Metal sulfide nanoparticle-based dual barcode-triggered DNAzyme cascade for multiplex miRNA detection in a single assay

Single miRNAs are not specific and accurate enough to meet the strict diagnosis requirements in practice. Therefore, simultaneous monitoring of multiplexed miRNA in biological samples can not only improve the accuracy and specificity of bioassays but also avoid the squandering of valuable biological specimens. Herein, we designed a metal sulfide nanoparticle-based dual barcode-triggered DNAzyme cascade strategy for the sensitive and simultaneous multiplex miRNA detection in a single assay. Firstly, the capture probes (H1, H2) specifically recognize targets (miRNA-21, miRNA-141), exposing the stem of H1 and H2. Then, with the introduction of a detection probe (CuS-H3, ZnS-H4), the exposed H1 and H2 catalyze the hairpin assembly (CHA) reaction, realizing target miRNA recycling, and forming H1/H3-CuS and H2/H4-ZnS complexes. Subsequently, the formed H1/H3-CuS and H2/H4-ZnS complexes are encoded on magnetic beads through the biotin/streptavidin interaction. The CuS and ZnS nanoparticles captured by magnetic beads release thousands of Cu²⁺ and Zn²⁺via the cation exchange reaction. Finally, the released Cu²⁺ and Zn²⁺ specially activate the DNAzyme of the catalytic and molecular beacon (CAMB) system. The CAMB system affords an amplified fluorescence signal output by cycling and regenerating the metal ion-dependent DNAzyme to realize multiple enzymatic turnovers. Benefiting from target recycling, nanoparticle amplification, and catalytic and molecular beacon amplification, there is substantial amplification and the target miRNAs can be detected at 0.06 fM (miRNA-21) and 0.048 fM (miRNA-141) in a single assay. Furthermore, the high selectivity and accuracy of the assay were proved by practical analysis of different cancer cells, which exhibited good practicability in multiplex miRNA detection in clinical sera. The results indicate that the proposed strategy holds great potential for the sensitive detection of multiplex cancer biomarkers and offers the opportunity for future applications in clinical diagnosis.

Rapid detection of miRNA via development of consecutive adenines (polyA)-based electrochemical biosensors

Herein, we report rapid electrochemical detection of miRNA let-7a based on a DNA probe consisting of a polyA and Fc-co-labeled harpin structure (the polyA-H probe). The polyA-H probe could be facilely immobilized on Au surfaces through the interactions between polyA and Au, followed by its pre-hybridization with a single strand (S1). The probe's surface density could be optimized for minimizing steric hindrance via changing the polyA block length. The target let-7a could be rapidly amplified via loop-mediated isothermal amplification (LAMP) with four simplified primers, followed by inducing the formation of dimeric i-motif (DIM) structure via H⁺-induced rapid folding of two C-rich sequences of motif strand 1 and strand 2. It was found that, after introducing the as-formed DIM to hybridize the S1, the immobilized polyA₂₀-H probe could rapidly revert to its hairpin structure, sending out a turn-on electrochemical signal of the Fc. The total time for detecting the let-7a was around 80 min, obviously less than that of most of electrochemical DNA sensors reported previously. The biosensor showed a linear relationship of the current response to the let-7a in the range of 10 fM to 50 nM with a limit of detection (LOD) of 5.1 fM. Our biosensors were further tested using human serum spiked with the let-7a and the extracts of the breast adenocarcinoma cells spiked with and without the let-7a, respectively. Satisfied results were obtained. This study shows a potential promising future of development of electrochemical biosensors for rapid detection of miRNAs in the application of clinical practice.

