lysis of RAW 264.7 cells when subject to LT treatment. Thus, we decided to use another cell line that is also susceptible to LT induced cell death but at a slower lysis rate than RAW 264.7. LT does not appear to cause instant lysis on human promyelocytic leukemia cell line HL-60 but is cytotoxic when HL-60 cells are differentiated into macrophage-like cells with PMA [23]. Differentiated HL-60 cells were pre-treated with 3MA for 1 hour followed by introduction of LT. Cells pre-treated with 3MA showed accelerated cell death compared to control cells at all the time points tested [17]. This suggests that autophagy may function as a defense mechanism against LT intoxication. While 3MA is often used as a specific inhibitor of autophagy [15], it also has effects on various aspects of metabolism that is unrelated to autophagy [24]. More studies need to be conducted to further understand the role of autophagy in LT intoxication.
LT is recognized as a critical virulence factor in
During autophagy, isolation membranes or phagophores elongate to sequester cytoplasmic components and become enclosed to form a double membrane autophagosome. Herein, we reported LT induced autophagosome formation in cells as demonstrated by the punctuate GFP-LC3 distribution in the cytoplasm and the corresponding increase in the punctuate counts. Another frequently used method as an indicator of autophagy is the monitoring of LC3-II conversion. LC3-II protein associates tightly to autophagosome and was determined to be correlated with autophagosome in cells [8]. Indeed, LT-treated cells displayed enhanced LC3-II conversion, which is a typical representative of autophagosome formation. As expected, PA was determined to be a critical component for autophagy induction. By itself, PA caused a moderate increase in LC3-II levels compared with non-treated controls. This could be attributed to a self-protection response of the host cells upon PA exposure. However, cells treated with LT (PA + LF) caused a dramatic increase in LC3-II levels [17]. This could be mainly the result of cellular stress and defence mechanism against the rapid toxic effects of LT. LT activity is believed to persist longer in the cells than PA alone, as indicated by its continuous enzymatic cleavage of substrate in the cells for 4-5 days [12, 26]. The prolonged presence of active LF in the cytoplasm may possibly play a contributing role in the dramatic increase of autophagy.
Autophagy may function as a defensive mechanism against toxins or invading pathogens but may also be exploited by microbes for survival/replication or even leading to death of host cells. In our study, autophagy was determined to be beneficial to differentiated human promyelocytic leukemia HL-60 cells exposed to LT as cells blocked from autophagy expressed accelerated cell death [17]. Probably similar to the cellular response to
Meanwhile, circumstantial evidence from other non-autophagy related LT studies also suggests a possible link between lethal toxin and autophagy [27, 28]. As described earlier, autophagy proceeds from nascent vacuoles to become degradative autophagosomes by acquiring lysosomal proteins, including lysosome associated membrane protein (LAMP)-1 [29]. The maturation culminates with the subsequent fusion of the autophagome with lysosome to form autolysosome where it then degrades and releases its contents into the cytoplasm. LAMP-1 protein is also a major component of lysosome [30]. Kuhn et al analysed the proteomic profile of macrophages treated with LT and reported that LAMP1 protein was one of the highly upregulated protein [27], conceivably to increase lysosome capacity for fusing with autophagosomes and binding to late autophagosomes. In another separate study, several compounds were tested for its ability to modulate LT-induced cell death in macrophages [28]. Interestingly, the presence of rapamycin, an autophagy inducer, protected macrophages from LT-induced cell death. In contrast, macrophages co-treated with autophagy inhibitors, wortmannin or LY294002, exhibited accelerated cell death upon treatment with LT. Although autophagy was not part of their experimental design [28], it is worthy to note that the only compound tested in that study that protected macrophage from LT death in that experiment is a well known autophagy inducer, rapamycin. The results from these studies are in agreement with our current findings that LT activate autophagy and it may function as a cellular defense mechanism against LT intoxication.
