DNA Nanostructure-based Interfacial engineering for PCR-free ultrasensitive electrochemical analysis of microRNA. Sci Rep. 2012;2:867. [PMID: 23162691 PMCID: PMC3499757 DOI: 10.1038/srep00867]

Electrochemical detection of nucleic acids, proteins, small molecules and cells using a DNA-nanostructure-based universal biosensing platform

The occurrence and prognosis of many complex diseases, such as cancers, is associated with the variation of various molecules, including DNA at the genetic level, RNA at the regulatory level, proteins at the functional level and small molecules at the metabolic level (defined collectively as multilevel molecules). Thus it is highly desirable to develop a single platform for detecting multilevel biomarkers for early-stage diagnosis. Here we report a protocol on DNA-nanostructure-based programmable engineering of the biomolecular recognition interface, which provides a universal electrochemical biosensing platform for the ultrasensitive detection of nucleic acids (DNA/RNA), proteins, small molecules and whole cells. The protocol starts with the synthesis of a series of differentially sized, self-assembled tetrahedral DNA nanostructures (TDNs) with site-specifically modified thiol groups that can be readily anchored on the surface of a gold electrode with high reproducibility. By exploiting the rigid structure, nanoscale addressability and versatile functionality of TDNs, one can tailor the type of biomolecular probes appended on individual TDNs for the detection of specific molecules of interest. Target binding occurring on the gold surface patterned with TDNs is quantitatively translated into electrochemical signals via a coupled enzyme-based catalytic process. This uses a sandwich assay strategy in which biotinylated reporter probes recognize TDN-bound target biomolecules, which then allow binding of horseradish-peroxidase-conjugated avidin (avidin-HRP). Hydrogen peroxide (H2O2) is then reduced by avidin-HRP in the presence of TMB (3,3',5,5'-tetramethylbenzidine) to generate a quantitative electrochemical signal. The time range for the entire protocol is ∼1 d, whereas the detection process takes ∼30 min to 3 h.

Integrated Magneto-Electrochemical Sensor for Exosome Analysis

Extracellular vesicles, including exosomes, are nanoscale membrane particles that carry molecular information on parental cells. They are being pursued as biomarkers of cancers that are difficult to detect or serially follow. Here we present a compact sensor technology for rapid, on-site exosome screening. The sensor is based on an integrated magneto-electrochemical assay: exosomes are immunomagnetically captured from patient samples and profiled through electrochemical reaction. By combining magnetic enrichment and enzymatic amplification, the approach enables (i) highly sensitive, cell-specific exosome detection and (ii) sensor miniaturization and scale-up for high-throughput measurements. As a proof-of-concept, we implemented a portable, eight-channel device and applied it to screen extracellular vesicles in plasma samples from ovarian cancer patients. The sensor allowed for the simultaneous profiling of multiple protein markers within an hour, outperforming conventional methods in assay sensitivity and speed.

Hybridization chain reaction amplification for highly sensitive fluorescence detection of DNA with dextran coated microarrays

Microarrays of biomolecules hold great promise in the fields of genomics, proteomics, and clinical assays on account of their remarkably parallel and high-throughput assay capability. However, the fluorescence detection used in most conventional DNA microarrays is still limited by sensitivity. In this study, we have demonstrated a novel universal and highly sensitive platform for fluorescent detection of sequence specific DNA at the femtomolar level by combining dextran-coated microarrays with hybridization chain reaction (HCR) signal amplification. Three-dimensional dextran matrix was covalently coated on glass surface as the scaffold to immobilize DNA recognition probes to increase the surface binding capacity and accessibility. DNA nanowire tentacles were formed on the matrix surface for efficient signal amplification by capturing multiple fluorescent molecules in a highly ordered way. By quantifying microscopic fluorescent signals, the synergetic effects of dextran and HCR greatly improved sensitivity of DNA microarrays, with a detection limit of 10fM (1×10(5) molecules). This detection assay could recognize one-base mismatch with fluorescence signals dropped down to ~20%. This cost-effective microarray platform also worked well with samples in serum and thus shows great potential for clinical diagnosis.

