Nucleotide detection mechanism and comparison based on low-dimensional materials: A review
M. Mustafa Azeem
Muhammad Shafa2 
Muhammad Aamir
Muhammad Zubair
Basma Souayeh
Mir Waqas Alam- 1Department of Civil, Architectural, and Environmental Engineering, Missouri University of Science and Technology, Rolla, MO, United States
- 2Yunnan Key Laboratory of Metal-Organic Molecular Materials and Devices, Kunming University, Kunming, Yunnan, China
- 3Department of Basic Science, Deanship of Preparatory Year, King Faisal University, Hofuf, Saudi Arabia
- 4Mechanical and Nuclear Engineering Department, University of Sharjah, Sharjah, United Arab Emirates
- 5Department of Physics, College of Science, King Faisal University, Al Ahsa, Saudi Arabia
The recent pandemic has led to the fabrication of new nucleic acid sensors that can detect infinitesimal limits immediately and effectively. Therefore, various techniques have been demonstrated using low-dimensional materials that exhibit ultrahigh detection and accuracy. Numerous detection approaches have been reported, and new methods for impulse sensing are being explored. All ongoing research converges at one unique point, that is, an impetus: the enhanced limit of detection of sensors. There are several reviews on the detection of viruses and other proteins related to disease control point of care; however, to the best of our knowledge, none summarizes the various nucleotide sensors and describes their limits of detection and mechanisms. To understand the far-reaching impact of this discipline, we briefly discussed conventional and nanomaterial-based sensors, and then proposed the feature prospects of these devices. Two types of sensing mechanisms were further divided into their sub-branches: polymerase chain reaction and photospectrometric-based sensors. The nanomaterial-based sensor was further subdivided into optical and electrical sensors. The optical sensors included fluorescence (FL), surface plasmon resonance (SPR), colorimetric, and surface-enhanced Raman scattering (SERS), while electrical sensors included electrochemical luminescence (ECL), microfluidic chip, and field-effect transistor (FET). A synopsis of sensing materials, mechanisms, detection limits, and ranges has been provided. The sensing mechanism and materials used were discussed for each category in terms of length, collectively forming a fusing platform to highlight the ultrahigh detection technique of nucleotide sensors. We discussed potential trends in improving the fabrication of nucleotide nanosensors based on low-dimensional materials. In this area, particular aspects, including sensitivity, detection mechanism, stability, and challenges, were addressed. The optimization of the sensing performance and selection of the best sensor were concluded. Recent trends in the atomic-scale simulation of the development of Deoxyribonucleic acid (DNA) sensors using 2D materials were highlighted. A critical overview of the challenges and opportunities of deoxyribonucleic acid sensors was explored, and progress made in deoxyribonucleic acid detection over the past decade with a family of deoxyribonucleic acid sensors was described. Areas in which further research is needed were included in the future scope.
1 Introduction
Deoxyribonucleic acid (DNA) carries the genetic information constituent of deoxyribose and nitrogenous bases known as nucleotides or fragments of DNA (Wilkins, 1956). These nucleotides contain genetic information that can encode life (Stegmann, 2005). As its size is comparable to the nanoscale, the double helix structure was reported in 1953 by Watson and Crick (1953). This well-known DNA double helix is formed from pairs of complementary single-stranded DNA (ssDNA). Double-stranded DNA (dsDNA) is a pair of bonded ssDNA (Watson and Crick, 1953).
Structural nanotechnology has made significant progress in terms of the rapid sensitivity of DNA sequences (Zhou et al., 2020). Each existing DNA is unique, indicating that DNA sequence is crucial for detecting, and it has been studied in the fight against sporadic pandemics. A small part of the DNA that holds genetic information is known as a gene. A complete DNA sequence of DNA is imperative for the fabrication of vaccines. Over the past two decades, many new methodologies have been developed for the detection of DNA, which has ultimately assisted in portable point-of-care diagnostics. Indigenous DNA is negatively charged (Zhang et al., 2007), which can be manipulated by several strategies, such as creating an electric field; thus, it behaves like electrons to attract positively charged particles (Liu and Hu, 2007). Therefore, the identification of specific DNA sequences is a crucial task achieved using modern nanotechnology, which consequently opens a new era of exploration ranging from detection to gene mutation. DNA sensors are capable of detecting changes in the form of electrical signals generated through the immune system in response to any perturbation. They convert biochemical reactions into a signal for further detection. Currently, integrated multiscale simulation and experimental techniques are used to study biosensing applications in a variety of interdisciplinary fields (Quan et al., 2018; Mohammadi et al., 2021; Babar et al., 2022).
