Sensitive Detection of Nucleic Acids with Rolling Circle Amplification and Surface-Enhanced Raman Scattering Spectroscopy

SERS microfluidic chip integrated with double amplified signal off-on strategy for detection of microRNA in NSCLC

In this work, based on Fe3O4@AuNPs and double amplified signal Off-On strategy, a simple and sensitive SERS microfluidic chip was constructed to detect microRNA associated with non-small cell lung cancer (NSCLC). Fe3O4@AuNPs have two advantages of SERS enhanced and magnetic adsorption, the introduction of microfluidic chip can realize double amplification of SERS signal. First, the binding of complementary ssDNA and hpDNA moved the Raman signaling molecule away from Fe3O4@AuNPs, at which point the signal was turned off. Second, in the presence of the target microRNA, they were captured by complementary ssDNA and bound to them. HpDNA restored the hairpin conformation, the Raman signaling molecule moved closer to Fe3O4@AuNPs. At this time, the signal was turned on and strong Raman signal was generated. And last, through the magnetic component of SERS microfluidic chip, Fe3O4@AuNPs could be enriched to realize the secondary enhancement of SERS signal. In this way, the proposed SERS microfluidic chip can detect microRNA with high sensitivity and specificity. The corresponding detection of limit (LOD) for miR-21 versus miR-125b was 6.38 aM and 7.94 aM, respectively. This SERS microfluidic chip was promising in the field of early detection of NSCLC.

Deep Learning Assisted Surface-Enhanced Raman Spectroscopy (SERS) for Rapid and Direct Nucleic Acid Amplification and Detection: Toward Enhanced Molecular Diagnostics

Surface-enhanced Raman scattering (SERS) has evolved into a robust analytical technique capable of detecting a variety of biomolecules despite challenges in securing a reliable Raman signal. Conventional SERS-based nucleic acid detection relies on hybridization assays, but reproducibility and signal strength issues have hindered research on directly amplifying nucleic acids on SERS surfaces. This study introduces a deep learning assisted ZnO-Au-SERS-based direct amplification (ZADA) system for rapid, sensitive molecular diagnostics. The system employs a SERS substrate fabricated by depositing gold on uniformly grown ZnO nanorods. These nanorods create hot spots for the amplification of the target nucleic acids directly on the SERS surface, eliminating the need for postamplification hybridization and Raman reporters. The limit of detection of the ZADA system was superior to those of the conventional amplification methods. Clinical validation of the ZADA system with coronavirus disease 2019 (COVID-19) samples from human patients yielded a sensitivity and specificity of 92.31% and 81.25%, respectively. The integration of a deep learning program further enhanced sensitivity and specificity to 100% and reduced SERS analysis time, showcasing the potential of the ZADA system for rapid, label-free disease diagnosis via direct nucleic acid amplification and detection within 20 min.

Current strategies of plasmonic nanoparticles assisted surface-enhanced Raman scattering toward biosensor studies

With the progressive nanofabrication technology, plasmonic nanoparticles (PNPs) have been increasingly deployed in the field of biosensing. PNPs have favorable biocompatibility, conductivity, and tunable optical properties. In addition, the localized surface plasmon resonance (LSPR) of PNPs plays a vital role in surface-enhanced Raman scattering (SERS). PNPs-based SERS biosensing enables wide-ranging applications for sensitive detection and high spatial and temporal resolution imaging. Numerous reviews of PNPs in the field of SERS biosensing highlight the fabrication or applications in one or more fields. However, the specific strategies for the SERS biosensor construction had not been summarized systematically. Thus, this work offers a comprehensive overview of SERS enhancement strategies based on PNPs, with a focus on SERS label-free detection along with label detection sensing construction, as well as its challenges and future trends.

