Parallel Polyadenine Duplex Formation at Low pH Facilitates DNA Conjugation onto Gold Nanoparticles

Chiroptical hybrid nanomaterials based on metal nanoparticles and biomolecules

Chirality at the nanoscale has recently attracted renewed attention from the scientific community. As a result, various strategies have been proposed to develop chiral nanomaterials based on metal nanoparticles and chiral biomolecules such as DNA, amino acids, or proteins. We review herein the past and recent literature related to the functionalization of metal nanoparticles with various chiral biomolecules and their assembly into biomaterials with chiroptical response. We divide the review into two main parts, according to the class of biomolecules. We first discuss mechanisms employed to obtain chiral bioconjugates based on metal nanoparticles and amino acids or their derivatives (peptides and proteins), including mechanisms for chirality transfer from chiral biomolecules to achiral nanoparticles. We also review the use of amino acids/peptides as either chiral inducers for the growth of chiral nanoparticles or templates for the chiral arrangement of achiral nanoparticles. In the second part we present an overview of methods to prepare bioconjugates comprising DNA and metal nanoparticles, as well as selected examples of helical nanoparticle arrangements that employ DNA as a chiral template.

Gold Nanoparticles Coated with Nucleic Acids: An Overview of the Different Bioconjugation Pathways

Gold-based nanomaterials have marked the last few decades with the emergence of new medical technologies presenting unique features. For instance, the conjugation of gold nanoparticles (AuNPs) and nucleic acids has allowed the creation of nanocarriers with immense promise for gene therapy applications. Although the use of lipid particles as RNA delivery vectors has been broadly explored, this review aims to focus on the limited models reported for the conjugation of RNA with AuNPs. This is nonetheless unexpected regarding the manifold strategies existing to conjugate DNA to gold nanoparticles, which are exhaustively listed in this paper. Furthermore, new processes such as fast microwave and freezing methods have been described very recently, and it therefore seemed necessary to review these recent but promising conjugation pathways and to pick out those applicable to RNA. Indeed, RNA is considerably more attractive than DNA for therapeutic purposes, but its low stability involves numerous difficulties in the construction of effective nanodevices. However, from the many approaches developed for DNA, it turns out that just two of them are frequently used for the building of RNA delivery platforms based on gold: the salt-aging method with thiolated RNA strands and physisorption. However, both approaches present strong limitations such as the low stability of the Au-S bond and the potential cytotoxicity of polycations. To conclude, this general assessment highlights that the exploration of innovating approaches implying different chemistries is needed for the creation of more robust and shapeable AuNPs-RNA conjugates.

Advanced Synthesis of Spherical Nucleic Acids: A Limit-Pursuing Game with Broad Implications

Spherical nucleic acids (SNAs) consist of DNA strands arranged radially and packed densely on the surface of nanoparticles. Due to their unique properties, which are not found in naturally occurring linear or circular DNA, SNAs have gained widespread attention in fields such as sensing, nanomedicine, and colloidal assembly. The rapidly evolving applications of SNAs have driven a modernization of their syntheses to meet different needs. Recently, several advanced approaches have emerged, enabling ultrafast, quantitative, and low-cost SNA synthesis with maximal DNA grafting through "counterintuitive" processes like freezing and dehydration. This concept paper discusses these critical developments from a synthetic perspective, focusing on their underlying mechanisms and broad implications, with a goal of inspiring future research in related fields.

Oligoadenine Strand Functionalized Polyacrylamide Hydrogel Film Exhibiting pH-Triggered High-Degree Inverse Shape Deformations

Smart shape-memory DNA hydrogels, which can respond to various types of external stimuli and undergo macroscopic shape deformations, have shown great potential in various applications. By constructing free-standing films, the deformation and response properties of these hydrogels can be further enhanced, and visualized deformation can be achieved. However, DNA hydrogels that can exhibit rapid and high-degree shape deformations, such as the inverse shape deformations, are still lacking. Herein, free-standing oligoadenine strand-functionalized polyacrylamide hydrogel films were developed that can exhibit reversible and high degree of inverse shape deformation upon cyclic pH changes. The oligoadenine strands exhibit a pH-stimulated reversible conformational transition between a flexible single-stranded state and parallel duplex A-motif structures, resulting in their role change in the film from negatively charged side chains to "head-to-head" crosslinking structures, driving a high degree of inverse shape deformation with a relative bending angle change of 223.7 % of the film, which is more than 5 times that of a film driven by pH-responsive i-motif structures, facilitating the development of bilayer hydrogel film actuators with potential in flexible sensors and robots.

