Poly-adenine-based programmable engineering of gold nanoparticles for highly regulated spherical DNAzymes

A multi-channel electrochemical biosensor based on polyadenine tetrahedra for the detection of multiple drug resistance genes

Antimicrobial resistance poses a serious threat to human health due to the high morbidity and mortality caused by drug-resistant microbial infections. Therefore, the development of rapid, sensitive and selective identification methods is key to improving the survival rate of patients. In this paper, a sandwich-type electrochemical DNA biosensor based on a polyadenine-DNA tetrahedron probe was constructed. The key experimental conditions were optimized, including the length of polyadenine, the concentration of the polyadenine DNA tetrahedron, the concentration of the signal probe and the hybridization time. At the same time, poly-avidin-HRP80 was used to enhance the electrochemical detection signal. Finally, excellent biosensor performance was achieved, and the detection limit for the synthetic DNA target was as low as 1 fM. In addition, we verified the practicability of the system by analyzing E. coli with the MCR-1 plasmid and realized multi-channel detection of the drug resistance genes MCR-1, blaNDM, blaKPC and blaOXA. With the ideal electrochemical interface, the polyA-based biosensor exhibits excellent stability, which provides powerful technical support for the rapid detection of antibiotic-resistant strains in the field.

Recent Advances in Electrochemiluminescence Biosensors for MicroRNA Detection

Electrochemiluminescence (ECL) as an analytical technology with a perfect combination of electrochemistry and spectroscopy has received considerable attention in bioanalysis due to its high sensitivity and broad dynamic range. Given the selectivity of bio-recognition elements and the high sensitivity of the ECL analysis technique, ECL biosensors are powerful platforms for the sensitive detection of biomarkers, achieving the accurate prognosis and diagnosis of diseases. MicroRNAs (miRNAs) are crucial biomarkers involved in a variety of physiological and pathological processes, whose aberrant expression is often related to serious diseases, especially cancers. ECL biosensors can fulfill the highly sensitive and selective requirements for accurate miRNA detection, prompting this review. The ECL mechanisms are initially introduced and subsequently categorize the ECL biosensors for miRNA detection in terms of the quenching agents. Furthermore, the work highlights the signal amplification strategies for enhancing ECL signal to improve the sensitivity of miRNA detection and finally concludes by looking at the challenges and opportunities in ECL biosensors for miRNA detection.

Triblock PolyA-Mediated Protein Biosensor Based on a Size-Matching Proximity Hybridization Analysis

The antibodies in the natural biological world utilize bivalency/multivalency to achieve a higher affinity for antigen capture. However, mimicking this mechanism on the electrochemical sensing interface and enhancing biological affinity through precise spatial arrangement of bivalent aptamer probes still pose a challenge. In this study, we have developed a novel self-assembly layer (SAM) incorporating triblock polyA DNA to enable accurate organization of the aptamer probes on the interface, constructing a "lock-and-key-like" proximity hybridization assay (PHA) biosensor. The polyA fragment acts as an anchoring block with a strong affinity for the gold surface. Importantly, it connects the two DNA probes, facilitating one-to-one spatial proximity and enabling a controllable surface arrangement. By precisely adjusting the length of the polyA fragment, we can tailor the distance between the probes to match the molecular dimensions of the target protein. This design effectively enhances the affinity of the aptamers. Notably, our biosensor demonstrates exceptional specificity and sensitivity in detecting PDGF-BB, as confirmed through successful validation using human serum samples. Overall, our biosensor presents a novel and versatile interface for proximity assays, offering a significantly improved surface arrangement and detection performance.

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-directed assembly of nanomaterials and their biomedical applications

In the past decades, DNA has been widely used in the field of nanostructures due to its unique programmable properties. Besides being used to form its own diverse structures such as the assembly of DNA origami, DNA can also be used for the assembly of nanostructures with other materials. In this review, different strategies for the functionalization of DNA on nanoparticle surfaces are listed, and the roles of DNA in the assembly of nanostructures as well as the influencing factors are discussed. Finally, the biomedical applications of DNA-assembled nanostructures were summarized. This review provided new insight into the application of DNA in nanostructure assembly.