Low-dimensional (LD) materials are a class of materials with extraordinary characteristics (Babar et al., 2022). They include graphene and carbon nanotubes (CNT), MXenes (Ti2C3), hexagonal boron nitride (h-BN), molybdenum disulfide (MoS2), and reduced graphene oxide (rGO), etc. (Mohammadi et al., 2021). They have displayed they are being used in a variety of applications. Currently, LD based sensors are replacing traditional sensors (Wu et al., 2022). LD materials are used for protective coating and biosensors due to their tunable, electrical, and optical, and excellent mechanical properties. They are also being used as substrate materials in electronic sensors due to their multilayered structures. Additionally, these materials modify their surface chemistry through associated functional groups due to which they respond to a specific analyte (Bolotsky et al., 2019). Other than normal 2D structures, very new types of nanostructured materials with improved optical properties have been reported (Kim and Benelmekki, 2019). They have diverse industrial applications, particularly suitable for biomolecular sensing. These are known as “smart nanosheets or nanoscrolls” (Kim et al., 2014; Kim and Benelmekki, 2018; Kim and Benelmekki, 2019; Benelmekki and Kim, 2023).
To achieve global market demand, the fabrication of DNA sensors should possess a low cost, low range of detection (LOD), simple and low processing time with high speed, and high selectivity. There are two main types of DNA detection techniques: conventional spectrophotometric and polymerase chain reactions (PCRs), and modern nanomaterial-based sensors, which are further subdivided into optical and electrical sensors. Optical sensors based on fluorescence (FL), surface plasmon resonance (SPR), colorimetric, and surface-enhanced Raman scattering (SERS) techniques, whereas electrical sensors based on electrochemical luminescence (ECL), chip-based, and field-effect transistors (FET) are described in Figure 1.
FIGURE 1. Division of nucleotide sensors.
Detection methods based on electrical sensors have been gaining attention in the global market owing to their high multiplexing capability, high sensitivity, and wide dynamic range. The major contribution of biosensor involves a transduction mechanism for detection. The transducer transforms the electrical signal from the analyte and amplify it. Conventional sensors have low accuracy and expensive and complex instrumentation whereas nanomaterial-based sensors are more compatible and provide a proficient detection. However, the optical method is commonly used because it has numerous defects, such as it is difficult to reliably profile low-abundance genes, and it requires expensive fabrication of these optical devices and complex bioinformatics tools for fluorescence signal identification. FET-based nano electronic devices have attracted much attention owing to their small scale, simple design, and better performance compared with conventional devices.
Because of the discovery of DNA sensors, efforts have been made to demonstrate and optimize them for portable point-of-care applications. The continuous demand and advancement of nanotechnology has been pointed out by experts, and the DNA sensor market is predicted to reach up to 28 billion dollars. This set an annual growth rate of 8.4% in 2022, as illustrated in Figure 2. In particular, Figure 2 represents data rooted from Scopus using search title as “DNA/RNA/Nucleic acid sensor” and immunosensor/antibody sensor, and “Enzyme’’ sensor (Mujawar et al., 2020).
FIGURE 2. Representation of biosensors in the US industry and annual budget expenses (Mujawar et al., 2020).
2 DNA sensors and types
A sensor is a combination of receptor-transducer, which converts the biochemical response to signals emitted from the source. Moreover, DNA sensors monitor involving biomolecular processes. A biosensor consists of an analyte, bioreceptor, transducer, electronics, and display setup (Naresh and Lee, 2021).
