PolyA-Mediated DNA Assembly on Gold Nanoparticles for Thermodynamically Favorable and Rapid Hybridization Analysis

Recent advances in nucleic acid-functionalized metallic nanoparticles

Nucleic acid-functionalized metallic nanoparticles (N-MNPs) precisely integrate the advantageous characteristics of nucleic acids and metallic nanomaterials, offering various abilities such as resistance to enzymatic degradation, penetration of physiological barriers, controllable mobility, biomolecular recognition, programmable self-assembly, and dynamic structure-function transformation. These properties demonstrate significant potential in the field of biomedical diagnostics and therapeutics. In this review, we examine recent advancements in the construction and theranostic applications of N-MNPs. We briefly summarize the methodologies employed in the conjugation of nucleic acids with metallic nanoparticles and the formation of their superstructural assemblies. We highlight recent representative applications of N-MNPs in biomolecular diagnosis, imaging, and smart delivery of theranostic agents. We also discuss challenges currently faced in this field and provide an outlook on future development directions and application prospects.

DNA-Engineered Coating for Protecting the Catalytic Activity of Platinum Nanozymes in Biological Systems

Nanozymes, exemplified by metal nanoparticles, have shown promise in the fields of biological diagnostics and therapeutics. However, their practical application is often hindered by aggregation or deactivation in complex biological systems. Here, we develop a DNA-engineered nanozyme coating to preserve the peroxidase-like catalytic activity of platinum nanoparticles in complex biological environments. We employed thiol-modified single-stranded DNA to coat the platinum nanoparticles through metal-sulfur interaction. We found that the negatively charged DNA coating prevents the aggregation of platinum nanoparticles in high-salt environments. Moreover, the DNA coating functions as a molecular sieve, inhibiting non-specific protein adsorption while preserving substrate access to the catalytic interface, thus sustaining high peroxidase-like catalytic activity in serum. As a proof of concept, we demonstrate miRNA detection in serum samples with a detection limit of 1 fM. This approach offers a versatile strategy for molecular diagnostics of nanozymes in complex biological environments.

Multicomponent nucleic acid enzymes as signal amplification strategy for the detection of microRNA based on fluorescence resonance energy transfer

A novel and simple methodology is introduced that allows accurate and highly sensitive detection of microRNAs (miRNAs), taking advantage of an amplification strategy based on multicomponent nucleic acid enzymes (MNAzymes), combined with a fluorescence resonance energy transfer (FRET) phenomenon. For this purpose, a fluorescent dye (FAM) has been selected as an energy donor, while gold nanoparticles (AuNPs) are employed as energy acceptors, located close to each other through hybridisation with the substrate. The research object was miR146a, which is a biomarker whose overexpression in milk is associated with inflammation in bovine mammary glands caused by bovine mastitis. The presence of a genetic target activates the MNAzyme cleavage capability, splitting the substrate into two parts. Hence, the presence of the target increases the distance between donor and acceptor, recovering the quenched fluorescence. Experimental parameters have been optimised, achieving a limit of detection (LOD) of only 2.3 fM (highly competitive as compared to other similar approaches) and a wide linear response range between 15.9 fM and 10 nM. In addition, the proposed methodology allows discriminating miR146a from other similar miRNAs differing in a single base mismatch. Detection of miR146a has been successfully carried out in spiked raw milk samples.

Rapid Thermal Drying Synthesis of Nonthiolated Spherical Nucleic Acids with Stability Rivaling Thiolated DNA

Attaching DNA oligonucleotides to gold nanoparticles (AuNPs) to prepare spherical nucleic acids (SNAs) has offered tremendous insights into surface chemistry with resulting bioconjugates serving as critical reagents in biosensors and nanotechnology. While thiolated DNA is generally required to achieve stable conjugates, we herein communicate that using a thermal drying method, a high DNA density and excellent SNA stability was achieved using nonthiolated DNA, rivaling the performance of thiolated DNA such as surviving 1 M NaCl, 2 month stability in 0.3 M NaCl and working in 50 % serum. A poly-adenine block with as few as two consecutive terminal adenine bases is sufficient for anchoring on AuNPs. By side-by-side comparison with the salt-aging method, the conjugation mechanism was attributed to competitive adenine adsorption at high temperature along with an extremely high DNA concentration upon drying. Bioanalytical applications of nonthiolated SNAs were validated in both solution and paper-based sensor platforms, facilitating cost-effective applications for SNAs.

From Structure to Application: The Evolutionary Trajectory of Spherical Nucleic Acids

Since the proposal of the concept of spherical nucleic acids (SNAs) in 1996, numerous studies have focused on this topic and have achieved great advances. As a new delivery system for nucleic acids, SNAs have advantages over conventional deoxyribonucleic acid (DNA) nanostructures, including independence from transfection reagents, tolerance to nucleases, and lower immune reactions. The flexible structure of SNAs proves that various inorganic or organic materials can be used as the core, and different types of nucleic acids can be conjugated to realize diverse functions and achieve surprising and exciting outcomes. The special DNA nanostructures have been employed for immunomodulation, gene regulation, drug delivery, biosensing, and bioimaging. Despite the lack of rational design strategies, potential cytotoxicity, and structural defects of this technology, various successful examples demonstrate the bright and convincing future of SNAs in fields such as new materials, clinical practice, and pharmacy.