Direct ultrasensitive electrochemical biosensing of pathogenic DNA using homogeneous target-initiated transcription amplification

Sensitive and specific methodologies for detection of pathogenic gene at the point-of-care are still urgent demands in rapid diagnosis of infectious diseases. This work develops a simple and pragmatic electrochemical biosensing strategy for ultrasensitive and specific detection of pathogenic nucleic acids directly by integrating homogeneous target-initiated transcription amplification (HTITA) with interfacial sensing process in single analysis system. The homogeneous recognition and specific binding of target DNA with the designed hairpin probe triggered circular primer extension reaction to form DNA double-strands which contained T7 RNA polymerase promoter and served as templates for in vitro transcription amplification. The HTITA protocol resulted in numerous single-stranded RNA products which could synchronously hybridized with the detection probes and immobilized capture probes for enzyme-amplified electrochemical detection on the biosensor surface. The proposed electrochemical biosensing strategy showed very high sensitivity and selectivity for target DNA with a dynamic response range from 1 fM to 100 pM. Using salmonella as a model, the established strategy was successfully applied to directly detect invA gene from genomic DNA extract. This proposed strategy presented a simple, pragmatic platform toward ultrasensitive nucleic acids detection and would become a versatile and powerful tool for point-of-care pathogen identification.

Elaborately designed diblock nanoprobes for simultaneous multicolor detection of microRNAs

Simultaneous detection of multiple biomarkers has important prospects in the biomedical field. In this work, we demonstrated a novel strategy for the detection of multiple microRNAs (miRNAs) based on gold nanoparticles (Au NPs) and polyadenine (polyA) mediated nanoscale molecular beacon (MB) probes (denoted p-nanoMBs). Novel fluorescent labeled p-nanoMBs bearing consecutive adenines were designed, of which polyA served as an effective anchoring block binding to the surface of Au NPs, and the appended hairpin block formed an upright conformation that favored the hybridization with targets. Using the co-assembling method and the improved hybridization conformation of the hairpin probes, we achieved high selectivity for specifically distinguishing DNA targets from single-base mismatched DNA targets. We also realized multicolor detection of three different synthetic miRNAs in a wide dynamic range from 0.01 nM to 200 nM with a detection limit of 10 pM. What's more, we even detected miRNAs in a simulated serum environment, which indicated that our method could be used in complex media. Compared with the traditional method, our strategy provides a promising alternative method for the qualitative and quantitative detection of miRNAs.

Constructing Higher-Order DNA Nanoarchitectures with Highly Purified DNA Nanocages

DNA nanostructures have attracted great attention due to their precisely controllable geometry and great potential in various areas including bottom-up self-assembly. However, construction of higher-order DNA nanoarchitectures with individual DNA nanostructures is often hampered with the purity and quantity of these "bricks". Here, we introduced size exclusion chromatography (SEC) to prepare highly purified tetrahedral DNA nanocages in large scale and demonstrated that precise quantification of DNA nanocages was the key to the formation of higher-order DNA nanoarchitectures. We successfully purified a series of DNA nanocages with different sizes, including seven DNA tetrahedra with different edge lengths (7, 10, 13, 17, 20, 26, 30 bp) and one trigonal bipyramid with a 20-bp edge. These highly purified and aggregation-free DNA nanocages could be self-assembled into higher-order DNA nanoarchitectures with extraordinarily high yields (98% for dimer and 95% for trimer). As a comparison, unpurified DNA nanocages resulted in low yield of 14% for dimer and 12% for trimer, respectively. AFM images cleraly presented the characteristic structure of monomer, dimer and trimer, impling the purified DNA nanocages well-formed the designed nanoarchitectures. Therefore, we have demonstrated that highly purified DNA nanocages are excellent "bricks" for DNA nanotechnology and show great potential in various applications of DNA nanomaterials.