Gold Nanoprobes for Robust Colorimetric Detection of Nucleic Acid Sequences Related to Disease Diagnostics

Gold nanoparticles (AuNPs) are highly attractive for applications in the field of biosensing, particularly for colorimetric nucleic acid detection. Their unique optical properties, which are highly sensitive to changes in their environment, make them ideal candidates for developing simple, rapid, and cost-effective assays. When functionalized with oligonucleotides (Au-nanoprobes), they can undergo aggregation or dispersion in the presence of complementary sequences, leading to distinct color changes that serve as a visual signal for detection. Aggregation-based assays offer significant advantages over other homogeneous assays, such as fluorescence-based methods, namely, label-free protocols, rapid interactions in homogeneous solutions, and detection by the naked eye or using low-cost instruments. Despite promising results, the application of Au-nanoprobe-based colorimetric assays in complex biological matrices faces several challenges. The most significant are related to the colloidal stability and oligonucleotide functionalization of the Au-nanoprobes but also to the mode of detection. The type of functionalization method, type of spacer, the oligo-AuNPs ratio, changes in pH, temperature, or ionic strength influence the Au-nanoprobe colloidal stability and thus the performance of the assay. This review elucidates characteristics of the Au-nanoprobes that are determined for colorimetric gold nanoparticles (AuNPs)-based nucleic acid detection, and how they influence the sensitivity and specificity of the colorimetric assay. These characteristics of the assay are fundamental to developing low-cost, robust biomedical sensors that perform effectively in biological fluids.

Oligo-Adenine Derived Secondary Nucleic Acid Frameworks: From Structural Characteristics to Applications

Oligo-adenine (polyA) is primarily known for its critical role in mRNA stability, translational status, and gene regulation. Beyond its biological functions, extensive research has unveiled the diverse applications of polyA. In response to environmental stimuli, single polyA strands undergo distinctive structural transitions into diverse secondary configurations, which are reversible upon the introduction of appropriate counter-triggers. In this review, we systematically summarize recent advances of noncanonical structures derived from polyA, including A-motif duplex, A-cyanuric acid triplex, A-coralyne-A duplex, and T ⋅ A-T triplex. The structural characteristics and mechanisms underlying these conformations under specific external stimuli are addressed, followed by examples of their applications in stimuli-responsive DNA hydrogels, supramolecular fibre assembly, molecular electronics and switches, biosensing and bioengineering, payloads encapsulation and release, and others. A detailed comparison of these polyA-derived noncanonical structures is provided, highlighting their distinctive features. Furthermore, by integrating their stimuli-responsiveness and conformational characteristics, advanced material development, such as pH-cascaded DNA hydrogels and supramolecular fibres exhibiting dynamic structural transitions adapting environmental cues, are introduced. An outlook for future developments is also discussed. These polyA derived, stimuli-responsive, noncanonical structures enrich the arsenal of DNA "toolbox", offering dynamic DNA frameworks for diverse future applications.