Progress on aptamer-based SERS sensors for food safety and quality assessment: methodology, current applications and future trends

It is well known that food safety has aroused extensive attentions from governments to researchers and to food industries. As a versatile technology based on molecular interactions, aptamer sensors which could specifically identify a wide range of food contaminants have been extensively studied in recent years. Surface-enhanced Raman spectroscopy integrated aptamer combines the advantages of both technologies, not only in the ability to specifically identify a wide range of food contaminants, but also in the ultra-high sensitivity, simplicity, portable and speed. To provide beneficial insights into the evaluation techniques in the field of food safety, we offer a comprehensive review on the design strategies for aptamer-SERS sensors in different scenarios, including non-nucleic acid amplification methods ("on/off" mode, sandwich mode, competition model and catalytic model) and nucleic acid amplification methods (hybridization chain reaction, rolling circle amplification, catalytic hairpin assembly). Meanwhile, a special attention is paid to the application of aptamer-SERS sensors in biological (foodborne pathogenic, bacteria and mycotoxins) and chemical contamination (drug residues, metal ions, and food additives) of food matrix. Finally, the challenges and prospects of developing reliable aptamer-SERS sensors for food safety were discussed, which are expected to offer a strong guidance for further development and extended applications.

Flexible Terahertz Metamaterial Biosensor for Ultra-Sensitive Detection of Hepatitis B Viral DNA Based on the Metal-Enhanced Sandwich Assay

The high sensitivity and specificity of terahertz (THz) biosensing are both promising and challenging in DNA sample detection. This study produced and refined a flexible THz MM biosensor for ultrasensitive detection of HBV in clinical serum samples based on a gold magnetic nanoparticle-mediated rolling circle amplification (GMNPs@RCA) sandwich assay under isothermal conditions. Typically, solid-phase RCA reactions mediated by circular padlock probes (PLPs) are triggered under isothermal conditions in the presence of HBV DNA, resulting in long single-stranded DNA (ssDNA) with high fidelity and specificity. Then, the resultant ssDNA was conjugated with detection probes (DPs) immobilized on gold nanoparticles (DP@AuNPs) to form GMNPs-RCA-AuNPs sandwich complexes. The HBV DNA concentrations were quantified by introducing GMNPs-RCA-AuNPs complexes into the metasurface of a flexible THz metamaterial-based biosensor chip and resulting in a red shift of the resonance peak of the THz metamaterials. This biosensor can lead to highly specific and sensitive detection with one-base mismatch discrimination and a limit of detection (LOD) down to 1.27E + 02 IU/ml of HBV DNA from clinical serum samples. The HBV DNA concentration was linearly correlated with the frequency shift of the THz metamaterials within the range of 1.27E + 02∼1.27E + 07 IU/ml, illustrating the applicability and accuracy of our assay in real clinical samples. This strategy constitutes a promising THz sensing method to identify virus DNA. In the future, it is hoped it can assist with pathogen identification and clinical diagnosis.

Fishing unfunctionalized SERS tags with DNA hydrogel network generated by ligation-rolling circle amplification for simple and ultrasensitive detection of kanamycin

Simple assay format-based SERS methods for sensitive target substance analysis is of great significance for the development of on-site monitoring biosensors. Herein, taking the typical antibacterial kanamycin (KANA) as a subject, a simple, highly sensitive and specific SERS aptasensor was developed by manipulating DNA hydrogel network to fish plasmonic core-shell nanoparticles. A competitive binding mode of aptamer, ligation-rolling circle amplification (L-RCA), gap-containing Au@Au nanoparticles (GCNPs) with embedded Raman reporters were integrated into the sensor. In the presence of KANA, the double stranded DNA (dsDNA) structure of the aptamer was disrupted, and the released primers were used to construct two kinds of circularized padlock probes (CPPs) which were partially complementary. DNA hydrogel network was formed through the intertwining and self-assembly of two RCA-generated single stranded DNA (ssDNA) chains, during which GCNPs and magnetic beads (MBs) were entangled and incorporated. Finally, KANA quantification was successfully achieved through the quantification of the DNA hydrogel. Overall, this novel SERS aptasensor realized a simple and ultrasensitive quantification of KANA down to 2.3 fM, plus excellent selectivity, and precision even for real food samples. In view of innovative fusion across L-RCA-based DNA hydrogel and SERS technique, the proposed method has promising potential for application in on-site detection and quantification of trace food contaminants.