Spatially nanoscale-controlled functional surfaces toward efficient bioactive platforms

Interest in well-defined surface architectures has shown a steady increase, particularly among those involved in biological applications where the reactivity of functional groups on the surface is desired to be close to that of the solution phase. Recent research has demonstrated that utilizing the self-assembly process is an attractive and viable choice for the fabrication of two-dimensional nanoscale-controlled architectures. This review highlights representative examples for controlling the spatial placement of reactive functional groups in the optimization of bioactive surfaces. While the selection is not comprehensive, it becomes evident that surface architecture is one of the key components in allowing efficient biomolecular interactions with surfaces and that the optimized lateral spacing between the immobilized molecules is crucial and even critical in some cases.

An electrochemical clamp assay for direct, rapid analysis of circulating nucleic acids in serum

The analysis of cell-free nucleic acids (cfNAs), which are present at significant levels in the blood of cancer patients, can reveal the mutational spectrum of a tumour without the need for invasive sampling of the tissue. However, this requires differentiation between the nucleic acids that originate from healthy cells and the mutated sequences shed by tumour cells. Here we report an electrochemical clamp assay that directly detects mutated sequences in patient serum. This is the first successful detection of cfNAs without the need for enzymatic amplification, a step that normally requires extensive sample processing and is prone to interference. The new chip-based assay reads out the presence of mutations within 15 minutes using a collection of oligonucleotides that sequester closely related sequences in solution, and thus allow only the mutated sequence to bind to a chip-based sensor. We demonstrate excellent levels of sensitivity and specificity and show that the clamp assay accurately detects mutated sequences in a collection of samples taken from lung cancer and melanoma patients.

Mach-Zehnder interferometer (MZI) point-of-care system for rapid multiplexed detection of microRNAs in human urine specimens

MicroRNAs have been identified as promising biomarkers for human diseases. The development of a point-of-care (POC) test for the disease-associated miRNAs would be especially beneficial, since miRNAs are unexpectedly well preserved in various human specimens, including urine. Here, we present the Mach-Zehnder interferometer-miRNA detection system capable of detecting multiple miRNAs in clinical urine samples rapidly and simultaneously in a label-free and real-time manner. Through measurement of the light phase change, the MZI sensor provides an optical platform for fast profiling of small molecules with improved accuracy. We demonstrate that this system could specifically detect target miRNAs (miR-21, and let-7a), and even identify the single nucleotide polymorphism of the let-7 family of miRNAs from synthetic and cell line samples. The clinical applicability of this system is confirmed by simultaneously detecting two types of miRNAs in urine samples of bladder cancer patients in a single reaction, with a detection time of 15 min. The POC system can be expanded to detect a number of miRNAs of different species and should be useful for a variety of clinical applications requiring at or near the site of patient care.

Point-of-care testing in the diagnosis of gastrointestinal cancers: Current technology and future directions

Point-of-care (POC) tests enable rapid results and are well established in medical practice. Recent advances in analytical techniques have led to a new generation of POC devices that will alter gastrointestinal diagnostic pathways. This review aims to identify current and new technologies for the POC diagnosis of gastrointestinal cancer. A structured search of the Embase and Medline databases was performed. Papers reporting diagnostic tests for gastrointestinal cancer available as a POC device or containing a description of feasibility for POC application were included. Studies recovered were heterogeneous and therefore results are presented as a narrative review. Six diagnostic methods were identified (fecal occult blood, fecal proteins, volatile organic compounds, pyruvate kinase isoenzyme type M2, tumour markers and DNA analysis). Fecal occult blood testing has a reported sensitivity of 66%-85% and specificity greater than 95%. The others are at a range of development and clinical application. POC devices have a proven role in the diagnosis of gastrointestinal cancer. Barriers to their implementation exist and the transition from experimental to clinical medicine is currently slow. New technologies demonstrate potential to provide accurate POC tests and an ability to diagnose gastrointestinal cancer at an early stage with improved clinical outcome and survival.