2.1 Conventional sensors (Cs)
2.1.1 Spectrophotometric sensor (Sps)
The interaction of light with matter, known as spectrometry, is an ancient technique that has been used in the fields of chemistry and biomedicine because of its low cost, simplicity, and convenience. This has led to the analytical detection of DNA derivatives, such as nucleic acids and nucleotides, owing to the presence of double bond systems as a consequence of these bonds responding to ultraviolet light in the spectrum. This type of specific absorbance will be helpful for the quantitative measurement of DNA by spectrophotometry in the form of micrograms/mL. The absorbance phenomenon corresponds to the transition of electrons from either the anti-bonding (π*) state to the non-bonding (n) state or from the anti-bonding (π*) state to the bonding state (π) associated with a specific energy (Mujawar et al., 2020). Infect nucleic acids have maximum absorbance of UV light at a wavelength of 260 nm; thus, a solution of DNA is exposed to quantify the exposed sample. The drawback of this methodology is that there is a considerably weak signal for single-stranded nucleic acids owing to the lack of bonding, anti-bonding, and non-bonding states. Furthermore, this technique cannot describe the detailed sequences of nucleic acids. As nucleic acids absorb UV light at 260 nm, the compound containing them absorbs UV at 280 nm. The purity of the sample can be calculated by the ratio of absorbance measurement following the criteria for being pure, i.e.,
2.1.2 Polymerase chain reaction-based sensor (PCRs)
Polymerase chain reaction (PCR) is an in vitro technique that can detect and amplify small DNA segments. Through this technique, millions of copies are developed in a fraction of the time. This method was proposed in early 1980 (Cantor, 1998), and has been used globally in various fields, such as food quality insurance, genetics, molecular biology, and forensic science. It is a well-established amplification technique during which millions of amplitudes are generated from a small segment of DNA in a short interval of time. Although it is a low-cost and universally used method, constraints, such as indirect melting temperature measurements and premier annealing, hinder their applications. Furthermore, specific amplification will only occur within a narrow range of reaction conditions that ultimately cause the failure of the PCR testing methodology.
For the sample preparation, errors in the volume of reagents significantly alter the result of the polymerase chain reactions cycle that may disrupt the melting temperature, premier annealing, and amplification. All of the building blocks of PCR hinder portability, as these types of measurements cannot be performed outside the laboratory in a well-controlled environment. Signal transduction mechanisms are another significant barrier that prevents PCR from becoming a popular portable device without the use of expensive instruments, such as PCR machines, and complicated processes, including electrophoresis. All these challenges limit the use of PCR as a portable device. Therefore, a simple modification was introduced using a colorimetric assay for the reserved transcription of DNA fragments known as real-time PCR (rt-PCR). RT-PCR was first described in 1990, and a schematic description is shown in Figure 3, which displays a comparison of the different PCR techniques. Conventional PCR, also known as end-point PCR for analysis of DNA amplification, was conducted at the end of fluorescent marking, whereas amplified DNA was analyzed during each cycle, also known as real-time PCR (Wang et al., 2018b). In general PCR, the fragmentation of DNA is pulled through the gel matrix using a centrifugal electric field that separates DNA segments. This process is called electrophoresis. The second PCR test known as qPCR is quantitative PCR, and it is a much more dynamic range of analysis than that of conventional PCR. It is also a modified form of PCR to qualitatively analyze the DNA by the introduction of florescent dyes during PCR cycles. The output of rPCR is typically displayed in the form of sinusoidal followed by a plateau. Digital PCR (dPCR) follows the random distribution of particles over numerous partitions. Each partition acts as an individual PCR through fluorescence detection. Poisson’s statistics were applied to the sample partitions to calculate the concentration of the target sequence from the proportion of the amplified positive concentration. The process constitutes independent partitioning and amplification followed by florescence detection.
FIGURE 3. Comparison of different PCR-based techniques (Quan et al., 2018).
2.2 Nanomaterial’s base sensors (NMBs)
Nanomaterial-based sensors are considered efficient sensors with excellent signal absorption strength due to quantum effects. They have a high surface-to-volume ratio and higher optical and magnetic properties which make them reasonably good for sensing all types of analytes (Santhanam et al., 2020). Numerous NMBs have been used for DNA biocompatibility because of their higher signal detection capability and transduction technology which converts signals from an analyte during its biochemical reaction (Hlongwane et al., 2019). DNA sensing using NMBs has been included in the following sections.