Optical bio-sensing of DNA methylation analysis: an overview of recent progress and future prospects

DNA methylation as one of the most important epigenetic modifications has a critical role in regulating gene expression and drug resistance in treating diseases such as cancer. Therefore, the detection of DNA methylation in the early stages of cancer plays an essential role in disease diagnosis. The majority of routine methods to detect DNA methylation are very tedious and costly. Therefore, designing easy and sensitive methods to detect DNA methylation directly and without the need for molecular methods is a hot topic issue in bioscience. Here we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation. In addition, various types of labeled and label-free reactions along with the application of molecular methods and optical biosensors have been surveyed. Also, the effect of nanomaterials on the sensitivity of detection methods is discussed. Furthermore, a comprehensive overview of the advantages and disadvantages of each method are provided. Finally, the use of microfluidic devices in the evaluation of DNA methylation and DNA damage analysis based on smartphone detection has been discussed.

Here, we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation.

Formation of Visible Aggregates between Rolling Circle Amplification Products and Magnetic Nanoparticles as a Strategy for Point-of-Care Diagnostics

Visual detection of rolling circle amplification products (RCPs) has been achieved by specific aggregation with magnetic nanoparticles. The method presented here reliably generates aggregates in 1.5 h; these are visible to the naked eye in samples containing at least 0.4 fmol of RCPs. In addition, alternate current susceptometry and absorbance spectroscopy have also been used to quantify the amplified products. The specificity of the detection method was tested, and no non-specific aggregation was detected in samples containing up to 20 fmol of non-complementary amplified DNA. This method is a versatile tool for detecting pathogenic DNA in point-of-care diagnostics, with no readout equipment required. However, chips and automated assays can be used in conjugation with the developed method since detection and quantification can be achieved by commercially available readout instruments.

Electrospun Nanofibers for Cancer Therapy

Lately, a remarkable progress has been recorded in the field of electrospinning for the preparation of numerous types of nanofiber scaffolds. These scaffolds present some remarkable features including high loading capacity and encapsulation efficiency, superficial area and porosity, potential for modification, structure for the co-delivery of various therapies, and cost-effectiveness. Their present and future applications for cancer diagnosis and treatment are promising and pioneering. In this chapter we provide a comprehensive overview of electrospun nanofibers (ESNFs) applications in cancer diagnosis and treatment, covering diverse types of drug-loaded electrospun nanofibers.

Fluorescent and electrochemical dual-mode detection of Chikungunya virus E1 protein using fluorophore-embedded and redox probe-encapsulated liposomes

The critical goal of sensitive virus detection should apply in the early stage of infection, which may increase the probable survival rate. To achieve the low detection limit for the early stage where a small number of viruses are present in the sample, proper amplified signals from a sensor can make readable and reliable detection. In this work, a new model of fluorescent and electrochemical dual-mode detection system has been developed to detect virus, taking recombinant Chikungunya virus E1 protein (CHIK-VP) as an example. The hydrophobic quantum dots (QDs) embedded in the lipid bilayer of liposome and methylene blue (MB) encapsulated in the inner core of liposomes played a role of dual-signaling modulator. After CHIK-VP addition, the nanocomposites and APTES-coated Fe₃O₄ nanoparticles (Fe₃O₄ NPs) were conjugated with antibodies to form a sandwich structure and separated from the medium magnetically. The nanoconjugates have been burst out by chloroform as surfactant, and both the QDs and MB are released from the liposome and were then monitored through changes in the fluorescence and electrochemical signals, respectively. These two fluorometric and electrochemical signals alteration quantified the CHIK-VP in the range of femtogram to nanogram per milliliter level with a LOD of 32 fg mL⁻¹, making this liposomal system a potential matrix in a virus detection platform.