MicroRNA Detection: Current Technology and Research Strategies

The relatively new field of microRNA (miR) has experienced rapid growth in methodology associated with its detection and bioanalysis as well as with its role in -omics research, clinical diagnostics, and new therapeutic strategies. The breadth of this area of research and the seemingly exponential increase in number of publications on the subject can present scientists new to the field with a daunting amount of information to evaluate. This review aims to provide a collective overview of miR detection methods by relating conventional, established techniques [such as quantitative reverse transcription polymerase chain reaction (RT-qPCR), microarray, and Northern blotting (NB)] and relatively recent advancements [such as next-generation sequencing (NGS), highly sensitive biosensors, and computational prediction of microRNA/targets] to common miR research strategies. This should guide interested readers toward a more focused study of miR research and the surrounding technology.

Cancer biomarker detection: recent achievements and challenges

We provide an overview covering the existing challenges and latest developments in achieving high selectivity and sensitivity cancer-biomarker detection.

Sensitive mutant DNA biomarker detection based on magnetic nanoparticles and nicking endonuclease assisted fluorescence signal amplification

Amplified fluorescence target DNA detection was developed combining nicking endonuclease assisted target recycling and magnetic nanoparticles with low background signal.

Advancing the speed, sensitivity and accuracy of biomolecular detection using multi-length-scale engineering

Rapid progress in identifying disease biomarkers has increased the importance of creating high-performance detection technologies. Over the last decade, the design of many detection platforms has focused on either the nano or micro length scale. Here, we review recent strategies that combine nano- and microscale materials and devices to produce large improvements in detection sensitivity, speed and accuracy, allowing previously undetectable biomarkers to be identified in clinical samples. Microsensors that incorporate nanoscale features can now rapidly detect disease-related nucleic acids expressed in patient samples. New microdevices that separate large clinical samples into nanocompartments allow precise quantitation of analytes, and microfluidic systems that utilize nanoscale binding events can detect rare cancer cells in the bloodstream more accurately than before. These advances will lead to faster and more reliable clinical diagnostic devices.

DNA nanostructure-based universal microarray platform for high-efficiency multiplex bioanalysis in biofluids

Microarrays of biomolecules have greatly promoted the development of the fields of genomics, proteomics, and clinical assays because of their remarkably parallel and high-throughput assay capability. Immobilization strategies for biomolecules on a solid support surface play a crucial role in the fabrication of high-performance biological microarrays. In this study, rationally designed DNA tetrahedra carrying three amino groups and one single-stranded DNA extension were synthesized by the self-assembly of four oligonucleotides, followed by high-performance liquid chromatography purification. We fabricated DNA tetrahedron-based microarrays by covalently coupling the DNA tetrahedron onto glass substrates. After their biorecognition capability was evaluated, DNA tetrahedron microarrays were utilized for the analysis of different types of bioactive molecules. The gap hybridization strategy, the sandwich configuration, and the engineering aptamer strategy were employed for the assay of miRNA biomarkers, protein cancer biomarkers, and small molecules, respectively. The arrays showed good capability to anchor capture biomolecules for improving biorecognition. Addressable and high-throughput analysis with improved sensitivity and specificity had been achieved. The limit of detection for let-7a miRNA, prostate specific antigen, and cocaine were 10 fM, 40 pg/mL, and 100 nM, respectively. More importantly, we demonstrated that the microarray platform worked well with clinical serum samples and showed good relativity with conventional chemical luminescent immunoassay. We have developed a novel approach for the fabrication of DNA tetrahedron-based microarrays and a universal DNA tetrahedron-based microarray platform for the detection of different types of bioactive molecules. The microarray platform shows great potential for clinical diagnosis.

Multivalent capture and detection of cancer cells with DNA nanostructured biosensors and multibranched hybridization chain reaction amplification

Sensitive detection of cancer cells plays a critically important role in the early detection of cancer and cancer metastasis. However, because circulating tumor cells are extremely rare in peripheral blood, the detection of cancer cells with high analytical sensitivity and specificity remains challenging. Here, we have demonstrated a simple, sensitive and specific detection of cancer cells with the detection sensitivity of four cancer cells, which is lower than the cutoff value with respect to correlation with survival outcomes as well as predictive of metastatic disease in clinical diagnostics. We re-engineered the hybridization chain reaction (HCR) to multibranched HCR (mHCR) that can produce long products with multiple biotins for signal amplification and multiple branched arms for multivalent binding. The capturing gold surface is modified with DNA tetrahedral probes, which provide superior hybridization conditions for the multivalent binding. The synergetic effect of mHCR amplification and multivalent binding lead to the high sensitivity of our detection platform.