2.2.1 Optical sensors (Ops)
These biosensors measure changes in optical properties, such as resonance, reflectance, absorbance, and luminescence from the sensor surface. This system measures the fluorescence from nanomaterials based on the detection of DNA hybridization (Vikrant et al., 2019). The optical sensors have been attracted due to their efficient detection level. The materials used in these detectors effectively amplify the detection signal. We summarized a few optical techniques used for developing nanomaterial-based DNA biosensors.
2.2.1.1 Fluorescence-based DNA sensors (FBs)
In such sensors, a fluorescent nanomaterial, known as the transducer, is conjugated with a DNA molecule acting as a target molecule. A fluorescence spectrophotometer was used to measure the fluorescence emitted from the nanomaterial conjugated with the target DNA, which is known as fluorescence resonance energy transfer (FRET) (Ploetz et al., 2016). In this technique, excited electrons were transferred from DNA to nanomaterials at resonance separated by a nanoscale distance without emission of a photon; this process is called fluorescence quenching (FQ). In the presence of the probe and target DNA, both combine to form a hybrid that leads to a change in the fluorescence intensity of the nanomaterials, similar to the aptamer/DNA sensor. Figure 4 shows a scheme of target detection based on FRET with reduced graphene quantum dots (GQDs) combined with probe (complementary) DNA (single-stranded). A spectrophotometer was used to measure the resonance intensity at the graphene monolayer surface. The FRET signal emerging from the layer was analyzed for the DNA structures. Initially, inorganic GQDs reaction with NaBH4 (sodium borohydride) results in reduced GQDs called (rGQDs) followed by connecting DNA (cDNA). This reaction is further divided into three steps. In the first step single strand DNA (ssDNA) interact with GQDs via a condensation reaction. Later, this interaction is absorbed through electrostatic stacking making a base pair of ssDNA-rGQDs/GO. Lastly, the base pair interact with the target DNA (tDNA). This tDNA is replaced by a single-based mismatched DNA (mDNA) making a double-strand DNA (dsDNA)-rGQDs compound detached to produce florescence recovery (Qian et al., 2014).
FIGURE 4. Schematic of a universal fiuorescence based sensor mechanism for the detection of DNA -FRET between GQDs and graphene oxide (GO) (Qian et al., 2014).
An overview of the variety of recently reported FRET-based DNA detection techniques is listed in Table 1. This table shows the complete information reading type of materials used, techniques and strategies of DNA detection, limit of detection, and range of analyte concentration. Herein, we can conclude that by using a tetrahedral DNA framework, we can achieve a DNA detection limit of 1 fM (Li et al., 2020b) while using Cu (I)-catalyzed alkyne-azide cycloaddition (CuAAC) as a fluorescent nanomaterial can achieve a detection range of 0.22 fM reported by Zheng et al. (2020). Furthermore, Zhang D et al. (2020) reported a 23.8 aM level detection limit using the composition of magnetic beads (MBs) that contain phosphate- Zr4+-carboxylate/Cu(II) Br/EDTA for lung cancer DNA. Another finding of magnetic nanoparticle-based on poly-enzyme nanobeads fluorescence assay show high detection of 1.6 aM, which is the highest ever reported by FRET techniques (Lapitan et al., 2019).
TABLE 1. Overview of FRET-based DNA detection techniques.