Rolling circle amplification promoted magneto-controlled photoelectrochemical biosensor for organophosphorus pesticides based on dissolution of core-shell MnO2 nanoflower@CdS mediated by butyrylcholinesterase

A photoelectrochemical (PEC) aptasensing platform is devised for sensitive detection of an organophosphorus pesticide based on dissolution of core-shell MnO₂ nanoflower@CdS (MnO₂ NF@CdS) by thiocholine (TCh). TCH is produced from the butyrylcholinesterase-acetylthiocholine system, accompanied by target-triggered rolling circle amplification (RCA). The core-shell MnO₂ NF@CdS with excellent PEC performance was synthesized and employed as a photo-sensing platform. The target was detected on a functionalized magnetic probe with the corresponding aptamer. Upon malathion introduction, the aptamer was detached from the magnetic beads, while capture DNA (cDNA, with primer fragment) remained on the beads. The primer fragment in cDNA can trigger the RCA reaction to form a long single-stranded DNA (ssDNA). Furthermore, a large number of butyrylcholinesterase (BChE) were assembled on the long ssDNA strands through the hybridization with the S₂-Au-BChE probe. Thereafter, TCh generated from hydrolysis of ATCh by BChE can reduce MnO₂ NF (core) to Mn²⁺ and release the CdS nanoparticles (shell) from the platform electrode, significantly enhancing the PEC signal. Under optimal conditions, the proposed aptasensor exhibited high sensitivity for malathion with a low detection limit of 0.68 pg mL^-1. Meanwhile, it also presents outstanding specificity, reproducibility, and stability. Importantly, the sensing platform provides a new concept for detection of pesticide. Graphical abstract Herein, this work devised a photoelectrochemical (PEC) aptasensing platform for sensitive detection of organophosphorus pesticide based on dissolution of core-shell MnO₂ nanoflower@CdS (MnO₂ NF@CdS) by the as-produced thiocholine (TCh) from the butyrylcholinesterase-acetylthiocholine system, accompanying with the target-triggered rolling circle amplification (RCA).

Surface Enhanced Raman Spectroscopy for DNA Biosensors-How Far Are We?

A sensitive and accurate identification of specific DNA fragments (usually containing a mutation) can influence clinical decisions. Standard methods routinely used for this type of detection are PCR (Polymerase Chain Reaction, and its modifications), and, less commonly, NGS (Next Generation Sequencing). However, these methods are quite complicated, requiring time-consuming, multi-stage sample preparation, and specially trained staff. Usually, it takes weeks for patients to obtain their results. Therefore, different DNA sensors are being intensively developed by many groups. One technique often used to obtain an analytical signal from DNA sensors is Raman spectroscopy. Its modification, surface-enhanced Raman spectroscopy (SERS), is especially useful for practical analytical applications due to its extra low limit of detection. SERS takes advantage of the strong increase in the efficiency of Raman signal generation caused by a local electric field enhancement near plasmonic (typically gold and silver) nanostructures. In this condensed review, we describe the most important types of SERS-based nanosensors for genetic studies and comment on their potential for becoming diagnostic tools.

A dual-cycling fluorescence scheme for ultrasensitive DNA detection through signal amplification and target regeneration

In this work, we propose an ultrasensitive fluorescence strategy for DNA detection. This method utilizes a molecular beacon (MB), a hairpin probe (HP), and an enzyme to trigger dual-cycling reactions (cycles I and II). In cycle I, the target is repeatedly used to amplify the fluorescence emission through hybridizations with the MB and cleavage reactions achieved by the enzyme. In cycle II, hybridization reactions between the HP and a segment of the MB continuously regenerate the target to trigger more cycle I reactions, leading to an enhanced fluorescent signal. The detection limit of the method is determined to be as low as 50 fM within 45 min, which is 2 to 3 orders of magnitude lower than that of the conventional fluorescence strategies. The method also shows a high selectivity over mismatched and random DNA sequences. The signal amplification mechanism of the strategy offers insights into constructing efficient and ultrasensitive biosensors for various applications.