Physical and biochemical insights on DNA structures in artificial and living systems

CONSPECTUS: Highly specific DNA base-pairing is the basis for both fulfilling its genetic role and constructing novel nanostructures and hybrid conjugates with inorganic nanomaterials (NMs). There exist many remarkable differences in the physical properties of single-stranded (ss) and double-stranded (ds) DNA, which play important roles in regulation of biological processes in nature. Rapid advances in nanoscience and nanotechnology pose new questions on how DNA and DNA structures interact with inorganic nanomaterials or cells and animals, which should be important for their biological and biomedical applications. In this Account, we intend to provide an overview on many facets of DNA and DNA structures in artificial and living systems, with the focus on their properties and functions at the interfaces of inorganic nanomaterials and biological systems. ssDNA, dsDNA, and DNA nanostructures interact with NMs in different ways. In particular, gold nanoparticles and graphene oxide exhibit strikingly different affinity toward ssDNA and dsDNA. Such binding differences can be coupled with optical properties of NMs. For example, DNA hybridization can effectively modulate the plasmonic and catalytic properties of gold nanoparticles. By exploitation of these interactions, there have been many ways for sensitive transduction of biomolecular recognition for various sensing applications. Alternatively, modulation of the properties of DNA and DNA structures with NMs has led to new tools for genetic analysis including genotyping and haplotyping. Self-assembled DNA nanostructures have emerged as a new type of NMs with pure biomolecules. These nanostructures can be designed in one, two, or three dimensions with various sizes, shapes, and geometries. They also have characteristics of uniform size, precise addressability, excellent water solubility, and biocompatibility. These nanostructures provide a new toolbox for biophysical studies with unparalleled advantages, for example, NMR-based protein structure determination and single-molecule studies. Also importantly, DNA nanostructures have proven highly useful in various applications including biological detection, bioreactors, and nanomedicine. In particular, DNA nanostructures exhibit high cellular permeability, a property that is not available for ssDNA and dsDNA, which is required for their drug delivery applications. DNA and DNA structures can also form hybrids with inorganic NMs. Notably, DNA anchored at the interface of inorganic NMs behaves differently from that at the macroscopic interface. Several types of DNA-NM conjugates have exerted beneficial effects for bioassays and in vitro translation of proteins. Even more interestingly, hybrid nanoconjugates demonstrate distinct properties under the context of biological systems such as cultured cells or animal models. These unprecedented properties not only arouse great interest in studying such interfaces but also open new opportunities for numerous applications in artificial and living systems.

CMOS-compatible silicon nanowire field-effect transistors for ultrasensitive and label-free microRNAs sensing

MicroRNAs (miRNAs) have been regarded as promising biomarkers for the diagnosis and prognosis of early-stage cancer as their expression levels are associated with different types of human cancers. However, it is a challenge to produce low-cost miRNA sensors, as well as retain a high sensitivity, both of which are essential factors that must be considered in fabricating nanoscale biosensors and in future biomedical applications. To address such challenges, we develop a complementary metal oxide semiconductor (CMOS)-compatible SiNW-FET biosensor fabricated by an anisotropic wet etching technology with self-limitation which provides a much lower manufacturing cost and an ultrahigh sensitivity. This nanosensor shows a rapid (< 1 minute) detection of miR-21 and miR-205, with a low limit of detection (LOD) of 1 zeptomole (ca. 600 copies), as well as an excellent discrimination for single-nucleotide mismatched sequences of tumor-associated miRNAs. To investigate its applicability in real settings, we have detected miRNAs in total RNA extracted from lung cancer cells as well as human serum samples using the nanosensors, which demonstrates their potential use in identifying clinical samples for early diagnosis of cancer.