Terminal deoxynucleotidyl transferase (TdT) based template-free signal amplification for the detection of exosomes in MUC1-positive cells

The Mucin1 (MUC1) protein, involved in cytoprotective and signaling pathways, is abnormally elevated in various cancers, making it a key cancer indicator. Exosomes, which reflect the status of their originating cells, offer potential for cancer diagnosis. Thus, developing a method to detect MUC1-positive exosomes is crucial for the early diagnosis of certain cancers. In this study, we developed a highly sensitive, specific, and simple UV-visible signal amplification method to detect MUC1-positive exosomes using terminal deoxynucleotidyl transferase (TdT). Initially, exosomes were captured on magnetic beads using a CD63 aptamer(apt). The Primer-AuNPs-MUC1 apt complex which we synthesized by low pH loading method was then attached MUC1 proteins on the surface of the exosomes to create a sandwich structure. TdT catalyzed the extension of Biotin-dATP at the 3' end of the primer, introducing multiple biotin sites into the sandwich structure. These sites subsequently bound multiple streptavidin-horseradish peroxidase (streptavidin-HRP), which catalyzed the oxidative color change of the substrate, which can be detected by colorimetric method. This method can detect A549 exosomes in the range of 1.4E+6 to 4.2E+8 particles/mL and shows high specificity for cell lines with different MUC1 expression. Additionally, it successfully distinguished cholangiocarcinoma (CCA) patients (n=11) from healthy individuals (n=7) in clinical serum assays, demonstrating good performance in real sample detection.

Sunflower Pollen-Derived Microspheres Selectively Absorb DNA for microRNA Detection

Herein, we report the finding that a naturally sunflower pollen-derived microspheres (HSECs) with hierarchical structures can selectively absorb polyC and polyA with high efficiency and affinity. HSECs exhibit the capability to selectively absorb polyC and polyA ssDNA under neutral and acidic conditions. It has been observed that the presence of metal cations, specifically Ca2+, enhances the absorption efficiency of HSECs. Mechanically, this absorption phenomenon can be attributed to both electrostatic interactions and cation-π interactions. Such an appealing property enables the functionalization of HSECs for broad potential biomedical applications, such as microRNA detection.

Short-stranded DNA segment-modulated LAMP/H+ as signal transducer to guide CHA-cooperated amplifiable electrochemical biosensing

BACKGROUND

Modulating loop-mediated isothermal amplification (mLAMP) by short-stranded DNA segment trigger (T) to generate byproducts H+ ions (mLAMP/H+) as signal transducer is intriguing for developing catalytic hairpin assembly (CHA)-cooperated amplifiable electrochemical biosensors. This would be a big challenge for traditional LAMP that is basically suitable for amplifying long-stranded oligonucleotides up to 200-300 nt. To address this inherent limitation of traditional LAMP, many researchers have put in efforts to explore improvements in this that would allow LAMP to be used for a wider range of target species amplification.

RESULTS

Here in this work, we are inspired to explore two-step loop-mediated amplification, firstly forming T-activated double-loop dumbbell structure (DLDS) intermediate by a recognition hairpin and a hairpin precursor, and next DLDS-guided mLAMP process with the aid of two primers to yield mLAMP/H+ during successive DNA incorporation via nucleophilic attacking interaction. To manipulate the mLAMP/H+-directed transduction of input T, a pH-responsive triplex strand is designed with the ability of self-folding in Hoogsteen structure at slightly acidic conditions, resulting in the dehybridization of a fuel strand (FS) to participate in CHA between two hairpins on the modified electrode surface, in which FS is repetitively displaced and recycled to fuel the progressive CHA events. In the as-assembled dsDNA complexes, numerous electroactive ferrocene labels are immobilized in the electrode sensing interface, thereby generating significantly amplified electrochemical current signal that can sense the presented and varied T.

SIGNIFICANCE

It is clear that we have creatively constructed a unique electrochemical biosensor for disease detection. Benefited from the rational combination of mLAMP and CHA, our electrochemical strategy is highly sensitive, specific and simplified, and would provide a new paradigm to construct various mLAMP/H+-based biosensors for other short-stranded DNA or microRNAs markers.

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.