Development of a CRISPR/Cas12a-mediated aptasensor for Mpox virus antigen detection

The emergence and rapid spread of Mpox (formerly monkeypox) have caused significant societal challenges. Adequate and appropriate diagnostics procedures are an urgent necessity. Herein, we discover a pair of aptamers through the systematic evolution of ligands by exponential enrichment (SELEX) that exhibit high affinity and bind to different sites towards the A29 protein of the Mpox virus. Subsequently, we propose a facile, sensitive, convenient CRISPR/Cas12a-mediated aptasensor for detecting the A29 antigen. The procedure employs the bivalent aptamers recognition, which induces the formation of a proximity switch probe and initiates subsequent cascade strand displacement reactions, then triggers CRISPR/Cas12a DNA trans-cleavage to achieve the sensitive detection of Mpox. Our method enables selective and ultrasensitive evaluation of the A29 protein within the range of 1 ng mL-1 to 1 μg mL-1, with a limit of detection (LOD) at 0.28 ng mL-1. Moreover, spiked A29 protein recovery exceeds 96.9%, while the detection activity remains above 91.9% after six months of storage at 4 °C. This aptasensor provides a novel avenue for exploring clinical diagnosis in cases involving Mpox as facilitating development in various analyte sensors.

Programmably engineered stochastic RNA nanowalker for ultrasensitive miRNA detection

A programmably engineered stochastic RNA nanowalker powered by duplex-specific nuclease (DSN) is developed. By utilizing poly-adenine-based spherical nucleic acids (polyA-SNA) to accurately regulate the densities of DNA tracks, the nanowalker showcases its capability to identify miRNA-21, miRNA-486, and miRNA-155 with quick kinetics and attomolar sensitivity, positioning it as a promising option for cancer clinical surveillance.

Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective

DNA-modified gold nanoparticles (AuNPs) play a pivotal role in bio-nanotechnology, driving advancements in bio-sensing, bio-imaging, and drug delivery. Synthetic protocols have focused on maximizing the receptor density on particles by fine-tuning chemical conditions, particularly for DNA. Despite their significance, the understanding of hybridization kinetics on functionalized AuNPs is lacking, particularly how this kinetics depends on DNA density and to what extent it varies from particle-to-particle. This study explores the molecular mechanisms of DNA hybridization on densely coated AuNPs by employing a combination of single-molecule microscopy and coarse-grained molecular dynamics simulations providing a quantification of the molecular rate constants for single particles. Our findings demonstrate that DNA receptor density and the presence of spacer strands profoundly impact association kinetics, with short spacers enhancing association rates by up to ∼15-fold. In contrast, dissociation kinetics are largely unaffected by receptor density within the studied range. Single-particle analysis directly reveals variability in hybridization kinetics, which is analyzed in terms of intra- and inter-particle heterogeneity. A coarse-grained DNA model that quantifies hybridization kinetics on densely coated surfaces further corroborates our experimental results, additionally shedding light on how transient base pairing within the DNA coating influences kinetics. This integrated approach underscores the value of single-molecule studies and simulations for understanding DNA dynamics on densely coated nanoparticle surfaces, offering guidance for designing DNA-functionalized nanoparticles in sensor applications.

Proximity hybridization induced bipedal DNA walker and rolling circle amplification for label-free electrochemical detection of apolipoprotein A4

Apolipoprotein A4 (Apo-A4) is considered as a prospective molecular biomarker for diagnosis of depression due to its neurosynaptic toxicity. We develop a proximity hybridization-induced DNAzyme-driven bipedal DNA walker strategy for Apo-A4 quantification based on rolling circle amplification (RCA) triggered by poly adenine binding to Ag nanoparticles (AgNPs). With the help of DNAzyme, the free-running bipedal DNA walker can quickly and sequentially shear a molecular beacon that acts as a primer to initiate the RCA process, producing a large number of long DNA strands containing numerous adenines. The long repetitive adenine strands then absorb large amounts of AgNPs on the electrode interface, which is then electrochemically stripped of the AgNPs. The method has a linear detection range of 0.001 ∼ 100 ng mL-1 and a detection limit of 0.46 pg mL-1. The presented detection strategy is label-free, which allows high sensitivity and selectivity for detection of a wide range of protein targets by corresponding DNA-based affinity probes, which have potential applications in bioanalysis.

Towards rational design: Developing universal freezing routes for anchoring DNA onto gold nanoparticles

DNA-functionalized gold nanoparticles (AuNPs), also known as spherical nucleic acids, are widely used in the development of biosensors, resulting in anchoring DNA onto AuNPs being a crucial preparation step and a popular research topic. The latest freeze-anchoring method is a simple and time-saving alternative to traditional salt aging; however, its universal applicability remains limited. In this study, we explored the interfacial interaction between DNA and the AuNP surface and proposed various universal routes for promoting freezing anchoring. Among them, rational design has been considered as the core idea to overcome these limitations, particularly using non-thiolated DNA anchoring, which offers significant advantages such as being unmodified, cost-effective, and easily accessible. We emphasize the importance of sequence structure and preparation process optimization, which mainly considers differences in DNA conformation and electrostatic repulsion. Additionally, the prepared DNA-functionalized AuNPs exhibited complete biological hybridization capability, and the extreme limiting conditions for non-thiolated DNA freeze anchoring were clarified. In summary, this study enhances our understanding of the interfacial relationship between DNA and AuNPs in the freeze-anchoring process and can significantly advance the applications of DNA-functionalized AuNP-based biosensors.