Taken together, this study provides new insights into a hitherto undescribed effect of LT on cells; the induction of autophagic response in cells by PA and LT and the plausible role of autophagy in
Biosensor technology is a promising field where many outputs are continuously produced thanks to physicochemical techniques and biological materials developed every day. In this technology, a biological molecule interacts with the analyte on the biosensor and this generates a physicochemical signal which is detected by the transducer. Biosensor systems are divided into two classes in terms of biological molecules used, either catalytic-based which transforms the analyte or affinity-based which binds the analyte directly [1]. In terms of physicochemical signal transmitter, it can be designed as electrochemical, optic or piezoelectric. Systems that are combined within also continue to be open to development today. For example, both electrochemistry and optical measurements can be made in spectroelectrochemical techniques. Among these techniques, electrochemical systems [2], which are produced at low-costs without being interfered by the properties of the analyte solution, are used mostly.
The most important element of the biosensor is the biorecognition agent which shows the affinity for the analyte. These agents are of biological origin and are biomolecules with specific substrates such as proteins [3], enzymes [4], nucleic acids [5], antibodies [6], cells [7], cell surface channels. Biosensors can be designed by immobilizing these biomolecules on a suitable signal transmitter based on the working principle. When selecting the biorecognition agent, the specimen containing the analyte to be measured and the characteristics of the reaction that will take place should be considered. It is desired that the biorecognition agent has a maximum activity and that it has a low degree of denaturation.
The living organism’s structural and functional strategy is hidden in its genes. The gene structure is based on the bases that form nucleic acids, which are divided into two main groups according to their functions, are deoxyribonucleic acid (DNA) and ribonucleic acids (RNA) [8]. DNA carries the genetic information in the double helix structure that includes adenine (A), guanine (G), cytosine (C) and thymine (T) bases. RNA has two main differences when compared to DNA, which are the inclusion of uracil (U) instead of T and the single stranded nucleic acid structure different from DNA. DNA’s double helix structure is formed with hydrogen bonds between the DNA bases of the complementary chains. In the same chain, ester bases between the 5 ‘OH group on the pentose sugar of a nucleotide and the 3’ OH group of the other nucleotide sugar form the single chain structure (Figure 1).
Representation of the hydrogen bonds between DNA chains.
Thereby, U, A, G, C and T can be ordered in countless combinations to form genetic sequences. These sequences are copied and then transcribed in the ribosomes to take part in the synthesis of peptides and proteins by encoding one amino acid corresponding to all three bases.
Although they have different structures in different living organisms, the basic function of base sequences does not change. Erwin Chargaff showed that A-T and G-C base pairs in DNA sequences are mutually paired with hydrogen bond [9]. The important point here is that the hydrogen bonds formed between DNA helixes directly affect the physical properties of DNA, since there are three hydrogen bonds between G-C, while there are two hydrogen bonds between A-T. If the G-C ratio is high, it requires more energetic power to separate the double helix. This is a considerable structural characteristic for the electrochemical techniques.
On the other hand, RNA is a single chain nucleic acid produced by using DNA sequences. Besides the three main types of RNA in protein encoding (mRNA, tRNA and rRNA), there are also other types of RNAs that serve in post-translational modifications in DNA replication or as regulators. For example, small nuclear RNA (snRNA) involved in RNA cleavage, guide RNA (gRNA) involved in CRISPR-Cas9 system, micro RNA (miRNA), small interfering RNA (siRNA) and viral RNA. These different nucleic acids are worth to identify their function and structure [10].
Today, DNA or RNA analysis can be done quite precisely. Therefore, genetic sequences have a central role in diagnosis and treatment processes and they guide the scientists for development of new techniques. RNA and DNA sequences can be easily illuminated with polymerase chain reactions (PCR) and next-generation sequencing analyzers [11]. Like every method, these methods have limitations. For PCR, it is necessary to use consumables for reproduction and analysis of the nucleic acid sequences. This increases analysis costs and affects the analysis time. The disadvantages of the methods naturally make it inevitable to develop new and efficient methods. Although there are different nucleic acid analysis methods, simple and precise methods are needed. Bioelectronics systems are preferable as they are in the front line with their low cost, fast analysis time, minimum consumable requirement and lower margin of errors. Efficient properties of biological molecules with physicochemical transducer sensitivity increase the preferability. These basic mini analyzers are able to provide fast, low cost and precise analysis, based on the immobilizing biological molecules on a physicochemical transducer. The term biosensor is developed by immobilizing a biomolecule of biological origin that provides the biochemical reaction on a transducer. In terms of classification, it can be divided into different areas according to both the working principle of the biomolecule and the working principle of the transducer.