2.2.1.2 Surface plasmon resonance-based DNA sensors (SPRs)
It is one of the most common optical sensing techniques which is based on surface plasmon which are electromagnetic waves originating from the metal interface. In this sensor, the incident light stimulates the resonance of the conduction electrons at the interface of the positive and negative permittivity materials. AuNPs with positive charge conjugate with the target DNA that is negatively charged; light stimulus resonance phenomena occur between them using conduction electrons, and there is a change in dielectric constants that generate surface plasmons. The schematic diagram shows the detection method by SPR, where the prism, transducer surface composed of nanomaterials, plane polarized light as a stimulus, and detector are the main components of the SPR system. During the conversion of the association phase to the disassociation phase, the refractive index changes, which ultimately deviate from the exiting light from the prism, are correlated with the concentration of the analyte, as shown in Figure 5. Specifically, Figure 5 represents the experimental illustration of SPR techniques (A) and a variation in the critical angle as a function of the intensity (B) and the response of the sensor during the experiment. This method offers label-free techniques; however, there is variation in the refractive index owing to changes in the transducer surface temperature and composition, which may significantly alter the detection results (Patching, 2014).
FIGURE 5. (A) Schematic of SPR-based DNA sensing technique for measuring the binding of an analyte molecule (B) varation in critical angle as fuction of intensity of incident light, (C) Evolution of sonogram's response during SPR experiment (Patching, 2014).
The SPR detection performs the analysis of biomolecular interaction ranging from organic compounds to proteins and nucleic acids and viruses based on real-time. The detection is non-invasive. i.e., it can analyze transparent or colored samples effectively. They are a label-free, specific, and sensitive method that is dependent on the changes in the refractive index of the material surface. A small change in the refractive index may induce a false signal during the detection of an analyte. Nanomaterials are the most ideal material for their fabrication and better signal detection and amplification. Most importantly they are available commercially (Deng et al., 2017; Das et al., 2021).
An overview of the various SPR-based DNA detection techniques reported recently is displayed in Table 2. We have listed all possible information, for example, the type of materials, techniques, and strategy of DNA detection used, limit of detection, and range of analyte concentration. Therefore, by employing a sandwich-like assay based on the selective capture of specific DNA targets, subsequent signal amplification can be obtained by a secondary DNA probe linked to Au nanostars with a detection limit of 3 fM to 6.9 aM (Mariani et al., 2015). Another study reported that a highly sensitive polarization control-modulated plasmonic biosensor based on monolayer graphene with Au film
TABLE 2. SPRs based DNA detection techniques.
2.2.1.3 Colorimetric-based DNA sensors (CMs)
In this technique, color tags or enzymes are used for the detection of DNA compatible with the substrate. Alternatively, nucleic acids functionalized with nanomaterial-based assays can be used for the detection and quantification of DNA (Krishnan and Syed, 2022). During colorimetric analysis, colloidal solution gold nanoparticles (GNPs) exhibit different colors based on their distance from red to blue. The detection is done through a change in the wavelength of the electrolyzed DNA. The color of GNPs is dependent on their dispersion and this help researchers to visually investigate assays that change owing to a decrease in the average distance between nanomaterials (Li and Rothberg, 2004). This method is straightforward, low-cost, and easy to perform for rapid onsite diagnostics. They have a poor limit of detection and prototype design. This DNA detection equipment is commercially available and more economical than other clinical diagnostics. Figure 6 displays schematic illustration of calorimeter based on the GNPs dispersion and aggregation (Liu et al., 2013). A series of DNA samples were electrolyzed and had different concentrations up to 6Nm. The color of the GNPs is gradually changing from pale to blue with the addition of concentration. The wavelength of absorption spectrum is in the range of 550–750 nm. This method is designed to detect a DNA sequence.
FIGURE 6. (A) Calorimetric response of concentration of DNA (0-6 nM), (B) absorption spectrum as a function of wavelength of electrolyzed DNA (Liu et al.,2013).
An overview of the various colorimetric DNA detection techniques recently reported is listed in Table 3. We summarized the types of materials used, techniques and strategies of DNA detection, limit of detection, and range of analyte concentration. Therefore, by employing electrophoretic streptavidin-coated MBs assisted with a magnetic field, we could introduce a new method, which uses active hybridization with a detection limit of 0.1 fM (Tian et al., 2019). Another report showed that Fe3O4 nanosheets in DNA/Fe3O4 networks display peroxidase-like catalytic activity, thereby enhancing detection to an extreme limit of 13 aM, which is the highest limit that has been reported for colorimetric techniques (Tang et al., 2019).