Fabrication of magneto-controlled moveable architecture to develop reusable electrochemical biosensors

Electrochemical biosensors have been studied intensively for several decades. Numerous sensing concepts and related interface architectures have been developed. However, all such architectures suffer a trade-off: simple architectures favour usability, whereas complex architectures favour better performance. To overcome this problem, we propose a novel concept by introducing a magneto-controlled moveable architecture (MCMA) instead of the conventional surface-fixed architecture. As a model, human breast cancer cells were used in this study. The results showed that a detection range from 100 to 1 × 10⁶ cells could be achieved. Moreover, the whole detection cycle, including the measurement and the regeneration, could be completed in only 2 min. Thus, usability and excellent performance can be achieved in a single biosensor.

Functional DNA nanostructures for theranostic applications

There has been tremendous interest in constructing nanostructures by exploiting the unparalleled ability of DNA molecules in self-assembly. We have seen the appearance of many fantastic, "art-like" DNA nanostructures in one, two, or three dimensions during the last two decades. More recently, much attention has been directed to the use of these elegant nanoobjects for applications in a wide range of areas. Among them, diagnosis and therapy (i.e., theranostics) are of particular interest given the biological nature of DNA. One of the major barricades for the biosensor design lies in the restricted target accessibility at the solid-water interface. DNA nanotechnology provides a convenient approach to well control the biomolecule-confined surface to increase the ability of molecular recognition at the biosensing interface. For example, tetrahedral DNA nanostructures with thiol modifications can be self-assembled at the gold surface with high reproducibility. Since DNA tetrahedra are highly rigid and well-defined structures with atomic precision and versatile functionality, they provide scaffolds for anchoring of a variety of biomolecular probes (DNA, aptamers, peptides, and proteins) for biosensing. Significantly, this DNA nanostructure-based biosensing platform greatly increases target accessibility and improves the sensitivity for various types of molecular targets (DNA, RNA, proteins, and small molecules) by several orders of magnitude. In an alternative approach, DNA nanostructures provide a framework for the development of dynamic nanosensors that can function inside the cell. DNA tetrahedra are found to be facilely cell permeable and can sense and image specific molecules in cells. More importantly, these DNA nanostructures can be efficient drug delivery nanocarriers. Since they are DNA molecules by themselves, they have shown excellent cellular biocompatibility with minimal cytotoxicity. As an example, DNA tetrahedra tailored with CpG oligonucleotide drugs have shown greatly improved immunostimulatory effects that makes them a highly promising nanomedicine. By taking them together, we believe these functionalized DNA nanostructures can be a type of intelligent theranostic nanodevice for simultaneous sensing, diagnosis, and therapy inside the cell.

Functional DNA nanostructures for theranostic applications

There has been tremendous interest in constructing nanostructures by exploiting the unparalleled ability of DNA molecules in self-assembly. We have seen the appearance of many fantastic, "art-like" DNA nanostructures in one, two, or three dimensions during the last two decades. More recently, much attention has been directed to the use of these elegant nanoobjects for applications in a wide range of areas. Among them, diagnosis and therapy (i.e., theranostics) are of particular interest given the biological nature of DNA. One of the major barricades for the biosensor design lies in the restricted target accessibility at the solid-water interface. DNA nanotechnology provides a convenient approach to well control the biomolecule-confined surface to increase the ability of molecular recognition at the biosensing interface. For example, tetrahedral DNA nanostructures with thiol modifications can be self-assembled at the gold surface with high reproducibility. Since DNA tetrahedra are highly rigid and well-defined structures with atomic precision and versatile functionality, they provide scaffolds for anchoring of a variety of biomolecular probes (DNA, aptamers, peptides, and proteins) for biosensing. Significantly, this DNA nanostructure-based biosensing platform greatly increases target accessibility and improves the sensitivity for various types of molecular targets (DNA, RNA, proteins, and small molecules) by several orders of magnitude. In an alternative approach, DNA nanostructures provide a framework for the development of dynamic nanosensors that can function inside the cell. DNA tetrahedra are found to be facilely cell permeable and can sense and image specific molecules in cells. More importantly, these DNA nanostructures can be efficient drug delivery nanocarriers. Since they are DNA molecules by themselves, they have shown excellent cellular biocompatibility with minimal cytotoxicity. As an example, DNA tetrahedra tailored with CpG oligonucleotide drugs have shown greatly improved immunostimulatory effects that makes them a highly promising nanomedicine. By taking them together, we believe these functionalized DNA nanostructures can be a type of intelligent theranostic nanodevice for simultaneous sensing, diagnosis, and therapy inside the cell.