In electrochemical nucleic acid biosensor systems, the electrical signal occurs because of the interaction between the biorecognition agent and the analyte. As a result of the biochemical reaction, if an electron is formed, amperometric measurement can be performed. If a molecule is formed it can be detected by potentiometric or direct affinity-based binding can be measured as impedimetric/capacitive. When there is no molecule being exposed, only affinity-based biosensor systems can be designed amperometrically. In this design, when the interaction between biomolecules occurs, a secondary molecule (label) can generate an electrochemical signal. Measurements can be performed through the electrochemical activity of the label used here. Electrical conductivity is an extremely important parameter, especially in biosensor systems. Nucleic acids, on the other hand, can be considered as ideal transistors, because of their structure, they show conductive nanocable characteristics and are very efficient in use in electrochemical biosensors in order to be found in many different conformations. The DNA helix has between 3.4-angstrom base pairs, and the aromatic ring structure facilitates electron flow. This structure, that is the closeness between the bases, is similar to the Z-directional space of graphite and provides conductivity. Moreover, the π electrons on DNA also help electrical conductivity [10]. They help electrochemical conductivity due to structural variability.
On the other hand, beside the electroactivity of DNA, the electrochemical measurement method is important in the design of nucleic acid biosensors. Some electroactive secondary molecules can be used for the electrochemical detection. Mediators, which are frequently used in biosensor systems, can also be used to measure molecules that interact with DNA. Mediator is an intermediary molecule that facilitates electron exchange in an electrochemical reaction and lowers the reduction/oxidation potential of the detection system and also has regeneration potential [1]. The most important feature of a mediator is that it can signal in a low and narrow potential ranges. This feature increases the sensitivity of the biosensor since signaling of other electroactive species can be prevented in lower potentials.
Electroactive species can be determined using techniques such as differential pulse voltammetry (DPV) and cyclic voltammetry (CV) in studies that require the measurement of electroactive species, and the measurement of the amount of DNA through the reduction or oxidation of these species. The basic principle of the measurements is the presence of electroactive species on DNA (guanine base) or the formation of signals by binding some mediators or indicators to DNA. Indicators such as ruthenium complexes, ferrocene and methylene blue are often used for nucleic acid based biosensors. Measurement can be performed by chemically marking the DNA or RNA at the end or forming a complex with DNA helix. Measuring current generated by electroactive species in these electrochemical techniques is extremely important, but can also limit the effectiveness of measurement systems. In other electrochemical measurement systems where mediators are not used, different electrochemical techniques that can measure nucleic acid binding or conformational changes may be used. These methods are performed in redox probe solutions to characterize electrode surface. Here, CV is capable of measuring physical changes on the surface with the help of a redox probe. When the sensitivity of CV in affinity based non-electroactive detections is insufficient, electrochemical impedance spectroscopy (EIS) or capacitance (C) measurement can also be used in affinity-based nucleic acid biosensors. These two methods are really sensitive methods to detect biomolecules, charge transfers and mass transfers with reaction kinetics and also are affected by electrode surface charges [12]. Therefore, nucleic acid length, base composition, and conformational changes after target molecule binding had to be considered before study design. Moreover, the negatively charged redox probe usage reduces the interference of the redox probe interaction between nucleic acid in the measurement.
Another advantage of nucleic acids is that there is no denaturation or loss of activity like proteins. The most important point to consider here is to take measures to reduce the effectiveness of DNase and RNase enzymes that break down nucleic acids. Some examples of methods that can be used when designing a biosensor system with nucleic acids are given in the following pages.