Label-free SERS detection of apolipoprotein A4 based on DNAzyme-driven molecular machine

Apolipoprotein A4 has a wide range of synaptic toxicity and can be used as a reliable molecular biomarker for the detection of depressive disorder. It has certain clinical requirements for simple, rapid and selective detection of apolipoprotein A4. Here, based on the DNA biped walker driven by DNAzyme, we designed a label-free surface-enhanced Raman scatting sensor for rapid detection of apolipoprotein A4. Compared with the typical DNA walker, the biped DNA walker has the advantages of large walking range and high magnification efficiency. The magnesium-dependent DNAzyme drives the DNA walker, which can cut the MBs sequentially. The resulting MBs fragments were then hybridized with AuNPs modified by repetitive adenine to make Au NPs proliferate on the substrate surface, resulting in a large number of cycles. Using 736 cm-1 adenine as the internal marker, surface enhanced Raman scattering analysis showed that the linear detection range of human apolipoprotein A4 was 10∼1000 ng mL-1, the detection limit was 4.7 pg/mL, and it had significant specificity, which could meet the needs of clinical detection and showed great application potential.

A fuel-initiated DNA molecular machine for microRNA detection in serum via poly-adenine-mediated spherical nucleic acids

MicroRNAs (miRNAs) have been identified as promising disease diagnostic biomarkers. However, it is challenging to sensitively detect miRNAs, especially in complex biological environments, due to their low abundance and small size. Herein, we have developed a DNA-fueled molecular machine for sensitive detection of miRNA-22 (miR-22) in undiluted serum by combining poly-adenine-mediated spherical nucleic acids (polyA-SNAs) with a toehold mediated strand displacement reaction (TMSDR). The polyA-SNAs are constructed by the assembly of diblock DNA probes on a AuNP surface through the high binding affinity of polyA to AuNPs. The surface density of the diblock DNA probe can be controlled by tuning the length of the polyA block, and the orientation of the diblock DNA probe can adopt an upright conformation, which is beneficial to target hybridization and TMSDRs. TMSDR is an enzyme-free target recycling amplification approach. Taking advantage of polyA-mediated SNAs and TMSDR, the operation of the molecular machine based on two successive TMSDRs on polyA20-SNAs is rapid and efficient, which can significantly amplify the fluorescence response for detection of miR-22 in an undiluted complex matrix. The developed sensor can detect as low as 10 pM of target miRNA/DNA in undiluted fetal bovine serum within 30 min. The synergetic effect of polyA-mediated SNAs and TMSDR presents a potential alternative tool for the detection of biomarkers in real biological samples.

Construction and bioanalytical applications of poly-adenine-mediated gold nanoparticle-based spherical nucleic acids

Owing to the versatile photophysical and chemical properties, spherical nucleic acids (SNAs) have been widely used in biosensing. However, traditional SNAs are formed by self-assembly of thiolated DNA on the surface of a gold nanoparticle (AuNP), where it is challenging to precisely control the orientation and surface density of DNA. As a new SNA, a polyadenine (polyA)-mediated SNA using the high binding affinity of consecutive adenines to AuNPs shows controllable surface density and configuration of DNA, which can be used to improve the performance of a biosensor. Herein, we first introduce the properties of polyA-mediated SNAs and fundamental principles regarding the polyA-AuNP interaction. Then, we provide an overview of current representative synthesis methods of polyA-mediated SNAs and their advantages and disadvantages. After that, we summarize the application of polyA-mediated SNAs in biosensing based on fluorescence and colorimetric methods, followed by discussion and an outlook of future challenges in this field.

DNA Hairpins and Stabilization of Gold Nanoparticles: Effect of Stem Length and Toehold Composition

This study investigates the effect of DNA hairpins on the stabilization of gold nanoparticles (AuNPs) against salt-induced aggregation (SIA) in label-free colorimetric biosensors. AuNPs were incubated with DNA hairpins of varying stem lengths and toehold sequences, followed by the addition of NaCl, before being subjected to ultraviolet-visible (UV-vis) measurement. Results showed that hairpins with longer stems generally provide better stabilization of AuNPs (18-bp >14-bp >10-bp). No improvement was observed for 14- and 18-bp hairpins with a toehold beyond 8A, which may be attributed to saturated adsorption of hairpins on the gold surface. For 14-bp hairpins with an 8-mer homopolymeric toehold, we observed a stabilization trend of A > C > G > T, similar to the reported trend of ssDNA. For variants containing ≥50% adenine as terminal bases, introducing cytosine or guanine as preceding bases could also result in strong stabilization. As the proportion of adenine decreases, variants with guanine or thymine provide less protection against SIA, especially for guanine-rich hairpins (≥6G) that could form G-quadruplexes. Such findings could serve as guidelines for researchers to design suitable DNA hairpins for label-free AuNP-based biosensors.