Point-of-care technologies for molecular diagnostics using a drop of blood

Molecular diagnostics is crucial for prevention, identification, and treatment of disease. Traditional technologies for molecular diagnostics using blood are limited to laboratory use because they rely on sample purification and sophisticated instruments, are labor and time intensive, expensive, and require highly trained operators. This review discusses the frontiers of point-of-care (POC) diagnostic technologies using a drop of blood obtained from a finger prick. These technologies, including emerging biotechnologies, nanotechnologies, and microfluidics, hold the potential for rapid, accurate, and inexpensive disease diagnostics.

Electrochemical monitoring of an important biomarker and target protein: VEGFR2 in cell lysates

Vascular endothelial growth factor receptor 2 (VEGFR2) is a potential cell-type biomarker in clinical diagnoses. Besides, it's the target protein of many tyrosine kinase inhibitors and its expression significantly associates with clinical performance of these inhibitors. VEGFR2 detection provides an early warning for diseases and a basis for therapy and drug screening. Some methods have been developed for VEGFR2 determination. However, they are usually performed indirectly and complexly. Herein, an electrochemical biosensing platform for VEGFR2 analysis has been first proposed. It can detect the total concentrations of the VEGFR2 protein in cells lysates directly and can be used to monitor the changes of VEGFR2 expression levels induced by treatments of different inhibitors. Moreover, the inhibitor-VEGFR2 interactions are illuminated through theoretical simulation. The simulation results agree well with the experimental data, indicating the veracity of the proposed method. The electrochemical detection methodology for VEGFR2 would be promising in clinical diagnosis and drug screening.

DNA-conjugated quantum dot nanoprobe for high-sensitivity fluorescent detection of DNA and micro-RNA

Herein, we report a convenient approach to developing quantum dots (QDs)-based nanosensors for DNA and micro-RNA (miRNA) detection. The DNA-QDs conjugate was prepared by a ligand-exchange method. Thiol-labeled ssDNA is directly attached to the QD surface, leading to highly water-dispersible nanoconjugates. The DNA-QDs conjugate has the advantages of the excellent optical properties of QDs and well-controlled recognition properties of DNA and can be used as a nanoprobe to construct a nanosensor for nucleic acid detection. With the addition of a target nucleic acid sequence, the fluorescence intensity of QDs was quenched by an organic quencher (BHQ2) via Förster resonance energy transfer. This nanosensor can detect as low as 1 fM DNA and 10 fM miRNA. Moreover, the QDs-based nanosensor exhibited excellent selectivity. It not only can effectively distinguish single-base-mismatched and random nucleic sequences but also can recognize pre-miRNA and mature miRNA. Therefore, the nanosensor has high application potential for disease diagnosis and biological analysis.

Binding-induced autonomous disassembly of aptamer-DNAzyme supersandwich nanostructures for sensitive electrochemiluminescence turn-on detection of ochratoxin A

The self-assembled DNA nanostructure has been one of the most interesting research areas in the field of nanoscience, and the application of the DNA self-assembled nanostructures in biosensing is still in the early stage. In this work, based on the target-induced autonomous disassembly of the aptamer-DNAzyme supersandwich nanostructures, we demonstrated a highly sensitive strategy for electrochemiluminescent (ECL) detection of ochratoxin A (OTA). The aptamer-DNAzyme supersandwich nanostructures, which exhibited significant ECL quenching effect toward the oxygen/persulfate (O2/S2O8(2-)) system, were self-assembled on the gold electrode surface. The presence of the target OTA and the exonuclease (RecJf) resulted in autonomous disassembly of the nanostructures and cyclic reuse of OTA, leading to efficient recovery of the ECL emission and highly sensitive detection of OTA. Our developed method also showed high selectivity against other interference molecules and can be applied for the detection of OTA in real red wine samples, which offers the proposed method opportunities for designing new DNA-based nanostructures for biosensing applications.