DNA-functionalized metal or metal-containing nanoparticles for biological applications

The conjugation of DNA molecules with metal or metal-containing nanoparticles (M/MC NPs) has resulted in a number of new hybrid materials, enabling a diverse range of novel biological applications in nanomaterial assembly, biosensor development, and drug/gene delivery. In such materials, the molecular recognition, gene therapeutic, and structure-directing functions of DNA molecules are coupled with M/MC NPs. In turn, the M/MC NPs have optical, catalytic, pore structure, or photodynamic/photothermal properties, which are beneficial for sensing, theranostic, and drug loading applications. This review focuses on the different DNA functionalization protocols available for M/MC NPs, including gold NPs, upconversion NPs, metal-organic frameworks, metal oxide NPs and quantum dots. The biological applications of DNA-functionalized M/MC NPs in the treatment or diagnosis of cancers are discussed in detail.

Robust noncovalent spherical nucleic acid enzymes (SNAzymes) for ultrasensitive unamplified electrochemiluminescence detection of endogenous myocardial MicroRNAs

Here we develop robust noncovalent spherical nucleic acid enzymes (SNAzymes) for direct electrochemiluminescence (ECL) detection of acute myocardial infarction (AMI) related endogenous microRNAs in both circulating blood and cardiomyocytes, which circumvents the need for time-consuming signal amplification widely used in previous counterparts. It mainly relies on the super peroxidase-like activity of the designed noncovalent SNAzymes, promoted by a few nucleotides flanking on the 3'-terminals of common parallel G-quadruplexes (G4). For this reason, an unmodified G4 with an A5T30 head is well chosen and then attached robustly onto bare AuNPs via microwave-assisted heating-drying. A probe strand is meanwhile attached onto SNAzymes, enabling the target microRNA-triggered formation of a Y-shaped junction together with a capture strand tethered to a DNA tetrahedron on the electrode surface. The utilization of this tetrahedral nanoscaffold favors the ECL readout and thereby contributes to high sensitivity of the sensing platform. In this way, an AMI-related microRNA, miR-499, can be probed in a wide linear range, with a detection limit of 33 aM and high selectivity over other analogues. Furthermore, our developed sensing platform is employed to analyze endogenous miR-499 in AMI patients' blood, revealing an apparently higher level than the mean value of the healthy. What it means to patients, heart injury, is elucidated by comparing the miR-499 levels of cardiomyocytes and other tissue cells, with endogenous miR-16 as an intrinsic reference.

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.

A Strong Acid-Induced DNA Hydrogel Based on pH-Reconfigurable A-Motif Duplex

Under a pH value lower than the pK_a of adenine (3.5), adenine-rich sequences (A-strand) form a unique parallel A-motif duplex due to the protonation of A-strand. At a pH above 3.5, deprotonation of adenines leads to the dissolution of A-motif duplex to A-strand single coil. This pH-reconfigurable A-motif duplex has been developed as a novel pH-responsive DNA hydrogel, termed A-hydrogel. The hydrogel state is achieved at pH 1.2 by the A-motif duplex bridging units, which are cross-linked by both reverse Hoogsteen interaction and electrostatic attraction. Hydrogel-to-solution transition is triggered by pH 4.3 due to the deprotonation-induced separation of A-motif duplex. The A-hydrogel system undergoes reversible hydrogel-solution transitions by subjecting the system to cyclic pH shifts between 1.2 and 4.3. An anti-inflammatory medicine, sulfasalazine (SSZ), which intercalates into A-motif duplex, is loaded into A-hydrogel. Its pH-controlled release from A-hydrogel is successfully demonstrated. The strong acid-induced A-hydrogel may fill the gap that other mild acid-responsive DNA hydrogels cannot do, such as protection of orally delivered drug in hostile stomach environment against strong acid (pH ~ 1.2) and digestive enzymes.

Selectivity of natural isoquinoline alkaloid assembler in programming poly(dA) into parallel duplex by polyvalent synergy

Ligand-induced assembly of disordered DNAs attracts much attention due to its potential action in transcription regulation and molecular switches-based sensors. Among natural isoquinoline alkaloids (NIAs), we screened out nitidine (NIT) as polyvalent-binding assembler to program poly(dA) into a parallel duplex assembly at neutral pH. The molecule planarity of NIAs was believed to be a determinant factor in programming the parallel poly(dA) assembly. Poly(dA) with more than six adenines can initiate the synergistic binding of NIT to generate the parallel assembly. It is expected that one A-A pair in duplex can bind one NIT molecule provided that poly(dA) is long enough, suggesting the pivotal role of the polyvalent synergy of NIT in programming the parallel poly(dA) assembly. A gold nanoparticles-based colorimetric method was also developed to screen NIT out of NIAs having the potential to construct the poly(dA) assembly. Our work will inspire more interest in developing polyadenine-based switches and sensors by concentrating NIT within the polyadenine parallel assembly.