TABLE 3. Colorimetric-based DNA detection techniques.
2.2.1.4 Surface-enhanced Raman scattering-based DNA sensors (SERSs)
In this technique, molecular vibrations which arise directly from analyte molecules were measured using Raman spectroscopy. Such types of resonance occur only when the target analyte is a nanostructure or a roughed metal surface. SERS sensing is based on the conjugation of nanomaterials and bioreceptor molecules (oligonucleotides) at the surface of a dye known as a Raman reporter or tag that enhances Raman signals during the detection of target DNA. SERS provides an enhanced Raman signal of 106–1014 order of magnitude owing to the electromagnetic interaction between the metal.
Nanostructures and the analyte. SERS-based biosensors have a comparatively low cost, high sensitivity, rapid results, and portability (Vikrant et al., 2019). Figure 7 shows the schematic setup for the detection of DNA based on AgNPs at the Si substrate as a sandwich-type sensing setup. Nanoparticles are functionalized with thiolated DNA as step 1, followed by conjugation of dye named Rhodamine as step 2. Therefore, a sandwich-like structure surrounded the target DNA by thiolated DNA and reported DNA that ultimately caused the formation of capture/target/reporter DNA ready for SERS detection as step 3, as shown in Figure 7. The optical sensors are summarized in Figure 8. Each optical sensor has been summarized in the flow chart.
FIGURE 7. Schematic of the fabrication route for SERS sensor and variation of Raman shift as a function of intensity (Jiang et al., 2012).
FIGURE 8. Division of optical sensors (Vikrant et al., 2019).
An overview of the various SERS-based DNA detection techniques reported recently is listed in Table 4. It contains the complete information type of materials used, techniques, a strategy of DNA detection, limit of detection, and range of analyte concentration. Thus, a detection limit of 10 uM–10 fM can be achieved by AuNPs on the surface of graphene oxide (GO) linking via hybridization (Khalil et al., 2019). He et al. (2019) reported a novel detection ratiometric sensor based on glucose oxidase (GOx) on Au and Si nanoflower substrates that enhances the detection to an extreme limit of 7.75 aM, which is the highest limit for colorimetric techniques. Table 4 lists earlier studies on SERS-based DNA sensors.
TABLE 4. SERS-based DNA detection techniques.
2.2.2 Electrochemical sensors (ECs)
2.2.2.1 Electro-chemiluminescence based DNA sensors (ECLs)
In this technique, chemical luminescence and electrochemical processes are combined and named as electro-chemiluminescence (ECL), which results in the emission of light. This photo emission occurs owing to the excitation and de-excitation of electrons between the ground and excited states stimulated by the electrochemical reaction in solution. Light is emitted because of the transfer of exergonic electrons at the electrode surface. This phenomenon is also known as electrogenerated chemical luminescence. The wavelength of the light emitted from the excited and relaxed states corresponds to the energy gap of the molecules. ssDNA is commonly used as a bioreceptor and printed screen, and pencil graphite glassy carbon, and gold are used as the working electrodes in the assembly of DNA sensors. Figure 9 shows the simple strategy and mechanism of detection. This design comprises a target DNA fragment that hybridizes with MBs, where streptadivine and biotin are used as linkers, and the ruthenium probe is conjugated at the other end (Figure 9A). This magnetic bead-assisted ECL reaction occurs in the presence of tripropylamine, where the ruthenium probe Ru (bpy)32+ amplifies the signal isothermally (Zhou et al., 2014).
FIGURE 9. (A) Schematic illustration of magnetic based (MB) ECL for hepatitis B antigen model and nucleic acid target ,whereas antibody of nucleic acids are labeled with biotin and Ru(bpy), (B) MB based ECL measurement and detection system (Zhou et al. 2014).
Table 5 presents an overview of the various ECL-based DNA detection techniques reported in the last decade. Herein, we summarize the detection limit of 19.05 aM for biosensor based on the in situ generation of Cu nanoclusters as luminophores and TiO2 as a coreaction accelerator (Liao et al., 2018). Zhang et al. (2020e) constructed MXene (Ti3C2Tx)-based impedimetric aptasensing nanosheets and iron phthalocyanine quantum dots for an enhanced high detection sensitivity of up to 4.3 aM as compared to the individual component-based ECL technique.