With 5 different base sequences on nucleic acids, the potential for an almost unlimited sequence is theoretically available. Their use as both a biorecognition agent and a target molecule to be analyzed is among its advantages. By its ability to form a complementary structure even within itself, it shows the feature of an analyte-biorecognition agent.
In studies where DNA is used as a biorecognition agent, biosensor systems can be designed by measuring molecules that interact directly or indirectly with DNA. Especially in genetic analysis, DNA determinations have been performed based on complementary base pairings (Figure 2).
Schematic representation of the DNA as biorecognition receptor.
Chen et al. [13] developed a DNA biosensor whose signal was increased in triplicate for the determination of transgenic soybeans. Signal enhancement was performed as rolling circle amplification (RCA). In the biosensor system Chronocoulometry was used to detect DNAs via electrode surface charges. Firstly, Fe3O4@Au magnetic nanoparticles were produced and the electrode was modified with SH modified DNAs to capture the target DNA sequence. After this immobilization on carbon electrode and incubated by dropping target DNA, complementary DNA forms a double structure with the target DNA. Afterwards, the double helix was cut and removed with ExoIII and 4 single-stranded ssDNA with a gold nanoparticle cube in the center was added to the free cutted ends, and binding was achieved with the help of Phi29 DNA polymerase and T4. [Ru(NH3)6]3+, which forms a complex with anionic phosphates, is used as a complex mediator specifically bound on this quaternary structure. The amount of DNA was determined chronocoulometrically over the electrochemical signals generated by the ruthenium complex. A linear calibration curve was obtained between 10−16 and 10−7 M, and LOD was calculated as 4.5 × 10−17 M. Target DNA analysis took 2 hours. By the help of this complex DNA analysis, the authors managed to develop an ultra-sensitive system. Sensitivity is increased with the DNA immobilization steps used here. However, since the study requires a repetitive enzyme treatment, it seems costly and time consuming in developmental process.
Nucleic acid biosensors can also be developed by using enzymes used in DNA analysis. In recent years, studies using the CRISPR-Cas9 system are used in biotechnological studies as a genetic editing molecule. Uygun et al. [14] developed an impedimetric graphene oxide electrode modified with CRISPR-dCas9 for the determination of the target circulating tumor DNA molecules containing the PIK3CA exon 9 mutation, which is used as a biomarker in breast cancer and is referred to as a liquid biopsy biomarker. In this study, deactivated Cas9 (dCas9) proteins without exonuclease activity, were used as biorecognition receptor by modifying them with a sgRNA that would recognize the target ctDNA sequence. Graphene oxide electrodes were modified with dCas9 and sgRNA, consequently. In this way, the modification for ctDNA analysis is completed. The short analysis time (40 seconds) needed was a great advantage. The impedimetric measurement method with a 1.92 nM LOD in the range of 2–20 nM ctDNA concentration has been developed.
Because of the charges on the DNA, analysis of cations, where the bases show selectivity, can be detected. In another biosensor study, due to its negatively charged structure, the ability of chelating properties of DNAs for metal ions is used. Zhang et al. [15] used DNA molecules for the determination of mercury ions. DNA probes modified with the DNA sulfur group formed a self-assembly monolayer on the gold electrode. Afterwards, the electrode modified with the reporter DNA, which has a gold nanoparticle in the center, was measured by binding mercury ions. Both impedance and CV were used in the study. The linear measuring range was set as 1–200 nM and the LOD was calculated as 0.05 nM. By this study, thanks to the use of DNA molecules, the mercury molecule was determined with a relative standard deviation of 3% within real samples.