Surface immobilization strategies for the development of electrochemical nucleic acid sensors

Following the recent pandemic and with the emergence of cell-free nucleic acids in liquid biopsies as promising biomarkers for a broad range of pathologies, there is an increasing demand for a new generation of nucleic acid tests, with a particular focus on cost-effective, highly sensitive and specific biosensors. Easily miniaturized electrochemical sensors show the greatest promise and most typically rely on the chemical functionalization of conductive materials or electrodes with sequence-specific hybridization probes made of standard oligonucleotides (DNA or RNA) or synthetic analogues (e.g. Peptide Nucleic Acids or PNAs). The robustness of such sensors is mostly influenced by the ability to control the density and orientation of the probe at the surface of the electrode, making the chemistry used for this immobilization a key parameter. This exhaustive review will cover the various strategies to immobilize nucleic acid probes onto different solid electrode materials. Both physical and chemical immobilization techniques will be presented. Their applicability to specific electrode materials and surfaces will also be discussed as well as strategies for passivation of the electrode surface as a way of preventing electrode fouling and reducing nonspecific binding.

Spatiotemporal Monitoring of Subcellular mRNAs In Situ via Polyadenine-Mediated Dual-Color Sticky Flares

Spatiotemporal monitoring of multiple low-abundance messenger RNAs (mRNAs) is vitally important for the diagnosis and pathologic analysis of cancer. However, it remains a clinical challenge to monitor and track multiple mRNAs location simultaneously in situ at subcellular level with high efficiency. Herein, we proposed polyA-mediated dual-color sticky flares for simultaneous imaging of two kinds of intracellular mRNA biomarkers. Two kinds of fluorescent DNA specific for GalNac-T mRNA and c-Myc mRNA were functionalized onto gold nanoparticles (AuNPs) through efficient polyadenine (polyA) attachment. By tuning polyA length, the lateral spacing and densities of DNA on AuNPs could be precisely engineered. Compared to the traditional thio-DNA-modified nanoprobes, the uniformity, detection sensitivity, and response kinetics of sticky flares were greatly improved, which enables live-cell imaging of mRNAs with enhanced efficiency. With a sticky-end design, the fluorescent DNA could dynamically trace mRNAs after binding with target mRNAs, which realized spatiotemporal monitoring of subcellular mRNAs in situ. Compared to one target mRNA imaging mode, the multiple target imaging mode allows more accurate diagnosis of cancer. Furthermore, the proposed polyA-mediated dual-color sticky flares exhibit excellent cell entry efficiency and low cytotoxicity with a low-cost and simple assembling process, which provide a pivotal tool for multiple targets imaging in living cells.

programmably engineered FRET-nanoflare for ratiometric live-cell ATP imaging with anti-interference capability

Herein, we present a poly-adenine (polyA)-mediated programmably engineered FRET-nanoflare for ratiometric intracellular ATP imaging with anti-interference capability. The programmable polyA attachment is advantageous in enhancing the signal response for ATP. Moreover, the FRET-based nanoflare is capable of avoiding false-positive signals due to probe degradation in a complex environment, which has great potential for clinical diagnosis.

A sandwich-type electrochemical immunosensor based on spherical nucleic acids-templated Ag nanoclusters for ultrasensitive detection of tumor biomarker

The accurate determination of tumor biomarkers in blood is of vital significance in the diagnosis and therapy of tumor disease. In this research, an innovative sandwich-type electrochemical immunosensor is designed for the ultrasensitive determination of tumor biomarker AFP using spherical nucleic acids-templated silver nanoclusters (AgNCs) sensing platform. For this purpose, on one hand, DNA functionalized gold nanoparticles (AuNPs@DNA) is selected not only as the cross-linker to immobilize the primary antibody (anti-AFP antibody 1, Ab1) to obtain AuNPs@DNA-Ab1, but also as the template for synthesizing AgNCs on AuNPs to form AuNPs@DNA-AgNCs. On the other hand, p-sulfonated calix[4]arene (pSC₄) modified Au is chosen to immobilize the secondary antibody (anti-AFP antibody 2, Ab2) through host-guest recognition between Ab2 and pSC₄. When AFP is encountered, the immunoreaction signal can be significantly amplified by the electrochemical reduction of AgNCs. Under optimal circumstances, the sandwich-type electrochemical immunosensor exhibits broad limit of linearity from 0.001 to 100 ng mL^-1 (R² = 0.997) and low detection limit of 7.74 fg mL^-1 (S/N = 3). The immunosensor possesses excellent repeatability and selectivity, offering a novel method for sensitive clinical diagnosis of tumor markers in human hepatocellular carcinoma.

Mechanical Stability of DNA Corona Phase on Gold Nanospheres

Noncovalent adsorption of biopolymers on the surface of gold nanoparticles (AuNPs) forms a corona phase that drastically diversify AuNP functions. However, mechanical stabilities of such corona phase are still obscure, hindering the application of biopolymer-coated AuNPs. Here, using optical tweezers, we have observed, for the first time, that DNA corona phase adsorbed on a 5 nm AuNP via two (dA)21 strands in proximity can withstand an average desorption force of 40 pN, which is higher than the stall force of DNA/RNA polymerases. This suggests a new role for AuNPs to modulate replications or transcriptions after binding to prevalent poly(dA) segments in eukaryotic genomes. We have also revealed that with increasing AuNP size (1.8-10 nm), DNA corona becomes harder to remove, likely due to the larger surfaces and flatter facets on bigger AuNPs. These findings provide guidance to design AuNP corona that can withstand harsh environments for biological and materials applications.