DNA-Guided Metallization of Nanomaterials and Their Biomedical Applications

Precise control of the structure of metallic nanomaterials is critical for the advancement of nanobiotechnology. As DNA (deoxyribonucleic acid) can readily modify various moieties, such as sulfhydryl, carboxyl, and amino groups, using DNA as a directing ligand to modulate the morphology of nanomaterials is a promising strategy. In this review, we focus on the use of DNA as a template to control the morphology of metallic nanoparticles and their biomedical applications, discuss the use of DNA for the metallization of gold and silver, explore the factors that influence the process, and outline its biomedical applications. This review aims to provide valuable insights into the DNA-guided growth of nanomaterials. The challenges and future directions are also discussed.

DNA-Based Molecular Machines

Artificial molecular machines have found widespread applications ranging from fundamental studies to biomedicine. More recent advances in exploiting unique physical and chemical properties of DNA have led to the development of DNA-based artificial molecular machines. The unprecedented programmability of DNA provides a powerful means to design complex and sophisticated DNA-based molecular machines that can exert mechanical force or motion to realize complex tasks in a controllable, modular fashion. This Perspective highlights the potential and strategies to construct artificial molecular machines using double-stranded DNA, functional nucleic acids, and DNA frameworks, which enable improved control over reaction pathways and motion behaviors. We also outline the challenges and opportunities of using DNA-based molecular machines for biophysics, biosensing, and biocomputing.

Sensitive detection of microRNAs using polyadenine-mediated fluorescence spherical nucleic acids and a microfluidic electrokinetic signal amplification chip

The identification of tumor-related microRNAs (miRNAs) exhibits excellent promise for the early diagnosis of cancer and other bioanalytical applications. Therefore, we developed a sensitive and efficient biosensor using polyadenine (polyA)-mediated fluorescent spherical nucleic acid (FSNA) for miRNA analysis based on strand displacement reactions on gold nanoparticle (AuNP) surfaces and electrokinetic signal amplification (ESA) on a microfluidic chip. In this FSNA, polyA-DNA biosensor was anchored on AuNP surfaces via intrinsic affinity between adenine and Au. The upright conformational polyA-DNA recognition block hybridized with 6-carboxyfluorescein-labeled reporter-DNA, resulting in fluorescence quenching of FSNA probes induced by AuNP-based resonance energy transfer. Reporter DNA was replaced in the presence of target miRNA, leading to the recovery of reporter-DNA fluorescence. Subsequently, reporter-DNAs were accumulated and detected in the front of with Nafion membrane in the microchannel by ESA. Our method showed high selectivity and sensitivity with a limit of detection of 1.3 pM. This method could also be used to detect miRNA-21 in human serum and urine samples, with recoveries of 104.0%–113.3% and 104.9%–108.0%, respectively. Furthermore, we constructed a chip with three parallel channels for the simultaneous detection of multiple tumor-related miRNAs (miRNA-21, miRNA-141, and miRNA-375), which increased the detection efficiency. Our universal method can be applied to other DNA/RNA analyses by altering recognition sequences.

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FSNA assisted microfluidic chip was developed for miRNAs detection.

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Three different miRNAs were detected simultaneously.

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The excellent sensitivity and specificity were displayed toward miRNAs.

Self-Protected DNAzyme Walker with a Circular Bulging DNA Shield for Amplified Imaging of miRNAs in Living Cells and Mice

Abnormal expression of miRNAs is often detected in various human cancers. DNAzyme machines combined with gold nanoparticles (AuNPs) hold promise for detecting specific miRNAs in living cells but show short circulation time due to the fragility of catalytic core. Using miRNA-21 as the model target, by introducing a circular bulging DNA shield into the middle of the catalytic core, we report herein a self-protected DNAzyme (E) walker capable of fully stepping on the substrate (S)-modified AuNP for imaging intracellular miRNAs. The DNAzyme walker exhibits 5-fold enhanced serum resistance and more than 8-fold enhanced catalytic activity, contributing to the capability to image miRNAs much higher than commercial transfection reagent and well-known FISH technique. Diseased cells can accurately be distinguished from healthy cells. Due to its universality, DNAzyme walker can be extended for imaging other miRNAs only by changing target binding domain, indicating a promising tool for cancer diagnosis and prognosis.