To observe the complementary base pairing and post translational modifications, secondary conjugates such as antibody or enzyme can be used in the DNA based biosensor studies. Huang et al. [16] developed a biosensor to determine DNA methylation levels. In this study, the methylation level was determined with the help of a bioconjugate modified by a secondary antibody. This conjugate is formed on graphene oxide layers that target CpG and have horseradish peroxidase (HRP)-labeled anti-5-methylcytosine antibodies. The signal generated by HRP is directly proportional to the presence of methyl groups, and DPV was used in this enzymatic reaction-based study. Hydroquinone as a mediator, i.e. electron transmitter, also reduced the reaction voltage and made it more selective. Then, the measurement was carried out on the complex of the bioconjugate with cytosine containing methyl groups. While the biosensor reaches 1 fM LOD value, it can measure in the linear range between 1 fM and 10 nM. The preparation process of the biosensor took approximately 5 hours. In this study, since DNA methylation is performed by measuring the enzyme activity on the bioconjugate, the measurement efficiency is based on the performance of the antibody, enzyme and the mediator.
Jahandari et al. [17] developed a biosensor modified with gold nanoparticles for DNA-based Temodal (anticancer drug) determination. They also modified dsDNA molecules electrochemically on the gold nanoparticles deposited on the pencil graphite electrode. The binding of the Temodal to the DNA on the biosensor was measured by DPV. Here, the main measurement is not the Temodal measurement directly. As the intercalator agent binds to the DNA, the reduction potential of the guanine base on the DNA decreases due to the amount of Temodal that is bound to DNA. Temodal performed intercalation by the interaction of the minor groove on the DNA. In this system with a maximum measurement time of 8 minutes, a maximum recovery deviation of 5% was observed in real samples. Linearly, it showed 1 nM LOD with measurement performance between 5 nM and 45 μM. The performance and sensitivity of this study are directly proportional to the presence of guanine bases. The base ratio on DNA is important in the design of such studies.
Ebrahimi et al. [18] determined cadmium ions using ethyl green (EG) on a simple DNA-based biosensor system. EG can be used as a hybridization indicator in DNA studies. Cadmium is known as a toxic heavy metal and this heavy metal measurement is especially important for biological samples. Cadmium destabilizes the double helix by forming a bond through the N7 atom of the guanine base on DNA. Similarly, in this study, measurement was performed using differential pulse voltammetry signals of EG. The signal generated by DPV is the oxidation signal that occurs as the result of the release of EG by destabilizing double helix. In other words, EG among the DNA helix is released as the result of the binding of cadmium to DNA, and it forms a destabilized DNA signal with cadmium. Measurement of cadmium ions showed 0.3 pM LOD with a linear measurement between 1 pM and 1 nM and between 10 nM and 1 μM. The limitation of the study is the accumulation performance of EG on DNA. The degree of this accumulation determines the sensitivity. It is difficult to determine the low amounts of cadmium in drinking water with a relative standard deviation of 8%.
In biosensors developed with DNA, the properties of DNA hybrids can be used. Yang et al. [19] have developed an electrochemical biosensor for the determination of MCF-7 cells, which are breast cancer cells. In this biosensor, DNA molecules were used for modification. The system provided linear measurement between 100 and 1 million cells in 1 mL and the LOD was found to be 80 cells/mL. The biosensor system was developed as a sandwich-type and the signal was made more sensitive with nanomaterials on antibodies labeled with DNA. With the 3D nanomaterials used in the design of the system, the modification steps are quite highly complex and difficult in terms of workload. In the study, the electrode was first modified with 3D-graphenes and then was modified with gold nanocages with antibody on the carbon nanotubes and immobilized on the electrode. DNA fragments labeled with a secondary antibody bonded on MCF-7 bound on these antibodies, and the measurement was performed with DPV. Here, MCF-7 measurement was performed by DNA hybridization, that is, by measuring the degree of binding of the complement bound to the ssDNA labeled with the last bound antibody.
Saeedfar et al. [20] developed a biosensor using multi-walled carbon nanotubes modified with gold nanoparticles to determine the sex of Arowana fish. The process of determining the sex of the Arowana fish before maturation is quite difficult. Arowana is an ancient and very expensive fish. This biosensor was developed as it is a very advantageous approach for the fish farming industry to distinguish the gender of the fish in time. For this, a hybridization-based approach has been adopted. Carbon nanotubes were used as a hybridization agent by complexing with ruthenium (III) chloride hex ammoniate in this study. DNA determination was performed between 10−21 M and 10−9 M and 1.55 × 10−21 M was the lowest detection limit.