Tetrahedral DNA-directed core-satellite assembly as SERS sensor for mercury ions at the single-particle level

To monitor the deteriorating mercury emissions, it is imperative to propose methods for detecting mercury ions (Hg²⁺) with sensitivity and selectivity. The SERS spectral-resolved single-particle detection approach can be carried out using dark-field optical microscopy (DFM) combined with Raman spectroscopy. Herein, we have designed a novel yet convenient single-particle detection assay for quantifying Hg²⁺ using DFM-correlated Raman spectroscopy. In the assay, a tetrahedral DNA-directed core-satellite nanostructure is used as the SERS probe. Especially, one edge of the tetrahedron is made up of a single-stranded DNA containing a Hg²⁺ aptamer, which reconfigures upon the specific recognition of Hg²⁺. As a result, the interparticle distance reduces from 4.5 to 1.2 nm, thus generating Raman signal enhancement. As a proof of concept, Hg²⁺ was detected in a linear range from 1 to 100 nM based on the variation in SERS intensity. Furthermore, the experimental results were supported by the finite difference time domain (FDTD) calculations. Owing to its high sensitivity and selectivity, this method was further employed to detect Hg²⁺ in practical tap water and lake water samples, revealing that the single-particle detection strategy holds great promise for Hg²⁺ analysis in real environment analysis.

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.

Spherical nucleic acids: Organized nucleotide aggregates as versatile nanomedicine

Spherical nucleic acids (SNAs) are composed of a nanoparticle core and a layer of densely arranged oligonucleotide shells. After the first report of SNA by Mirkin and coworkers in 1996, it has created a significant interest by offering new possibilities in the field of gene and drug delivery. The controlled aggregation of oligonucleotides on the surface of organic/inorganic nanoparticles improves the delivery of genes and nucleic acid-based drugs and alters and regulates the biological profiles of the nanoparticle core within living organisms. Here in this review, we present an overview of the recent progress of SNAs that has speeded up their biomedical application and their potential transition to clinical use. We start with introducing the concept and characteristics of SNAs as drug/gene delivery systems and highlight recent efforts of bioengineering SNA by imaging and treatmenting various diseases. Finally, we discuss potential challenges and opportunities of SNAs, their ongoing clinical trials, and future translation, and how they may affect the current landscape of clinical practices. We hope that this review will update our current understanding of SNA, organized oligonucleotide aggregates, for disease diagnosis and treatment.

Proximity hybridization induced DNA assembly for label-free surface-enhanced Raman spectroscopic detection of carcinoembryonic antigen

In our research, label-free and surface-enhanced Raman dyes-free Raman spectroscopy which was used to detect carcinoembryonic antigen (CEA) according to poly adenine (Poly A)-regulated self-assembly methods was developed and studied. CEA induced partial hybridization of Ab-H2 and Ab-H1, and Ab-H1-CEA-Ab-H2 (a sandwich proximity CEA-DNA complex) was formed, which unfolded molecular beacon 1 (MB1) and modified the substrate. Subsequently, MB2-AuNPs were hybridized with MB1, and Ab-H1-CEA-Ab-H2 was released via toehold regulated displacements of DNA strands. Therefore, hybridization processes of MB2 and MB1 were induced and promoted by CEA-DNA complexes which worked as catalysts. The misplaced target then induced a next round of strand exchange, and the signals for determination of CEA were amplified by AuNPs absorbed on the substrate. It was indicated that the spectral characteristics of adenine at 736 cm^-1 were consistent with the SERS spectrum of DNA. Adenine acted as an internal marker for label-free SERS detection of CEA. Moreover, satisfactory stability and reproducibility were found. Meanwhile, the antibody could specifically recognize the corresponding antigen. Since adenine was dominant in SERS spectra, which was also proximal to Au surface, the sensitivity of the novel method was high without modifications. The analytical performance of this method in determining serum CEA was satisfactory.

Conformational transition in SPR experiments: impact of spacer length, immobilization mode and aptamer density on signal sign and amplitude

The spacer length and immobilization mode impact the Surface plasmon resonance (SPR) signal and affinity measured for small target/aptamer recognition. The signal could be positive, negative or null explained by refractive index increment deviation.

Functional nucleic acid biosensors utilizing rolling circle amplification

Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.

Triblock probe-polyA-probe electrochemical interfacial engineering for the sensitive analysis of RNAi plants

RNA interference (RNAi) is under fast development in agriculture and brings new challenge for GMO analysis. We developed a electrochemical biosensor for the analysis of GM maize samples based on a polyA-DNA capturing probe. Ultrasensitive detection of 10 fM RNA was realized.