MicroRNA-Triggered Deconstruction of Field-Free Spherical Nucleic Acid as an Electrochemiluminescence Biosensing Switch

Herein, a new field-free and highly ordered spherical nucleic acid (SNA) nanostructure was self-assembled directly by ferrocene (Fc)-labeled DNA tweezers and DNA linkers based on the Watson-Crick base pairing rule, which was employed as an electrochemiluminescence (ECL) quenching switch with improved recognition efficiency due to the high local concentration of the ordered nanostructure. Moreover, with a collaborative strategy combined with the advantages of both self-accelerated approach and pore confinement-enhanced ECL effect, the mesoporous silica nanospheres (mSiO₂ NSs) were prepared to be filled with rubrene (Rub) as ECL emitters and Pt nanoparticles (PtNPs) as coreaction accelerators (Rub-Pt@mSiO₂ NSs), which demonstrated high ECL response in the aqueous media (dissolved O₂ as coreactant). When the SNA nanostructure was immobilized on the Rub-Pt@mSiO₂ NSs-modified electrode, it presented a "signal off" state owing to the quenching effect of the Fc molecules. As a proof of concept, the SNA-based ECL switch platform was applied in the detection of microRNA let-7b (let-7b). Impressively, in the presence of the target let-7b, a deconstruction of the SNA nanostructure was actuated, causing the Fc to leave the electrode surface and achieved an extremely high ECL recovery ("signal on" state). Hence, a sensitive determination for let-7b was realized with a low detection limit of 1.8 aM ranging from 10 aM to 1 nM by employing the Rub-Pt@mSiO₂ NSs-based ECL platform combined with the target-triggered SNA deconstruction, which also offered an ingenious method for the further applications of biomarker analyses.

Synthesis of sea urchin-shaped Au nanocrystals by double-strand diblock oligonucleotides for surface-enhanced Raman scattering and catalytic application

It is of great significance to construct specially designed gold nanocrystals (AuNCs) with precisely controllable size and morphology to achieve an excellent physicochemical performance. In this work, sea urchin-shaped AuNCs with tunable plasmonic property were successfully synthesized by the hybridized double-strand poly adenine (dsPolyA) DNA-directed self-assembly technique. Hybridized dsPolyA as the directing template had suitable rigidity and upright conformation, which benefited the controllable formation of these anisotropic multi-branched AuNCs with the assistance of surfactant. The effects of essential conditions influencing the synthesis and precise morphology control were investigated in detail. COMSOL simulation was used to evaluate their electromagnetic field distribution according to their morphologies, and the result suggested that sea urchin-shaped AuNCs had abundant 'hot spots' for surface-enhanced Raman scattering (SERS) detection due to their regular nanoprotuberance structure. Finally, sea urchin-shaped AuNCs with excellent SERS and catalytic performance were applied for the quantitative analysis of food colorant and catalytic degradation of potential pollutants. The SERS enhancement factor of sea urchin-shaped AuNCs was up to 5.27 × 10⁶, and the catalytic degradation rate for 4-NP by these AuNCs was up to -0.13min^-1.

An enzyme-mediated universal fluorescent biosensor template for pathogen detection based on a three-dimensional DNA walker and catalyzed hairpin assembly

An enzyme-mediated universal fluorescent biosensor template for rapid detection of pathogens was developed based on the strategy of a three-dimensional (3D) DNA walker and catalyzed hairpin assembly (CHA) reaction. In the bacterial recognition step, a strand displacement reaction between bacteria and the double-stranded complex caused the release of the walker strand. The walker strand triggered the DNA walker to produce an enzyme fragment, and the DNA walker used gold nanoparticles (AuNPs) as the track to provide an excellent DNA ligand anchoring area. In the CHA step, the enzyme fragment induced the CHA cycle to yield fluorescence signals, which greatly enhanced the conversion ratio of trigger DNA and the sensitivity of the fluorescent biosensor. The effect of the distance and density of the DNA ligand was studied by adjusting the length of poly-adenine (PolyA), and was further explored by its reaction kinetics. By comparing the maximum reaction rate (Vmax), Michaelis constant (Km) and turnover number (Kcat), the optimized PolyA probe was assessed and identified. In this work, the optimized PolyA-DNA probe exhibited an outstanding sensitivity in Salmonella typhimurium (S. ty) detection, which is 11.9 times and 4.6 times higher than those of the SH-DNA and the MCH treated SH-DNA. Meanwhile, a detection limit of 28.1 CFU mL-1 was achieved in Escherichia coli (E. coli) detection. Furthermore, the biosensor achieved good selectivity and high repeatability with recoveries of 91%-115% for real sample detection. Considering these advantages, this template has great potential as a routine tool for pathogen detection and has wide applications in the field of global public health and food safety.

The nucleobase assisted pyrene functionalization of gold nanoparticles

Gold nanoparticles were functionalized with a pyrene fluorophore without compromising the functional behaviour of the fluorophore.

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.

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.