TABLE 5. ECL-based DNA detection techniques.
2.2.2.2 Microfluidic/PCR chip-based DNA sensors (MFCs)
Lab-on-a-chip (LOC) is a mini-integrated chip with small sensors in an array with an area of a few square centimeters. They are based on the micro-electrical-mechanical-based technology (MEMS) in the form of an integrated chip. These sensors are composed of a network of microfluidic channels in which the analyte can be manipulated at the microscale level. The compact design of microfluidic chips results in rapid heating and mixing; hence, providing ultrahigh sensitivity and portability for direct analysis of a crime scene (Temiz et al., 2015; Bruijns et al., 2016). This will also decrease the amount of analyte as well as reduces cross-contamination in the sealed environment. These systems are designed for single use, which will benefit from the chain of custody and contamination risk. A bandage-like flexible sensor that amplifies the DNA detection signal using microfluidic technology is shown in Figure 10. These sensors can be powered by body heat; thus, they are highly sensitive and portable for on-site detection (Bruijns et al., 2016). They are widely used for DNA amplification process and accelerate PCR process. They are small in dimension and instant detection and cost-effective instrument.
FIGURE 10. Schematic of the wearable microfluidic sensor for nucleic acids (Temiz et al., 2015; Yang et al., 2019).
An overview of the various microfluidic chip-based DNA detection techniques reported earlier is listed in Table 6. We can observe that biosensors based on microfluidic chips are designed as power-free chips. They follow the amplification of fluorescence signals after hybridization with laminar flow-assisted dendritic cells and have a detection limit of 0.045–0.45 pM (Kim et al., 2019). Microfluidic-based nucleic acid amplification tests as noise resistant quantitative PCR are used for rapid detection of ultralow-abundance DNA in real biofluids. They have the highest diagnostic limits of 0.05 aM to be reported for a microfluidic technique (Ye and De, 2017).
TABLE 6. Chip-based microfluidic DNA sensor detection techniques.
2.2.2.3 FET-based DNA sensors
FET biosensors are highly sensitive detectors based on 2D materials. They have high carrier mobility owing to their nanoscale dimensions and high volume-to-charge ratio. MXene-based biosensors are a combination of metal carbides and nitrides that have attracted attention because of their unique characteristics (Babar et al., 2022; Guo et al., 2011). They are used for analyte detection and biosensing applications (Yadav et al., 2021). A combination of MXene-graphene-based FET has been used to detect influenza and 2019-Ncov (Li et al., 2021). A multiscale computer simulation method and experimental approach were employed to investigate the characteristics of flat and crumpled graphene-based biosensors by Hwang et al. (2020) ,who found that the detection limits of buffer and human samples are 600 aM and 20 aM, respectively. Furthermore, the atomic-scale simulation results revealed that the deformation mechanism resulted in electrical hotspots in the channel. This technique can be used to develop reliable fast-track biosensors for medical applications. Figure 11 displays a cross-sectional representation of flat and crumpled graphene FET sensors over a Debye length, represented by the blue curve (Figure 11A), whereas Figure 11B shows the fabrication route. Debye screening is weaker in crumpled graphene, which makes it more sensitive for detecting DNA (Hwang et al., 2020). The insets show the distribution of energy over the K-space.
FIGURE 11. (A) Scheme of flat and crumpled graphene FET biosensor using single and double DNA strands over graphene surface. (B) Experimental route for fabrication and flow proces.