Sensitive electrochemical detection of oxytetracycline based on target triggered CHA and poly adenine assisted probe immobilization

Here, we developed a homogeneous electrochemical biosensor for the sensitive determination of antibiotic by the CHA reaction and the consecutive adenine mediated probe fixation. The binding of target to the target recognition sequences in the triple-helix DNA can release the trigger. It can initiate the catalytic hairpin assembly (CHA) to generate lots of mimic targets, which were labeled with electroactive substance ferrocene (Fc). Because the generated mimic target has consecutive sequence of adenines (PolyA), they can be self-assembled on the AuNPs modified electrode and finally realize electrochemical detection. Under optimal conditions, this developed biosensor achieved a satisfactory limit of detection of 0.089 nM (S/N = 3) and a linear range from 0.1 nM to 100 nM for sensitive detection of oxytetracycline with good specificity. The whole process is carried out in homogeneous solution, not only realizes signal amplification, but also avoids the complex modification process of electrode surface. Compared with some reported electrochemical sensors, the method is easier to operate and has good precision.

Sensitive Detection of Single-Nucleotide Polymorphisms by Solid Nanopores Integrated With DNA Probed Nanoparticles

Single-nucleotide polymorphisms (SNPs) are the abundant forms of genetic variations, which are closely associated with serious genetic and inherited diseases, even cancers. Here, a novel SNP detection assay has been developed for single-nucleotide discrimination by nanopore sensing platform with DNA probed Au nanoparticles as transport carriers. The SNP of p53 gene mutation in gastric cancer has been successfully detected in the femtomolar concentration by nanopore sensing. The robust biosensing strategy offers a way for solid nanopore sensors integrated with varied nanoparticles to achieve single-nucleotide distinction with high sensitivity and spatial resolution, which promises tremendous potential applications of nanopore sensing for early diagnosis and disease prevention in the near future.

Poly-Adenine-Based Spherical Nucleic Acids for Efficient Live-Cell MicroRNA Capture

Direct delivery of exogenous non-coding nucleic acids into living cells has attracted intense interest in biological applications. However, the cell entry efficiency and target capture ability remain to be improved. Herein, we report a method for compartmenting the nucleic acids on the surface of poly-adenine-based spherical nucleic acids (polyA-SNAs) for efficient capture of oncogenic microRNAs (miRNAs) in living cells. We find that polyA-SNAs exhibit high cell entry efficiency, which is insensitive to the configuration of the anti-miRNA sequences. By programming the length of polyAs, we precisely engineered the spatial configuration of the anti-miRNA sequences in polyA-SNAs. Compartmentalized polyA-SNAs bind to miRNAs with improved capture ability as compared to densely compacted SNAs. We further demonstrate that polyA-SNAs serve as high-efficacy miRNA sponges for capturing oncogenic miRNAs both in living cells and in mice. The efficient inhibition of miRNAs results in significant suppression of tumor growth.

Functional Nucleic Acid Nanomaterials: Development, Properties, and Applications

Functional nucleic acid (FNA) nanotechnology is an interdisciplinary field between nucleic acid biochemistry and nanotechnology that focuses on the study of interactions between FNAs and nanomaterials and explores the particular advantages and applications of FNA nanomaterials. With the goal of building the next-generation biomaterials that combine the advantages of FNAs and nanomaterials, the interactions between FNAs and nanomaterials as well as FNA self-assembly technologies have established themselves as hot research areas, where the target recognition, response, and self-assembly ability, combined with the plasmon properties, stability, stimuli-response, and delivery potential of various nanomaterials can give rise to a variety of novel fascinating applications. As research on the structural and functional group features of FNAs and nanomaterials rapidly develops, many laboratories have reported numerous methods to construct FNA nanomaterials. In this Review, we first introduce some widely used FNAs and nanomaterials along with their classification, structure, and application features. Then we discuss the most successful methods employing FNAs and nanomaterials as elements for creating advanced FNA nanomaterials. Finally, we review the extensive applications of FNA nanomaterials in bioimaging, biosensing, biomedicine, and other important fields, with their own advantages and drawbacks, and provide our perspective about the issues and developing trends in FNA nanotechnology.

Hydrophobic collapse-driven nanoparticle coating with poly-adenine adhesives

The mechanism underlying the strong adhesion between DNA with consecutive adenines (polyA) and Au nanoparticles (AuNPs) is experimentally and theoretically studied. We elucidate that the consecutive adenines collectively result in hydrophobic collapse in the adhesion process, which plays a pivotal role for the high adhesion affinity and specificity.

Programmable Engineering of DNA-AuNP Encoders Integrated Multimodal Coupled Analysis for Precision Discrimination of Multiple Metal Ions

A cross-responsive strategy (CRS) based on gold nanoparticles (AuNPs) through attaching various recognition receptors on the surface of AuNPs for identifying multiple analytes is presented, and the detection throughput and overall identification accuracy are improved. However, the CRS's recognition receptor cannot get comprehensive information from the target analytes limited in number and type, which determines the overall identification accuracy. Therefore, the practicability of the CRS runs into a bottleneck. Herein, we report a programmable DNA-AuNP encoder combined with a multimodal coupled analysis algorithm for high-throughput detection and accurate analysis of multiple metal ions. The programmable DNA-AuNP encoder breaks through the limitation of the recognition receptor's quantity. Furthermore, the multimodal signals from target metal ion-induced DNA-AuNP aggregation are related to and observed in the ultraviolet absorbance spectrum, surface potential, and particle diameter. The multimodal coupled analysis algorithm can reflect comprehensive information on the target analyte more completely. Finally, this study provides a highly generic tool for the cross-responsive strategy.