Poly-adenine-mediated spherical nucleic acids for strand displacement-based DNA/RNA detection

DNA-gold nanoparticles (AuNPs) conjugate is one of the most versatile bionanomaterials for biomedical and clinical diagnosis. However, to finely tune the hybridization ability and precisely control the orientation and conformation of surface-tethered oligonucleotides on AuNPs remains a hurdle. In this work, we developed a poly adenine-mediated spherical nucleic acid (polyA-mediated SNA) strategy by assembling di-block DNA probes on gold nanoparticles (AuNPs) to spatially control interdistance and hybridization ability of oligonucleotides on AuNPs. By modulating length of poly A bound on the SNA with different degrees of constructing, we presented significant improved biosensing performance including high hybridization efficiency, and expanded dynamic range of analytes with more sensitive detection limit. Furthermore, this polyA design could facilitate the programmable detection for DNA in serum environment and simultaneous multicolor detection of three different microRNAs associated with pancreatic carcinoma. The demonstration of the link between modulation of SNA assembly strategy and biodetection capability will increase the development of high performance diagnostic tools for translational biomedicine.

DNA Nanotechnology-Enabled Interfacial Engineering for Biosensor Development

Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly. We then summarize recent progress in DNA nanotechnology and efforts to harness DNA nanostructures to engineer various biological interfaces, with a particular focus on the use of framework nucleic acids. We also discuss the implementation of biosensors to detect physiologically relevant nucleic acids, proteins, small molecules, ions, and other biomarkers. This review highlights promising applications of DNA nanotechnology in interfacial engineering for biosensors and related areas.

Poly-adenine-mediated fluorescent spherical nucleic acid probes for live-cell imaging of endogenous tumor-related mRNA

Identification of tumor-related mRNA in living cells hold great promise for early cancer diagnosis and pathological research. Herein, we present poly-adenine (polyA)-mediated fluorescent spherical nucleic acid (FSNA) probes for intracellular mRNA detection with regulable sensitivities by programmably adjusting the loading density of DNA on gold nano-interface. Gold nanoparticles (AuNPs) functionalized with polyA-tailed recognition sequences were hybridized to fluorescent "reporter" strands to fabricate fluorescence-quenched FSNA probes. While exposed to target gene, the "reporter" strands were released from FSNA through strand displacement and fluorescence was recovered. With polyA20 tail as the attaching block, the detection limit of FSNA probes was calculated to be 0.31 nM, which is ~55 fold lower than that of thiolated probes without surface density regulation. Quantitative intracellular mRNA detection and imaging could be achieved with polyA-mediated FSNA probes within 2 hours, indicating their application potential in rapid and sensitive intracellular target imaging.

Polyadenine-Modulated DNA Conformation Monitored by Surface-Enhanced Raman Scattering (SERS) on Multibranched Gold Nanoparticles and Its Sensing Application

This work proposes a facile way to modulate the conformation of DNA from the "Lie-Down" to the "Stand-Up" conformation on the surface of multibranched gold nanoparticles (AuNPs). This is realized by regulating the length of polyadenine (polyA) linked to the DNA sequence and/or the hybridization of this sequence with the target DNA, and can be monitored by the Raman signal owing to the excellent performance of multibranched AuNPs (AuNSs) as a surface-enhanced Raman scattering (SERS) substrate and the distance change between the Raman reporter and the substrate. The probable mechanism, which depends on the repulsion of polyA from the sequence and the tip assembly, has also been probed through theoretical simulation using the finite difference time domain method. By virtue of this strategy, a conformation-transformation-based DNA@AuNS sensor is constructed for the identification of a specific oligonucleotide, which has been used for the detection of DNA sequences associated with Severe Acute Respiratory Syndrome (SARS). This strategy leads to a novel sensing platform with good extendibility for DNA analysis, and provides a powerful protocol for facilitating the cognition of DNA conformation on metal surfaces.

Bubble-Mediated Ultrasensitive Multiplex Detection of Metal Ions in Three-Dimensional DNA Nanostructure-Encoded Microchannels