T-Shaped Aptamer-Based LSPR Biosensor Using Ω-Shaped Fiber Optic for Rapid Detection of SARS-CoV-2

SARS-CoV-2, especially the variant strains, is rapidly spreading around the world. Rapid detection methods for the virus are crucial for controlling the COVID-19 epidemic. Herein, a localized surface plasmonic resonance (LSPR) biosensor based on Ω-shaped fiber optic (Ω-FO) was developed for dual assays of SARS-CoV-2 monitoring. Due to its strong ability to control the orientation and density, a new T-shaped aptamer exhibits enhanced binding affinity toward N proteins. After being combined on the fiber optic surface, the T-shaped aptamer sensitively captured N proteins of SARS-CoV-2 for a direct assay. Further, core-shell structured gold/silver nanoparticles functionalized with a T-shaped aptamer (apt-Ag@AuNPs) can amplify the signal of N protein detection for a sandwich assay. The real-time analytical feature of the dual assays endows time-dependent sensitivity enhancement behavior, which provides a guideline to save analytical time. With those characteristics, the LSPR biosensor has been successfully used to rapidly identify 39 healthy volunteers and 39 COVID-19 patients infected with the ancestral or variant SARS-CoV-2. With the help of simple pretreatment, we obtain a true negative rate of 100% and a true positive rate of 92.3% with a short analysis time of 45 min using the direct assay. Further, the LSPR biosensor could also broaden the detection application range to the surface of cold-chain foods using a sandwich assay. Thus, the LSPR biosensor based on Ω-FO was demonstrated to have broad application potential to detect SARS-CoV-2 rapidly.

Stabilization of Gold Nanoparticles by Hairpin DNA and Implications for Label-Free Colorimetric Biosensors

With extremely high extinction coefficients and other unique optical properties, gold nanoparticles (AuNPs) have received growing interest in developing biosensors. DNA hairpin structures are very popular probes for the detection of not only complementary DNA or RNA but also aptamer targets. This work aims to understand the effect of the structure and sequence of hairpin DNA for the stabilization of AuNPs and its implications in AuNP-based label-free colorimetric biosensors. A series of hairpin DNA with various loop sizes from 4 to 26 bases and sequences (random sequences, poly-A and poly-T) were tested, but they showed similar abilities to protect AuNPs from aggregation. Using hairpin DNA with a tail under the same conditions, optimal protection was achieved with a six-base or longer tail. DNA hairpins are likely adsorbed via their tail regions or with their terminal bases if no tail is present. Molecular dynamics simulations showed that the rigidity of the hairpin loop region disfavored its adsorption to AuNPs, while the flexible tail region is favored. Finally, a DNA sensing assay was conducted using different structured DNA, where hairpin DNA with a tail doubled the sensitivity compared to the tail-free hairpin.

Chiral Sum Frequency Generation Spectroscopy Detects Double-Helix DNA at Interfaces