A computational study on single-layer MXene that has potential applications as a DNA detection material with high sensitivity and effectiveness was conducted (Yadav et al., 2021). Computer simulation methods have frequently been used to understand the mechanisms and interactions of materials at the atomic scale (Mustafa et al., 2017; Azeem et al., 2018a; Azeem et al., 2018b; Azeem et al., 2019b; Azeem et al., 2019a; Azeem et al., 2020; Azeem et al., 2021; Mustafa Azeem et al., 2018; Mustafa Azeem et al., 2019). An overview of the various FET-based DNA detection techniques reported earlier is listed in Table 7. It is important to point here that LD material has displayed clear advantage on other materials used for designing sensors for health application because of their tunable band structure and ultrathin nature. They also display an improved detection sensitivity. LD materials have been emerged as promising candidate for health industry. Figure 12 summarize LD materials and their application in sensing applications. The division is based on the synthesis, preparation methods, electrochemical and optical properties. The fabrication process of these materials involves process of exfoliation that depends on the chemical environment. Moreover, intercalation constitute chemical vapor deposition (CVD) and electrochemical exfoliation. The material based on LD sensors are used in theranostics image guide application and diagnostics (Bolotsky et al., 2019).
TABLE 7. FET-based DNA detectors.
FIGURE 12. Preparation and synthesis of LD materials for optical and electrochemical applications (Bolotsky et al., 2019).
3 Challenges and commercial applications
Sensors play an important role in our daily life specifically in the healthcare sector as DNA detection and its diagnostic involve curing diseases. The current trend and developing sensors are now hot topics. They have increasing demand after the nCov-19. A big challenge involving the development of DNA detection sensors requires components with on-site and rapid detection and detection limit. Before commercialization, it is very important to handle the stability and reproducibility of the samples. Another major challenge concerns the storage as handling the short lifetime of the samples and re-usage. The conventional detection methods are based on PCR techniques which are very expensive and time-consuming. It is one of the big challenges that involve the detection of ultra-low concentrations of any analyte. Another challenge involves the response time for detection. Developing accurate and economical DNA sensors is a present concern. Presently, DNA detection with nanopore technology has resolved this issue and these materials have already displayed unique characteristics. Compared to conventional methods 2D materials-based FET sensors involve the electric field to create a charge to interact with DNA and change in current results in the form of a signal to detect.
4 Conclusion
Infectious diseases have posed a challenge in the past few years. Biosensing and biotechnology are emerging fields. In particular, DNA biosensors have potential research applications because of their chemical properties as well as reliable and fast detection.
We have reviewed different types of biosensors and listed the fabrication techniques and materials used to develop them. Conventional methods for developing in vitro diagnostics are time-consuming and require multiple trials and centralized technologies. There are diverse techniques and strategies for developing sensors, including, but not limited to, collecting samples, and implementing integrated diagnostics for biological applications. LD materials are considered as alternate to traditional materials due to their nanosized thickness and compatible nature. Currently, understanding nature of these materials in biological environment is major challenge. Critical challenges exist in transforming the optimal clinical treatment of infectious diseases from trial to translational research.
Author contributions
MAz prepared the initial draft and collected the literature review, and MS collected most of the information. MZ, MAa, BS, and MWA reviewed and proofread the manuscript. All the authors have approved this manuscript.
Funding
This work is supported by the Deanship of Scientific Research, Vice Presidency for Graduate Studies and Scientific Research, King Faisal University, Saudi Arabia, under the Reviewing Researcher Track (Grant No. 2389).
Acknowledgments
Authors would like to thank King Faisal University for supporting this research.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Publisher’s note
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Keywords: detection, deoxyribonucleic acid, sensors, polymerase chain reaction, surface plasmon resonance, field effect transistor, nucleotide sensors
Citation: Azeem MM, Shafa M, Aamir M, Zubair M, Souayeh B and Alam MW (2023) Nucleotide detection mechanism and comparison based on low-dimensional materials: A review. Front. Bioeng. Biotechnol. 11:1117871. doi: 10.3389/fbioe.2023.1117871
Received: 07 December 2022; Accepted: 13 February 2023;
Published: 02 March 2023.
Edited by:
Jeong-Hwan Kim, Yokohama City University, JapanReviewed by:
Weiling Song, Qingdao University of Science and Technology, ChinaQuanjiang Dong, Qingdao University Medical College, China
Copyright © 2023 Azeem, Shafa, Aamir, Zubair, Souayeh and Alam. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: M. Mustafa Azeem, mustafa@mst.edu; Muhammad Aamir, msadiq@kfu.edu.sa