Sensitive detection of microRNA by chronocoulometry and rolling circle amplification on a gold electrode

An integrated gold electrode fabricated on a polystyrene substrate was developed for quantitative detection of nucleic acids by rolling circle amplification and chronocoulometry.

Point-of-care nucleic acid detection using nanotechnology

Recent developments in nanotechnology have led to significant advancements in point-of-care (POC) nucleic acid detection. The ability to sense DNA and RNA in a portable format leads to important applications for a range of settings, from on-site detection in the field to bedside diagnostics, in both developing and developed countries. We review recent innovations in three key process components for nucleic acid detection: sample preparation, target amplification, and read-out modalities. We discuss how the advancements realized by nanotechnology are making POC nucleic acid detection increasingly applicable for decentralized and accessible testing, in particular for the developing world.

Self-assembled DNA tetrahedral optofluidic lasers with precise and tunable gain control

We have applied self-assembled DNA tetrahedral nanostructures for the precise and tunable control of the gain in an optofluidic fluorescence resonance energy transfer (FRET) laser. By adjusting the ratio of the donor and the acceptor attached to the tetrahedral vertices, 3.8 times reduction in the lasing threshold and 28-fold enhancement in the lasing efficiency were demonstrated. This work takes advantage of the self-recognition and self-assembly capabilities of biomolecules with well-defined structures and addressability, enabling nano-engineering of the laser down to the molecular level.

Supramolecular self-assemblies as functional nanomaterials

In this review, we survey the diversity of structures and functions which are encountered in advanced self-assembled nanomaterials. We highlight their flourishing implementations in three active domains of applications: biomedical sciences, information technologies, and environmental sciences. Our main objective is to provide the reader with a concise and straightforward entry to this broad field by selecting the most recent and important research articles, supported by some more comprehensive reviews to introduce each topic. Overall, this compilation illustrates how, based on the rules of supramolecular chemistry, the bottom-up approach to design functional objects at the nanoscale is currently producing highly sophisticated materials oriented towards a growing number of applications with high societal impact.

Self-assembly of DNA-based drug delivery nanocarriers with rolling circle amplification

DNA nanostructures have recently emerged as a type of drug delivery nanocarriers due to their suitable sizes, well-defined structures and low-toxicity. Here, we present a protocol for the assembly of DNA nanoribbon structures with rolling circle amplification (RCA) and delivery of CpG oligonucleotide. DNA nanoribbons with different dimensions and patterns were assembled with long RCA strands and several short staples. Significantly, we demonstrated they exhibited high-efficiency cellular uptake and improved immunostimulatory activity compared with ss- or ds- DNA.

Nanoscale spatial distribution of thiolated DNA on model nucleic acid sensor surfaces

The nanoscale arrangement of the DNA probe molecules on sensor surfaces has a profound impact on molecular recognition and signaling reactions on DNA biosensors and microarrays. Using electrochemical atomic force microscopy, we have directly determined the nanoscale spatial distribution of thiolated DNA that are attached to gold via different methods. We discovered significant heterogeneity in the probe density and limited stability for DNA monolayers prepared by the backfilling method, that is, first exposing the surface to thiolated DNA then "backfilling" with a passivating alkanethiol. On the other hand, the monolayers prepared by "inserting" thiolated DNA into a preformed alkanethiol monolayer lead to a more uniformly distributed layer of DNA. With high-resolution images of single DNA molecules on the surface, we have introduced spatial statistics to characterize the nanoscale arrangement of DNA probes. The randomness of the spatial distribution has been characterized. By determining the local densities surrounding individual molecules, we observed subpopulations of probes with dramatically different levels of "probe crowding". We anticipate that the novel application of spatial statistics to DNA monolayers can enable a framework to understand heterogeneity in probe spatial distributions, interprobe interactions, and ultimately probe activity on sensor surfaces.