Many DNA-based technologies involve the immobilization of DNA and therefore require a fundamental understanding of the DNA structure-function relationship at interfaces. We present three immobilization methods compatible with chiral sum frequency generation (SFG) spectroscopy at interfaces. They are the "anchor" method for covalently attaching DNA on a glass surface, the "island" method for dropcasting DNA on solid substrates, and the "buoy" method using a hydrocarbon moiety for localizing DNA at the air-water interface. Although SFG was previously used to probe DNA, the chiral and achiral SFG responses of single-stranded and double-stranded DNA have not been compared systemically. Using the three immobilization methods, we obtain the achiral and chiral C-H stretching spectra. The results introduce four potential applications of chiral SFG. First, chiral SFG gives null response from single-stranded DNA but prominent signals from double-stranded DNA, providing a simple binary readout for label-free detection of DNA hybridization. Second, with heterodyne detection, chiral SFG gives an opposite-signed spectral response useful for distinguishing native (D-) right-handed double helix from non-native (L-) left-handed double helix. Third, chiral SFG captures the aromatic C-H stretching modes of nucleobases that emerge upon hybridization, revealing the power of chiral SFG to probe highly localized molecular structures within DNA. Finally, chiral SFG is sensitive to macroscopic chirality but not local chiral centers and thus can detect not only canonical antiparallel double helix but also other DNA secondary structures, such as a poly-adenine parallel double helix. Our work benchmarks the SFG responses of DNA immobilized by the three distinct methods, building a basis for new chiral SFG applications to solve fundamental and biotechnological problems.

Freeze-Driven Adsorption of Poly-A DNA on Gold Nanoparticles: From a Stable Biointerface to Plasmonic Dimers

Increasing attention is paid to poly-adenine (poly-A) DNA-functionalized gold nanoparticles due to the high cost of thiols. Freezing is an effective approach for immobilizing poly-A DNA on gold nanoparticles, but its mechanism remains elusive. To cope with this issue, in this paper, some experimental insights are provided. It is shown that (1) the DNA loading density is independent of the length of poly-A. (2) DNA is densely packed on gold nanoparticles, and the biointerface is peculiarly stable, which is not in line with the existing "wrapping" model. (3) Using a DNA-staining dye, thiazole orange, it is shown that poly-A duplex structures are formed on the surface of gold nanoparticles, with evidence given by fluorescence and Raman measurements. An alternative model involving stable poly-A duplexes anchored by finite terminal adenines is proposed. Based on it, a strategy for constructing plasmonic dimers is developed, using freeze-driven adsorption of a DNA sequence with poly-adenine at both ends. This work provides insights into the reaction between poly-A DNA and AuNPs upon freezing and is expected to facilitate related research in biosensor development and nanotechnology.

Acid-Resistant and Physiological pH-Responsive DNA Hydrogel Composed of A-Motif and i-Motif toward Oral Insulin Delivery

An acid-resistant DNA hydrogel that is stable in an extremely acidic environment with pH as low as 1.2 has not been reported before, largely due to the instability of DNA-hybridized structures. To achieve this, adenine (A)-rich and cytosine (C)-rich oligonucleotides are rationally designed and integrated to form copolymers with acrylamide monomers via free-radical polymerization. In an acidic environment (pH 1.2-6.0), the generated copolymers form a hydrogel state, which is cross-linked by parallel A-motif duplex configurations (pH 1.2-3.0) and quadruplex i-motif structures (pH 4.0-6.0) due to the protonation of A and C bases, respectively. Specifically, the protonated A-rich sequences under pH 1.2-3.0 form a stable parallel A-motif duplex cross-linking unit through reverse Hoogsteen interaction and electrostatic attraction. Hemi-protonated C bases under mildly acidic pH (4.0-6.0) form quadruplex i-motif cross-linking configuration via Hoogsteen interaction. Under physiological pH, both A and C bases deprotonated, resulting in the separation of A-motif and i-motif to A-rich and C-rich single strands, respectively, and thereby the dissociation of the DNA hydrogel into the solution state. The acid-resistant and physiological pH-responsive DNA hydrogel was further developed for oral drug delivery to the hostile acidic environment in the stomach (pH 1.2), duodenum (pH 5.0), and small intestine (pH 7.2), where the drug would be released and absorbed. As a proof of concept, insulin was encapsulated in the DNA hydrogel and orally administered to diabetic rats. In vitro and in vivo studies demonstrated the potential usage of the DNA hydrogel for oral drug delivery.