Apart from DNA and proteins used in DNA determination, uncharged DNA variant known as Peptide Nucleic Acid (PNA) is also used. Unlike DNA, instead of a phosphate backbone, this molecule contains a backbone made of neutral amino acids. PNA of this nature can be used as potential probes for both DNA and RNA determination. The advantage of PNA is that it provides a great advantage in reducing the determination time. Tian et al. [21] used graphene field-effected transistors in their PNA-modified electrochemical biosensor study. In the DNA analysis study by measuring the gate voltage, it reached the level of 0.1 aM LOD and performed between 0.1 aM and 1 pM.
Due to their structural features, RNA biosensors can also be used in biosensor development, just like DNA biosensors. The structural differences of RNA with DNA were mentioned above. Apart from their metabolic functions, RNA and DNA are similar except for the difference in oxidation in ribose sugar. Studies have also been carried out which DNA and RNA can be used together in biosensor studies, especially using complementary DNAs for RNA analysis. In this section, RNA-based biosensors and types of studies are summarized.
Luo et al. [22] have developed an electrochemical DNA biosensor for exosomal miRNA analysis. The study was generally modified by adding a DNA probe modified with methylene blue (MB) over amino groups after the lysine amino acid was electrochemically coated on the glassy carbon electrode. Complementary to this probe, a ferrocene-modified secondary probe is attached. The biosensor was prepared for sample measurement by exosome extraction that releases miRNA to hybridize them to complementary chain and detected by labeled with Ferrocene (Fc). The variation of the Fc signal with the MB folded on itself indicates the miRNA and probe measurement, consequently. It shows performance at 2.3 fM level LOD and linear measurement range between 10 and 70 fM.
As a result, DNA and RNA have been used both as a recognition agent and as a target molecule with successful results. In some of these studies, the determination was carried out by measuring a secondary molecule on the basis of DNA hybridization. Besides, DNA analysis with the use of Cas proteins and DNA analysis with PNA were performed by using different methods and extremely low detection limits were reached.
Aptamers have caught a very rapid trend after their discovery. These artificial nucleic acids are produced by the systematic evolution of ligands by exponential enrichment (SELEX) method [5]. By being artificially produced, they show affinity for a wide range of target molecules. They achieve this affinity with easy physical changes. Aptamer sequences designed in the correct sequence for the target molecule work by binding to the target site by undergoing conformational change when the target molecule approaches. The conformational change can be measured by using a label or surface resistance, shown in Figures 3 and 4, respectively.
Labeled-aptamer based electrochemical biosensor technology.
Schematic representation of the impedimetric aptamer biosensor.
Ohno et al. [23] developed a label-free immunosensor-based aptamer-modified graphene FET. The researchers, who modified the G-FET with IgE aptamers, determined IgG by measuring the gate voltage on the FET. With a protein concentration measurement between 0.29 and 340 nM, a LOD value of 0.29 nM was reached. 47 nM isotherm value was observed as the Kd value. Since nonspecific binding of different proteins except this molecule was not observed.
In another study, Chen et al., [24] developed an aptamer-based biosensor for the electrochemical determination of Human epidermal growth factor (HER2). Differential pulse voltammetry was chosen as a measurement technique. In the study, after modifying the gold nanorod nanomaterials with palladium, they formed a bioconjugate for analysis by modifying it with an aptamer containing SH group and horse radish peroxidase (HRP). Later, they modified the gold electrode with DNA tetrahedrons. DNA tetrahedron is a nanoscale structure designed by using the complementary base pairing reactions of nucleic acids. They modified the single-stranded DNA aptamer from one corner of the DNA tetrahedron structure. DNA tetrahedron is preferred because of its mechanical structural rigidity and high affinity (5000 times higher for ssDNA aptamer). The DNA was dropped onto the tetrahedron-aptamer modified gold electrode, aptamer’s unbound ends were modified with BSA. After HER2 molecules were captured by the aptamer on the electrode, the bioconjugate was added on this modification and the biosensor was constructed???. HER2 measurement was performed indirectly through the conversion of HRP to hydrogen peroxide and the measurement of hydroquinone (mediator) added to the environment. In this study, researchers used the DNA tetrahedron structure and aptamer composite, thus HER2 recognition capacity was increased with this modification. The biosensor, with a working range of 10–200 ng/mL, provided the opportunity to make the analysis in 60 minutes. LOD was found to be 0.15 ng/mL.