Nanoscale Nucleic Acid Recognition at the Solid-Liquid Interface Using Xeno Nucleic Acid Probes

Challenges in reliable nucleic acid detection are manifold. The major ones are related to false positive or negative signals due to a lack of target specificity in detection and to low sensitivity, especially when a plethora of background sequences are present that can mask the specific recognition signal. Utilizing designed synthetic nucleic acids that are commonly called xeno nucleic acids could offer potential routes to meeting such challenges. In this article, we present the general framework of nucleic acid detection, especially for nanoscale applications, and discuss how and why the xeno nucleic acids could be truly an alternative to the DNA probes. Two specific cases, locked nucleic acid (LNA) and peptide nucleic acid (PNA), which are nuclease-resistant and can form thermally stable duplexes with DNA, are addressed. It is shown that the relative ease of the conformationally rigid LNA probe to be oriented upright on the substrate surface and of the nonionic PNA probe to result into high probe density assists in their use in nanoscale nucleic acid recognition. It is anticipated that success with these probes may lead to important developments such as PCR-independent approaches where the major aim is to detect a small number of target sequences present in the analyte medium.

A dandelion-like liposomes-encoded magnetic bead probe-based toehold-mediated DNA circuit for the amplification detection of MiRNA

The development of facile and sensitive miRNA quantitative detection methods is a central challenge for the early diagnosis of miRNA-related diseases. Herein, we propose a strategy for a liposome-encoded magnetic bead-based DNA toehold-mediated DNA circuit for the simple and sensitive detection of miRNA based on a toehold-mediated circular strand displacement reaction (TCSDR) coupled with a personal glucometer (PGM ). In this strategy, a glucoamylase-encapsulated liposomes (GELs)-encoded magnetic bead (GELs-MB) probe is designed to integrate target binding, magnetic separation, and signal response. Upon sensing the target miRNA-21, a GELs-MB probe-based toehold-mediated circular strand displacement reaction (TCSDR) was initiated with the help of fuel-DNA, constructing a DNA circuit system, and realizing target recycling amplification and the disassembly of the liposomes. The disassembled liposomes were finally removed via magnetic separation, and the encapsulated glucoamylase was liberated to catalyze amylose hydrolysis with multiple turnovers to glucose for a PGM readout. Benefiting from target recycling amplification initiated by the toehold-mediated DNA circuit and the liposome multiple-label amplification, a small quantity of target miRNA-21 can be transformed into a large glucose signal. The strategy realized the quantification of miRNA-21 down to a level of 0.7 fM without enzymatic amplification or precise instrumentation. Moreover, the high-density GELs-MB probe allows the sensitive detection of miRNA-21 to be accomplished within 1.5 h. Furthermore, this strategy exhibits the advantages of specificity and simplicity, since a toehold-mediated strand displacement reaction, magnetic separation and portable PGM were used. Importantly, this strategy has been demonstrated to allow the high-confidence quantification of miRNA. Therefore, with the advantages of low cost, ease of use, portability, and sensitivity, the reported method holds great potential for the early diagnosis of miRNA-related diseases.

Plasmonic molecular assays: Recent advances and applications for mobile health

Plasmonics-based biosensing assays have been extensively employed for biomedical applications. Significant advancements in use of plasmonic assays for the construction of point-of-care (POC) diagnostic methods have been made to provide effective and urgent health care of patients, especially in resourcelimited settings. This rapidly progressive research area, centered on the unique surface plasmon resonance (SPR) properties of metallic nanostructures with exceptional absorption and scattering abilities, has greatly facilitated the development of cost-effective, sensitive, and rapid strategies for disease diagnostics and improving patient healthcare in both developed and developing worlds. This review highlights the recent advances and applications of plasmonic technologies for highly sensitive protein and nucleic acid biomarker detection. In particular, we focus on the implementation and penetration of various plasmonic technologies in conventional molecular diagnostic assays, and discuss how such modification has resulted in simpler, faster, and more sensitive alternatives that are suited for point-of-use. Finally, integration of plasmonic molecular assays with various portable POC platforms for mobile health applications are highlighted.

Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application

Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.