The development of rapid and sensitive point-of-test devices for on-site monitoring of heavy-metal contamination has great scientific and technological importance. However, developing fast, inexpensive, and sensitive microarray sensors to achieve such a goal remains challenging. In this work, we present a DNA-nanostructured microarray (DNM) with a tubular three-dimensional sensing surface and an ordered nanotopography. This microarray enables enhanced molecular interaction toward the rapid and sensitive multiplex detection of heavy-metal ions. In our design, the use of DNA tetrahedral-structured probes engineers the sensing interface with spatially resolved and density-tunable sensing spots that improve the microconfined molecular recognition. A bubble-mediated shuttle reaction was used inside the DNM-functionalized microchannel to improve the target-capturing efficiency. Using this novel DNM biosensor, the sensitive and selective detection of multiple heavy-metal ions (i.e., Hg²⁺, Ag⁺, and Pb²⁺) was achieved within 5 min, the detection limit was down to 10, 10, and 20 nM for Hg²⁺, Ag⁺, and Pb²⁺, respectively. The feasibility of our DNM sensor was further demonstrated by probing heavy-metal ions in real water samples with a direct optical readout. Beyond metal ions, this unique DNM sensor can easily be extended to in vitro bioassays and clinical diagnostics.

Probing Cellular Molecules with PolyA-Based Engineered Aptamer Nanobeacon

Adenosine triphosphate (ATP) is a central metabolite that is of critical importance in many cellular processes. The development of sensitive and selective methods for the detection of ATP level in vivo is crucial in diagnostic and theranostic applications. In this work, we have developed a polyA-based aptamer nanobeacon (PAaptNB) with improved efficiency and speed of ATP analysis. We found that the dissociation constants and competitive binding kinetics of the PAaptNB could be programmably regulated by adjusting the polyA length. When the polyA length reached to 30 bases, a 10 μM detection limit for ATP assay with PAaptNB can be achieved (∼10-fold improvement compared with the conventional thiol-based aptamer nanobeacon). The feasibility of the PAaptNB for in vivo assay was further demonstrated by imaging intracellular ATP molecules. This study provides a new strategy to construct high-efficiency and high-speed biosensors for cellular molecules analysis, which holds great potential in bioanalysis and theranostic applications.

Theranostic DNAzymes

DNAzymes are catalytically active DNA molecules that are obtained via in vitro selection. RNA-cleaving DNAzymes have attracted significant attention for both therapeutic and diagnostic applications due to their excellent programmability, stability, and activity. They can be designed to cleave a specific mRNA to down-regulate gene expression. At the same time, DNAzymes can sense a broad range of analytes. By combining these two functions, theranostic DNAzymes are obtained. This review summarizes the progress of DNAzyme for theranostic applications. First, in vitro selection of DNAzymes is briefly introduced, and some representative DNAzymes related to biological applications are summarized. Then, the applications of DNAzyme for RNA cleaving are reviewed. DNAzymes have been used to cleave RNA for treating various diseases, such as viral infection, cancer, inflammation and atherosclerosis. Several formulations have entered clinical trials. Next, the use of DNAzymes for detecting metal ions, small molecules and nucleic acids related to disease diagnosis is summarized. Finally, the theranostic applications of DNAzyme are reviewed. The challenges to be addressed include poor DNAzyme activity under biological conditions, mRNA accessibility, delivery, and quantification of gene expression. Possible solutions to overcome these challenges are discussed, and future directions of the field are speculated.

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

Understanding the behavior of biomolecules on nanointerface is critical in bioanalysis, which is great challenge due to the instability and the difficulty to control the orientation and loading density of biomolecules. Here, we investigated the thermodynamics and kinetics of DNA hybridization on gold nanoparticle, with the aim to improve the efficiency and speed of DNA analysis. We achieved precise and quantitative surface control by applying a recently developed poly adenines (polyA)-based assembly strategy on gold nanoparticles (DNA-AuNPs). PolyA served as an effective anchoring block based on the preferential binding with the AuNP surface and the appended recognition block adopted an upright conformation that favors DNA hybridization. The lateral spacing and surface density of DNA on AuNPs can be systematically modulated by adjusting the length of polyA block. We found the stability of duplex on AuNP was enhanced with the increasing length of polyA block. When the length of polyA block reached to 40 bases, the thermodynamic properties were more similar to that of duplex in solution. Fast hybridization rate was observed on the diblock DNA-AuNPs and was increased along with the length of polyA block. We consider the high stability and excellent hybridization performance come from the minimization of the DNA-DNA and DNA-AuNP interactions with the use of polyA block. This study provides better understanding of the behavior of biomolecules on the nanointerface and opens new opportunities to construct high-efficiency and high-speed biosensors for DNA analysis.

The preparation of a recyclable catalyst of silver nanoparticles dispersed in a mesoporous silica nanofiber matrix

A recyclable catalyst of sliver nanoparticles well dispersed in mesoporous silica was successfully synthesized via a straight-forward strategy combining an electrospinning technique with post-calcination.