Single-stranded circular DNA theranostics

The past decade has witnessed the blossom of nucleic acid therapeutics and diagnostics (theranostics). Unlike conventional small molecule medicines or protein biologics, nucleic acid theranostics have characteristic features such as the intrinsic ability as “information drugs” to code and execute genetic and theranostic information, ready programmability for nucleic acid engineering, intrinsic stimulatory or regulatory immunomodulation, versatile functionalities, and easy conformational recovery upon thermal or chemical denaturation. Single-stranded circular DNA (circDNA) are a class of single-stranded DNAs (ssDNA) featured with their covalently-closed topology. In addition to the basic advantages of nucleic acids-based materials, such as low cost, biocompatibility, and simplicity of chemical modification, the lack of terminals in circDNA prevents exonuclease degradation, resulting in enhanced biostability relative to the corresponding linear ssDNA. circDNA has been explored for versatile theranostic applications. For instance, circDNA has been extensively studied as templates for bioanalytical signal amplification and the synthesis of nano-/micro-/macro- biomaterials via rolling circle amplification (RCA) and rolling circle transcription (RCT) technologies. circDNA has also been commonly used as the scaffolds for the self-assembly of versatile DNA origami. Finally, circDNA has been implemented as theranostic aptamers, miRNA inhibitors, as well as clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) gene editing donors. In this review article, we will discuss the chemistry, characteristic properties, and the theranostic applications of circDNA (excluding double-stranded circular DNA such as plasmids); we will also envision the challenges and opportunities in this research field.

Recent advances in biological detection with rolling circle amplification: design strategy, biosensing mechanism, and practical applications

Rolling circle amplification (RCA) is a simple and isothermal DNA amplification technique that is used to generate thousands of repeating DNA sequences using circular templates under the catalysis of DNA polymerase.

DNA Based and Stimuli-Responsive Smart Nanocarrier for Diagnosis and Treatment of Cancer: Applications and Challenges

The rapid development of multidrug co-delivery and nano-medicines has made spontaneous progress in tumor treatment and diagnosis. DNA is a unique biological molecule that can be tailored and molded into various nanostructures. The addition of ligands or stimuli-responsive elements enables DNA nanostructures to mediate highly targeted drug delivery to the cancer cells. Smart DNA nanostructures, owing to their various shapes, sizes, geometry, sequences, and characteristics, have various modes of cellular internalization and final disposition. On the other hand, functionalized DNA nanocarriers have specific receptor-mediated uptake, and most of these ligand anchored nanostructures able to escape lysosomal degradation. DNA-based and stimuli responsive nano-carrier systems are the latest advancement in cancer targeting. The data exploration from various studies demonstrated that the DNA nanostructure and stimuli responsive drug delivery systems are perfect tools to overcome the problems existing in the cancer treatment including toxicity and compromised drug efficacy. In this light, the review summarized the insights about various types of DNA nanostructures and stimuli responsive nanocarrier systems applications for diagnosis and treatment of cancer.

Fabrication and application of nanoporous anodic aluminum oxide: a review

Due to the unique optical and electrochemical properties, large surface area, tunable properties, and high thermal stability, nanoporous anodic aluminum oxide (AAO) has become one of the most popular materials with a large potential to develop emerging applications in numerous areas, including biosensors, desalination, high-risk pollutants detection, capacitors, solar cell devices, photonic crystals, template-assisted fabrication of nanostructures, and so on. This review covers the mechanism of AAO formation, manufacturing technology, the relationship between the properties of AAO and fabrication conditions, and applications of AAO. Properties of AAO, like pore diameter, interpore distance, wall thickness, and anodized aluminum layer thickness, can be fully controlled by fabrication conditions, including electrolyte, applied voltage, anodizing and widening time. Generally speaking, the pore diameter of AAO will affect its specific application to a large extent. Moreover, manufacturing technology like one/two/multi step anodization, nanoimprint lithography anodization, and pulse/cyclic anodization also have a major impact on overall array arrangement. The review aims to provide a perspective overview of the relationship between applications and their corresponding AAO pore sizes, systematically. And the review also focuses on the strategies by which the structures and functions of AAO can be utilized.

Self-Assembled DNA Nanoflowers Triggered by a DNA Walker for Highly Sensitive Electrochemical Detection of Staphylococcus aureus

With the development of DNA nanotechnology, DNA has been widely used to construct a variety of nanomachines. Among them, a DNA walker is a unique nanomachine that can move continuously along a specific orbit to fulfill diverse functions. In this paper, a dual signal amplification electrochemical biosensor based on a DNA walker and DNA nanoflowers is constructed for high sensitivity detection of Staphylococcus aureus (S. aureus). Two groups of double-stranded DNA are modified on the surface of a gold electrode. The binding of S. aureus with its aptamer induces the disintegration of the long double strands and releases the DNA walker. With the help of exonuclease III (Exo III), the DNA walker moves along the electrode surface and continuously hydrolyzes the anchored short double strands. The introduction of a specially customized circular DNA and phi29 DNA polymerase initiates the rolling circle amplification (RCA) reaction. DNA nanoflowers are formed at high local concentration of DNA in the solution, which provide binding sites for electroactive methylene blue (MB) and thus produce intense signal. Under the best conditions, the current response is linearly related to the logarithm of the concentration of S. aureus ranging from 60 to 6 × 10⁷ CFU/mL, and the detection limit is 9 CFU/mL. In addition, the proposed biosensor has achieved satisfactory results in the detection of actual water samples and diluted honey samples, which confirm the practicability of the biosensor and its application potential in environmental monitoring and food safety.