SERS Quantification and Characterization of Proteins and Other Biomolecules

Changes in protein expression levels and protein structure may indicate genomic mutations and may be related to some diseases. Therefore, the precise quantification and characterization of proteins can be used for disease diagnosis. Compared with several other alternative methods, surface-enhanced Raman scattering (SERS) spectroscopy is regarded as an excellent choice for the quantification and structural characterization of proteins. Herein, we review the main advance of using plasmonic nanostructures as SERS sensing platform for this purpose. Three design approaches, including direct SERS, indirect SERS, and SERS-encoded nanoparticles, are discussed in the direction of developing new precise approaches of quantification and characterization of proteins. While this Review is focused on proteins, in order to highlight concepts of SERS-based sensors also detection of other biomolecules will be discussed.

The effect of main urine inhibitors on the activity of different DNA polymerases in loop-mediated isothermal amplification

BACKGROUND

The use of rapid amplification methods to detect pathogens in biological samples is mainly limited by the amount of pathogens present in the sample and the presence of inhibiting substances. Inhibitors can affect the amplification efficiency by either binding to the polymerase, interacting with the DNA, or interacting with the polymerase during primer extension. Amplification is performed using DNA polymerase enzymes and even small changes in their activity can influence the sensitivity and robustness of molecular assays Methods: The main purpose of this research was to examine which compounds present in urine inhibit polymerases with strand displacement activity. To quantify the inhibition, we employed quantitative loop-mediated isothermal amplification Results: The authors found that the presence of BSA, Mg 2+, and urea at physiologically relevant concentrations, as well as acidic or alkaline conditions did not affect the activity of any of the tested polymerases. However, addition of salt significantly affected the activity of the tested polymerases.

CONCLUSION

These findings may aid in the development of more sensitive, robust, cost effective isothermal amplification based molecular assays suitable for both point-of-care testing and on-site screening of pathogens directly from unprocessed urine which avoid the need for long and tedious DNA purification steps prior to amplification.

Mismatch detection in DNA monolayers by atomic force microscopy and electrochemical impedance spectroscopy

Background: DNA hybridization is at the basis of most current technologies for genotyping and sequencing, due to the unique properties of DNA base-pairing that guarantee a high grade of selectivity. Nonetheless the presence of single base mismatches or not perfectly matched sequences can affect the response of the devices and the major challenge is, nowadays, to distinguish a mismatch of a single base and, at the same time, unequivocally differentiate devices read-out of fully and partially matching sequences.

Results: We present here two platforms based on different sensing strategies, to detect mismatched and/or perfectly matched complementary DNA strands hybridization into ssDNA oligonucleotide monolayers. The first platform exploits atomic force microscopy-based nanolithography to create ssDNA nano-arrays on gold surfaces. AFM topography measurements then monitor the variation of height of the nanostructures upon biorecognition and then follow annealing at different temperatures. This strategy allowed us to clearly detect the presence of mismatches. The second strategy exploits the change in capacitance at the interface between an ssDNA-functionalized gold electrode and the solution due to the hybridization process in a miniaturized electrochemical cell. Through electrochemical impedance spectroscopy measurements on extended ssDNA self-assembled monolayers we followed in real-time the variation of capacitance, being able to distinguish, through the difference in hybridization kinetics, not only the presence of single, double or triple mismatches in the complementary sequence, but also the position of the mismatched base pair with respect to the electrode surface.

Conclusion: We demonstrate here two platforms based on different sensing strategies as sensitive and selective tools to discriminate mismatches. Our assays are ready for parallelization and can be used in the detection and quantification of single nucleotide mismatches in microRNAs or in genomic DNA.

Isothermal Amplification of Nucleic Acids

Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.

Portable and sensitive quantitative detection of DNA using personal glucose meters and exonuclease III-assisted signal amplification

A portable and sensitive quantitative DNA detection method using personal glucose meters (PGMs) and Exonuclease III-assisted signal amplification was developed. In the presence of target DNA, a target recycling process that can release target and linker DNA was obtained. The released linker DNA was used to link capture DNA on magnetic beads and the DNA invertase. After the washing away of unbound target DNA and subsequent DNA-invertase conjugation, the bound DNA-invertase can be used to catalyze the hydrolysis of sucrose into glucose with millions of turnovers, which transforms the concentration of target DNA into the level of glucose monitored by PGMs. There was a linear relationship between the signal of PGM and the concentration of target DNA in the range of 0.5 pM to 100 pM. A correlation coefficient of 0.989 was obtained, and the relative standard deviation (RSD) was 4.1% for a concentration of 50 pM target DNA (n = 9). In addition, the method exhibits excellent sequence selectivity, being able to differentiate a single mismatch in the target DNA. What is more, there was almost no effect from biological complexes on detection performance, which suggests our method can be successfully applied to DNA detection in real biological samples.