Rationally Designed Multivalent Aptamers Targeting Cell Surface for Biomedical Applications

Specific interactions between ligands and receptors on cell surface play an important role in the cell biological process. Nucleic acid aptamers as commonly used ligands enable specific recognition and tight binding to membrane protein receptors for modulation of cell fate. Therefore, molecular probes with aptamers can be applied for cancer diagnosis and targeted therapy by targeting overexpression membrane proteins of cancer cells. However, because of their fast degradation and rapid glomerulus clearance in vivo, the applications of aptamers in physiological conditions remain challenged. Inspired by natural multivalent interactions, many approaches have been developed to construct multivalent aptamers to improve the performance of aptamers in complex matrices with higher binding affinity, more stability, and longer circulation time. In this review, we first introduce the aptamer generation from purified protein-based SELEX and whole cell-based SELEX for targeting the cell surface. We then highlight the approaches to fabricate multivalent aptamers and discuss their properties. By integrating different materials (including inorganic nanomaterials, diacyllipid, polymeric nanoparticles, and DNA nanostructures) as scaffolds with an interface modification technique, we have summarized four kinds of multivalent aptamers. After that, representative applications in biosensing and targeted therapy are illustrated to show the elevated performance of multivalent aptamers. In addition, we analyze the challenges and opportunities for the clinical practices of multivalent aptamers.

Microfluidic synthesis of high-valence programmable atom-like nanoparticles for reliable sensing

Synthesis of programmable atom-like nanoparticles (PANs) with high valences and high yields remains a grand challenge. Here, a novel synthetic strategy of microfluidic galvanic displacement (μ-GD) coupled with microfluidic DNA nanoassembly is advanced for synthesis of single-stranded DNA encoder (SSE)-encoded PANs for reliable surface-enhanced Raman scattering (SERS) sensing. Notably, PANs with high valences (e.g., n-valence, n = 12) are synthesized with high yields (e.g., >80%) owing to the effective control of interfacial reactions sequentially occurring in the microfluidic system. On the basis of this, we present the first demonstration of a PAN-based automatic analytical platform, in which sensor construction, sample loading and on-line monitoring are carried out in the microfluidic system, thus guaranteeing reliable quantitative measurement. In the proof-of-concept demonstration, accurate determination of tetracycline (TET) in serum and milk samples with a high recovery close to 100% and a low relative standard deviation (RSD) less than 5.0% is achieved by using this integrated analytical platform.

Proximity hybridization-triggered DNA assembly for label-free surface-enhanced Raman spectroscopic bioanalysis

We have developed a versatile label-free surface-enhanced Raman spectroscopic platform for detecting various biotargets via proximity hybridization-triggered DNA assembly based on the 736 cm^-1 Raman peak of adenine breathing mode. We initially immobilized the first probe to AuNPs and modified the second with poly adenine. Presence of target DNA or protein molecules assembled a sandwich complex that brought the poly adenine close to the AuNPs surface, generating Raman signals, that were proportional to target molecule concentration. These approach exhibits high sensitivity, with a detection limit of 5.4 pM, 47 fM, and 0.51 pg/mL for target DNA, thrombin and CEA, respectively. Owing to a one step proximity dependent complex formation, this technique is simple and can be completed within 40 min, making it a promising candidate for point-of-care testing applications.

A novel surface-enhanced Raman scattering (SERS) strategy for ultrasensitive detection of bacteria based on three-dimensional (3D) DNA walker

Bacteria seriously endanger human life and health, and the detection of bacteria is vital for the prevention and treatment of related diseases. Surface-enhanced Raman scattering (SERS) is considered as a powerful technique for bacterial detection due to the inherent richness of spectral data. In this work, a novel SERS strategy based on three-dimensional (3D) DNA walker was developed for quantitative analysis of Salmonella typhimurium (S. ty). The complimentary DNA of S.ty-recognizing aptamer (cApt) was replaced from the double-stranded DNA (dsDNA) of Apt@cApt in the presence of S.ty, which can trigger the endonuclease mediated "DNA walker" on the surface of gold modified magnetic nanoparticles (AuMNPs). The DNA residues on the surface of AuMNPs can bind to SERS tag through base complementary pairing, and the complex of "AuMNPs@SERS tag" can be separated from the fluid by an external magnetic field for SERS analysis. It was found that the SERS intensity showed a good linear relationship with both lower (10-10⁴ CFU/mL) and higher (10⁴-10⁶ CFU/mL) S.ty concentration. A superior limit of detection (LOD) as low as 4 CFU/mL was achieved due to the signal amplification effect of "DNA walker", and the preeminent selectivity of the proposed method was determined by the selectivity of the aptamer sequence. This strategy of separating the SERS tag from the biological matrix enables high stability and good repeatability of the SERS spectra, which presents a new method for SERS detection of biomaterials that can benefit various application scenarios.