Apart from large proteins, aptamer molecules are also used to identify small molecules. Aptamer molecules are particularly useful for the determination of molecules which are extremely difficult and demanding to identify easily. Swensen et al. [25] conducted real-time cocaine measurement in their biosensor study. This determination was carried out in approximately one minute. The microfluidic chip has been modified with cocaine-specific aptamers for cocaine binding. One end of the aptamer is modified with methylene blue. The sample, injected into the microfluidic chamber, was added to the fetal bovine serum with a flow, and the measurement was performed by binding to the aptamer. Rapid measurement is important for the rapid determination of this drug, which has a half-life of 60–90 minutes in serum. Besides the speed advantage, this system has a 20 pM LOD with a linear detection range of 10–2000 μM.
Apart from organic molecules, aptamer-based biosensors have also been developed for the determination of ions. Radi et al. [26] developed a biosensor system for the aptamer-based potassium determination. The gold electrode was made ready for potassium ion measurement after being modified with aptamers with SH at one end and Fc at the other. The biosensor had a measurement limit between 0.1 and 1 mM and reached a value of 0.015 LOD by using electrochemical impedance spectroscopy.
Besides the principle of binding aptamer molecules to a molecule, a bifunctional aptamer-based biosensor for determination of adenosine and lysozyme was developed by Deng et al. [27]. In their study, they performed the determination of adenosine and lysozyme on DNA/DNA duplex. The gold electrode was first modified by a probe with SH group (adenosine selective) and then a secondary probe (lysozyme selective) attached to this probe, and the modification was completed with a DNA loaded nanomaterial with a central gold nanoparticle. Finally, ruthenium complexes were added as electroactive species on this structure. After the primary probe captures adenosine with adenosine binding, the gold nanoparticle structure together with the secondary probe is separated from the biosensor. With lysozyme binding, the secondary structure is separated from the main structure by binding lysozyme. All these bonding and separation reactions were followed by the electrochemical activity of ruthenium complexes. Electrochemical measurement was carried out by CV. Lysozyme and adenosine bifunctional biosensor reached the LOD limits of 0.01 μg/mL and 0.02 nM, respectively. Measurements were made between 0.02 and 40 nM for adenosine and 10–60 μg/mL for lysozyme.
With aptamer nucleic acids, target biomolecules can be easily identified. Although aptamer molecules work similarly to antibodies, they can easily be modified with a secondary biomolecule. Molecules that do not have denaturation problems unlike proteins can be very useful in the development of biosensors, especially in the development of electrochemical biosensors. Electrochemical activation of electroactive species or direct aptamer binding to the target molecule can be measured impedimetrically. As a result, aptamer systems are suitable for affinity-based sensor development in biosensors (Table 1).