Enzymatical biomineralization of DNA nanoflowers mediated by manganese ions for tumor site activated magnetic resonance imaging

DNA nanoflower has been demonstrated as a promising DNA nanostructure for therapeutics and bioimaging primarily because of the programmable DNA sequence and unique structure. Herein, we report manganese ions mediated enzymatic biomineralization to prepare DNA-Mn hybrid nanoflower (DMNF). Paramagnetic Mn²⁺ was explored as the co-factor of DNA polymerase for the extension of long strand DNA. The biomimetic synthesis of DMNF was performed using the long strand DNA as template via nucleation and growth of Mn₂PPi. The morphology and size of DMNF were controllable by tuning reaction time and Mn²⁺ concentration. The aptamer sequence was encoded into circle template to achieve tumor-targeted DMNF, and cellular uptake assay demonstrated obvious aptamer-mediated internalization. DMNF showed enhanced T₁-weighted magnetic resonance (MR) imaging effect in acid environment for high tumor-specific MR imaging, and high spatial resolution imaging of kidneys and liver. Our work provides a facile enzymatically biomineral strategy to integrate multifunctional modules into one DNA structure and promotes the development of DNA nanostructure for precision medicine.

Molecular insights and novel approaches for targeting tumor metastasis

In recent years, due to the effective drug delivery and preciseness of tumor sites or microenvironment, the targeted drug delivery approaches have gained ample attention for tumor metastasis therapy. The conventional treatment approaches for metastasis therapy have reported with immense adverse effects because they exhibited maximum probability of killing the carcinogenic cells along with healthy cells. The tumor vasculature, comprising of vasculogenic impressions and angiogenesis, greatly depends upon the growth and metastasis in the tumors. Therefore, various nanocarriers-based delivery approaches for targeting to tumor vasculature have been attempted as efficient and potential approaches for the treatment of tumor metastasis and the associated lesions. Furthermore, the targeted drug delivery approaches have found to be most apt way to overcome from all the limitations and adverse effects associated with the conventional therapies. In this review, various approaches for efficient targeting of pharmacologically active chemotherapeutics against tumor metastasis with the cohesive objectives of prognosis, tracking and therapy are summarized.

In situ growth of nano-gold on anodized aluminum oxide with tandem nanozyme activities towards sensitive electrochemical nanochannel sensing

The growth of nano-gold tandem nanozymes on anodized aluminum oxide is successfully developed using poly-dopamine as an in situ reducing layer for electrochemical nanochannel sensing.

Static DNA Nanostructures For Cancer Theranostics: Recent Progress In Design And Applications

Among the various nano/biomaterials used in cancer treatment, the beauty and benefits of DNA nanocomposites are outstanding. The specificity and programmability of the base pairing of DNA strands, together with their ability to conjugate with different types of functionalities have realized unsurpassed potential for the production of two- and three-dimensional nano-sized structures in any shape, size, surface chemistry and functionality. This review aims to provide an insight into the diversity of static DNA nanodevices, including DNA origami, DNA polyhedra, DNA origami arrays and bioreactors, DNA nanoswitch, DNA nanoflower, hydrogel and dendrimer as young but promising platforms for cancer theranostics. The utility and potential of the individual formats in biomedical science and especially in cancer therapy will be discussed.