SERS-based approaches toward genetic profiling

In the last decade surface-enhanced Raman scattering (SERS) has experienced an important resurgence, and as a consequence it has seen wide application in the biological field, especially for DNA identification. SERS-based DNA detection can be carried out directly and indirectly and, in the latter approach, it relies on the use of SERS tags, whose role is to indirectly prove the recognition and binding of a specific oligonucleotide sequence. Herein, the role of SERS tags is analyzed focusing specifically on the use of DNA identification for genetic profiling.

Simultaneous and sensitive detection of dual DNA targets via quantum dot-assembled amplification labels

We describe a signal amplification assay for the simultaneous detection of HIV-1 and HIV-2 via a quantum dot (QD) layer-by-layer assembled polystyrene microsphere (PS) composite in a homogeneous format. The crucial point of this composite is the core-shell system. PS is utilized as the core and QDs as the shell. Based on the high affinity of streptavidin and biotin, QDs are assembled layer-by-layer on the surface of the PS as amplification labels. Biotinylated reporter probe is combined with the PS-QDs conjugate and then hybridized with target DNA immobilized on the surface of a 96-well plate. Using this approach, each target DNA corresponds to a large number of QDs and the fluorescence signal is greatly enhanced. Two QD colors (605 and 655 nm) are used to detect dual-target DNAs simultaneously. Taking advantage of the enzyme-free reaction and high sensitivity, this PS-QD-based sensor can be used in simple 'mix and detection' assays. Our results show that this technology has potential application in rapid point-of-care testing, gene expression studies, high-throughput screening and clinical diagnostics.

Development of rolling circle amplification based surface-enhanced Raman spectroscopy method for 35S promoter gene detection

In this study, we developed the genetically modified organism detection method by using the combination of rolling circle amplification (RCA) and surface-enhanced Raman spectroscopy (SERS). An oligonucleotide probe which is specific for 35S DNA promoter target was immobilised onto the gold slide and a RCA reaction was performed. A self-assembled monolayer was formed on gold nanorods using 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) and the second probe of the 35S DNA promoter target was immobilised on the activated gold coated slide surfaces. Probes on the nanoparticles were hybridised with the target oligonucleotide. Quantification of the target concentration was performed via SERS spectra of DTNB on the nanorods. SERS spectra of target molecules were enhanced through the RCA reaction and the detection limit was found to be 6.3fM. The sensitivity of the developed RCA-SERS method was compared with another method which had been performed without using RCA reaction, and the detection limit was found to be 0.1pM. The correlation between the target concentration and the SERS signal was found to be linear, within the range of 1pM to 10nM for the traditional assay and 100fM to 100nM for the RCA assay. For the developed RCA-SERS assay, the specificity tests were performed using the 35S promoter of Bt-176 maize gene. It was found out that the developed RCA-SERS sandwich assay method is quite sensitive, selective and specific for target sequences in model and real systems.

In situ polydopamine-assisted deposition of silver nanoparticles on a two dimensional support as an inexpensive and highly efficient SERS substrate

Versatile substrates were modified with polydopamine followed by in situ AgNP deposition to fabricate a cheap, flexible and disposable SERS substrate.

A linear DNA probe as an alternative to a molecular beacon for improving the sensitivity of a homogenous fluorescence biosensing platform for DNA detection using target-primed rolling circle amplification

Linear single-labeled DNA probes are used in this RCA-based fluorescence strategy for DNA detection, which could effectively avoid the fluorescence quenching between neighboring signal probes using hairpin probe as signal probe.