A Robust Au-C≡C Functionalized Surface: Toward Real-Time Mapping and Accurate Quantification of Fe2+ in the Brains of Live AD Mouse Models

Described here is that Au-C≡C bonds showed the highest stability under biological conditions, with abundant thiols, and the best electrochemical performance compared to Au-S and Au-Se bonds. The new finding was also confirmed by theorical calculations. Based on this finding, a specific molecule for recognition of Fe²⁺ was designed and synthesized, and used to create a selective and accurate electrochemical sensor for the quantification of Fe²⁺ . The present ratiometric strategy demonstrates high spatial resolution for real-time tracking of Fe²⁺ in a dynamic range of 0.2-120 μM. Finally, a microelectrode array with good biocompatibility was applied in imaging and biosensing of Fe²⁺ in the different regions of live mouse brains. Using this tool, it was discovered that the uptake of extracellular Fe²⁺ into the cortex and striatum was largely mediated by cyclic adenosine monophosphate (cAMP) through the CREB-related pathway in the brain of a mouse with Alzheimer's disease.

Dual-emission fluorescent silicon nanoparticle-based nanothermometer for ratiometric detection of intracellular temperature in living cells

In this article, we present a kind of dual-emission fluorescent nanothermometer, which is made of europium (Eu3+)-doped silicon nanoparticles (Eu@SiNPs), allowing the detection of intracellular temperature in living cells with high accuracy. In particular, the presented SiNP-based thermometer features dual-emission fluorescence (blue (455 nm) and red (620 nm) emission), negligible toxicity (cell viability of treated cells remains above 90% during 24 h of treatment) and robust photostability in living cells (i.e., preserving >90% of fluorescence intensity after 45 min of continuous UV irradiation). More significantly, the fluorescence intensity of the Eu@SiNPs exhibits a linear ratiometric temperature response in a broad range from 25 to 70 °C. Taking advantage of these attractive merits, the Eu@SiNP-based nanothermometer is able to accurately (∼4.5% change per °C) determine dynamic changes in intracellular temperature in a quantitative and long-term (i.e., 30 min) manner.

Poly-adenine regulated DNA density on AuNPs to construct efficient DNA walker for microRNA-21 detection

DNA-modified gold nanoparticles (AuNPs) are useful nanomaterials for detecting multiple molecules. However, their performance is greatly dependent on the density of probe DNA on the surface of AuNPs. Here, we used Poly-adenine (PolyA) to regulate the surface density of probe DNA to achieve a highly efficient DNA walking biosensor system to detection miRNA-21. The movement track of the biosensor system consists of PolyA-DNA probe was connected to AuNPs, and exonuclease III (Exo III) acted as a motor driving the walker movement to achieve signal amplification. By optimizing the length of PolyA, the surface density of probe DNA was changed, thereby affecting the target binding and enzymatic processing of the bound probes, which ultimately enhanced the sensitivity and reduced timeliness of the DNA walker. Furthermore, the designed PolyA-DNA probe exhibits an outstanding sensitivity, due to the effect of density regulation, which is 7.9 times and 11.1 times lower than those of the SH-DNA and the free-DNA, respectively. In addition, the hairpin structure of DNA probe locates fluorophore at a zone adjacent to AuNPs surface, which reduces the background signal by 1.1 times compared with traditional straight probe. In this work, the biosensor system shows a high selectivity towards miRNA-21. Moreover, the biosensor system has been demonstrated to be potentially useful for the miRNA-21 detection in human serum with the recoveries of 93.2%-110.0% and has high repeatability. Considering these advantages, this PolyA-regulated DNA walking biosensor system has great potential as a routine tool for miRNA detection and has wide applications in the field of biomedical analysis.

DNAzyme–gold nanoparticle-based probes for biosensing and bioimaging

The design and applications of DNAzyme–gold nanoparticle-based probes in biosensing and bioimaging are summarized here.

Turn-on detection of MicroRNA155 based on simple UCNPs-DNA-AuNPs luminescence energy transfer probe and duplex-specific nuclease signal amplification

A novel luminescence energy transfer (LET) probe for detection of tumor related microRNAs using NaGdF₄:Yb,Er@NaYF₄ upconversion nanoparticles (UCNPs) as energy donors and gold nanoparticles (AuNPs) as energy acceptors was developed. Using the double modified complementary DNA sequences of microRNA155 (miRNA155) as a bridge, NaGdF₄:Yb,Er@NaYF₄ UCNPs and AuNPs were conjugated to form NaGdF₄:Yb,Er@NaYF₄ UCNPs-DNA-AuNPs nanocomplexes (UCNPs-DNA-AuNPs) probe. The energy transfer would occur when the distance between donor and acceptor gets closer. In the presence of target miRNA155, DNA-RNA heteroduplexes appeared as product, but the luminescence intensity was not changed obviously. In the existence of duplex-specific nuclease (DSN), DSN could hydrolyze the DNA strand of DNA-RNA heteroduplexes, the bridge linked NaGdF₄:Yb,Er@NaYF₄ UCNPs and AuNPs was destroyed, which induced that the quenched luminescence intensity was recovered and RNA was released. The released miRNA155 could react with another UCNPs-DNA-AuNPs probe to form DNA-RNA heteroduplexes again. This cyclic reaction generates an amplification of luminescence signal for quantitative detection of miRNA155. Under the illumination of 980 nm laser, the concentration ranges from 0.1 nM to 15 nM and the detection of limits was 0.045 nM for detection of miRNA155. Moreover, the UCNPs-DNA-AuNPs probe was used in quantify miRNA155 in cell lysates with satisfactory results.