Fabrication of polydimethylsiloxane nanofluidic chips under AFM tip-based nanomilling process

In current research realm, polydimethylsiloxane (PDMS)-based nanofluidic devices are widely used in medical, chemical, and biological applications. In the present paper, a novel nanomilling technique (consisting of an AFM system and a piezoelectric actuator) was proposed to fabricate nanochannels (with controllable sizes) on PDMS chips, and nanochannel size was controlled by the driving voltage and frequency inputted to the piezoelectric actuator. Moreover, microchannel and nanochannel molds were respectively fabricated by UV lithography and AFM tip-based nanomilling, and finally, PDMS slabs with micro/nanochannels were obtained by transfer process. The influences of PDMS weight ratio on nanochannel size were also investigated. The bonding process of microchannel and nanochannel slabs was conducted on a homemade alignment system consisted of an optical monocular microscope and precision stages. Furthermore, the effects of nanochannel size on electrical characteristics of KCl solution (concentration of 1 mM) were analyzed. Therefore, it can be concluded that PDMS nanofluidic devices with multiple nanochannels of sub-100-nm depth can be efficiently and economically fabricated by the proposed method.

An ultrasensitive electrochemiluminescence biosensor for MicroRNA detection based on luminol-functionalized Au NPs@ZnO nanomaterials as signal probe and dissolved O2 as coreactant

In this work, the ZnO nanostars with excellent catalytic performance were firstly used as the coreaction accelerator of luminol-O₂ system to construct a biosensor for ultrasensitively detecting microRNA-21 (miRNA-21) in cancer cells. Specifically, ZnO nanostars could expedite the reduction of dissolved O₂, generating more reactive oxygen species (ROSs) to extremely promote electrochemiluminescence (ECL) luminous efficiency of luminol. Thus luminol-functionalized Au NPs@ZnO (L-Au NPs@ZnO) nanomaterials were employed as signal probe to fabricate sensing nano-platform for achieving significant ECL emission as "signal on" state. Moreover, upon the addition of a tiny minority of target miRNA-21, massive ferrocene (Fc) could be immobilized on the sensing interface through hybridization chain reaction (HCR) triggered-DNA dendrimers self-assembly, in which Fc consumed dissolved O₂ for prominently quenching the ECL emission of signal probe and then reached a "signal off" state. As a result, the biosensor performed a good linearity in 100 aM - 100 pM and a low limit of detection (LOD) down to 18.6 aM. In general, this work utilized a new coreaction accelerator as an efficient amplification approach for ultrasensitively detecting target analyses, providing a promising approach in luminol-centric ECL bioanalysis fields.

Biomimetic Nanochannel-Ionchannel Hybrid for Ultrasensitive and Label-Free Detection of MicroRNA in Cells

A biomimetic nanochannel-ionchannel hybrid coupled with electrochemical detector was developed for label-free and ultrasensitive detection of microRNA (miRNA) in cells. Probe single stranded DNA (ssDNA) was first immobilized on the outer surface of the nanochannel-ionchannel hybrid membrane, which can hybridize with the target miRNA in cells. Due to the unique mass transfer property of the hybrid, the DNA-miRNA hybridization kinetics can be sensitively monitored in real-time using the electrochemical technique. More importantly, due to the super small size of the ionchannels, the DNA probe immobilization and hybridization process can be carried out on the outer surface of the ionchannel side, which can effectively avoid the blockage and damage of channels and thus considerably enhance the reproducibility and accuracy of the method. Using this strategy, the miRNA ranging from 0.1 fM to 0.1 μM can be facilely detected with a low detection limit of 15.4 aM, which is much lower than most reported work. The present strategy provides a sensitive and label-free miRNA detection platform, which will be of great significance in biomedical research and clinical diagnosis.

Nanochannel-Ion Channel Hybrid Device for Ultrasensitive Monitoring of Biomolecular Recognition Events

We propose an in situ and label-free method for detection of biomolecular recognition events by use of a nanochannel-ion channel hybrid device integrated with an electrochemical detector. The aptamer is first immobilized on the outer surface of the nanochannel-ion channel hybrid. Its binding with target thrombin in solution considerably regulates the mass-transfer behavior of the device owing to the varied surface charge density and effective channel size. Via the electrochemical detector, the changed mass-transport property can be monitored in real time, which enables in situ and label-free detection of thrombin-aptamer recognition. The solution pH has a significant influence on detection sensitivity. Under optimal pH conditions, a detection limit as low as 0.22 fM thrombin can be achieved, which is much lower than most reported work. The present nanofluidic device provides a simple, ultrasensitive, and label-free platform for monitoring biomolecular recognition events, which would hold great potential in exploring the functions and reaction mechanisms of biomolecules in living systems.