Electrochemical method | Biorecognition receptor | Target | Linear range | LOD | Reference |
---|---|---|---|---|---|
Coul | Phi29 DNA polymerase and T4 | Transgenic soybeans DNA | 10−16 and 10−7 M | 4.5 × 10−17 M | [6] |
EIS | CRISP-dCas9 | PIK3CA | 2–20 nM | 1.92 nM | [7] |
CV | DNA | Hg2+ | 1–200 nM | 0.05 nM | [8] |
DPV | DNA-(HRP)-labeled IgG | DNA Methylation | 1 fM–10 nM | 1 fM | [9] |
DPV | AuNPSs-DNA | Temodal | 5 nM–45 μM | 1 nM | [10] |
DPV | DNA-ethyl green | Cd2+ | 1 pM–1 nM | 0.3 pM | [11] |
DPV | DNA-antibody-graphene | MCF-7 Cells | 102–106 cells/mL | 80 cells/mL | [12] |
DPV | DNA-ruthenium | Arowana fish gender (DNA) | 10−21–10−9 M | 1.55 × 10−21 M | [13] |
G-FET | DNA | PNA | 0.1 aM–1 pM | 0.1 aM | [14] |
DPV | DNA-MB, DNA-Fc | Exosomal miRNA | 10–70 fM | 2.3 fM | [15] |
G-FET | IgG aptamer | IgG | 0.29–340 nM | 0.29 nM | [17] |
DPV | DNA tetrahedron – aptamer | HER2 | 10–200 ng/mL | 0.15 ng/mL | [18] |
AC voltammetry | Cocaine aptamer | Cocaine | 10–2000 μM | 20 pM | [19] |
EIS | 5′-ferrocene(Fc)–DNA–SH-3′ | K+ | 0.1–1 mM | 0.015 mM | [20] |
CV | Adenosine-lysozyme aptamers | Lysozyme Adenosine | 10–60 μg/mL 0.02–40 nM | 0.01 μg/mL 0.02 nM | [21] |
Comparison of the nucleic acid based biosensors.
DPV: differential pulse voltammetry, EIS: electrochemical impedance spectroscopy, CV: cyclic voltammetry, Coul: coulometry, fc: ferrocene, PIK3CA: phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha, AuNPs: gold nanoparticles, G-FET: graphene field effect transistor, MB: methylene blue, HER2: human epidermal growth factor, AC: alternative current.
Biosensors are low cost analyzers with high potential to be miniaturized. They also provide short measurement time. Thanks to the numerous combinations of biorecognition receptor and transducers, biosensor systems can easily be adapted for the measurement of any kind of analyte. The biological activity of the biorecognition agent on the transducer is the critical element in a biosensor. Biomolecules with low probability of denaturation, adaptable to all kinds of measurements and strong electrical components should be selected for biosensor development. Nucleic acids meet the needs of biosensors at this point. They are advantageous biomolecules that can interact from metal ions to large proteins thanks to their multiple negative charges. Nucleic acids also have the potential to facilitate the determination of organic molecules, such as drugs and pesticides, which can enter between nucleic acid chains thanks to the electroactive guanine base in their structure. They can be used as simple biorecognition agents, similar to an unlimited antibody-antigen interaction, with the potential to be designed to synthetically show affinity for the target molecule. Another important feature of nucleic acids is the potential of their end portions to be modified by secondary signal transmitters without causing any deactivation. Apart from being both a biorecognition agent and an analyte molecule, their immobilization capacity also increases their usage and advantages. In conclusion, the fact that they can be used as a material which provides stability and ease of modification for analysis in biosensor systems puts nucleic acids one step further among other biorecognition agents.
We are grateful to thank The Scientific and Technological Research Council Of Turkey (TÜBİTAK) for the supports for giving the idea to write this chapter by awarded our TÜBİTAK-1001 217S353 project.
The authors declare no conflict of interest.
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Dr. Blumenberg’s research is focused on the epidermis, expression of keratin genes, transcription profiling, keratinocyte differentiation, inflammatory diseases and cancers, and most recently the effects of the microbiome on the skin. 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Thus proteomics, an area of research that detects all protein forms expressed in an organism, including splice isoforms and post-translational modifications, is more suitable than genomics for a comprehensive understanding of the biochemical processes that govern life. The most common proteomics applications are currently in the clinical field for the identification, in a variety of biological matrices, of biomarkers for diagnosis and therapeutic intervention of disorders. From the comparison of proteomic profiles of control and disease or different physiological states, which may emerge, changes in protein expression can provide new insights into the roles played by some proteins in human pathologies. Understanding how proteins function and interact with each other is another goal of proteomics that makes this approach even more intriguing. Specialized technology and expertise are required to assess the proteome of any biological sample. 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