DNAzyme-Functionalized Nanomaterials: Recent Preparation, Current Applications, and Future Challenges

DNAzyme-nanomaterial bioconjugates are a popular hybrid and have received major attention for diverse biomedical applications, such as bioimaging, biosensor development, cancer therapy, and drug delivery. Therefore, significant efforts are made to develop different strategies for the preparation of inorganic and organic nanoparticles (NPs) with specific morphologies and properties. DNAzymes functionalized with metal-organic frameworks (MOFs), gold nanoparticles (AuNPs), graphene oxide (GO), and molybdenum disulfide (MoS₂ ) are introduced and summarized in detail in this review. Moreover, the focus is on representative examples of applications of DNAzyme-nanomaterials over recent years, especially in bioimaging, biosensing, phototherapy, and stimulation response delivery in living systems, with their several advantages and drawbacks. Finally, the perspective regarding the future directions of research addressing these challenges is also discussed and highlighted.

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.

Comparison of Two DNA Aptamers for Dopamine Using Homogeneous Binding Assays

Dopamine is an essential neurotransmitter and its detection is important for bioanalytical chemistry. Two very different DNA aptamers have been reported for dopamine, one derived from an RNA aptamer (named Apt1) and other obtained via direct aptamer selection (named Apt2). In this study, we used four homogeneous binding assays to compare these two DNA dopamine aptamers. Thiazole orange (TO) fluorescence assay indicated that the Apt2 specifically bound with dopamine with a K_d of 2.37 μM, which was consistent with that from the isothermal titration calorimetry (ITC) assay. However, Apt1 had much less TO fluorescence change and also no signal from ITC. By labeling the two ends of the two aptamers by a fluorophore and a quencher, the aptamer beacons showed binding of dopamine only for Apt2. Finally, the label-free AuNP-based colorimetric assay showed no difference between these two aptamer sequences, and even non-binding random DNA showed the same response, indicating that AuNPs were not a good probe for detecting dopamine. According to the data, Apt1 does not appear to be able to bind dopamine specifically, while Apt2 showed specific binding and could be used for developing related biosensors.

Single-strand DNA-nanorod conjugates - tunable anisotropic colloids for on-demand self-assembly

Directed self-assembly uses different stimuli to initiate and control the interaction between nanocrystals. Protonation at reduced pH represents a convenient stimulus for initiating self-assembly. Prior work has focused on protonation-induced hydrogen bonding between peptide or amino acid functionalized nanocrystals for reversible cycling between dispersed and aggregated states. Here, we discuss a fundamentally different approach, in which changes in pH modify the nonspecific interparticle interaction between Au nanorods conjugated with single-stranded (ss) DNA. While electrostatic repulsion stabilizes dispersed suspensions at neutral pH, protonation in acidic solution modifies the DNA corona, turning the interaction between the rods attractive and triggering their self-assembly. Analysis of in-situ electron microscopy of ssDNA-Au nanorods in solution is consistent with a van der Waals attraction of charge-neutral monomers at acidic pH. The results demonstrate ssDNA-conjugated anisotropic nanostructures as versatile building blocks with stimuli-programmable interactions for on-demand self-assembly.

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.

Real-Time Electron Microscopy of Nanocrystal Synthesis, Transformations, and Self-Assembly in Solution

Solution-phase processes such as colloidal synthesis and transformations have enabled the formation of nanocrystals with exquisite control over size, shape, and composition. Self-assembly, in solution or at phase boundaries, can arrange such nanocrystal building blocks into ordered superlattices and dynamically reconfigurable "smart" materials. Ultimately, continued improvements in our ability to direct nanocrystal matter depend on progress in understanding colloidal chemistry and self-assembly in solution. The traditional approach for investigating the underlying, inherently dynamic processes involves sampling at different stages combined with ex situ characterization, for example, using electron microscopy. In situ studies have been restricted to a few methods capable of measuring in bulk liquids, either in reciprocal space by diffraction or scattering or using spatially averaging (e.g., optical) measurements. These strategies face clear limitations in obtaining mechanistic information, and they are unable to address heterogeneous systems that may harbor rich sets of configurations with different local properties. The development of microfabricated cells that hermetically encapsulate bulk solutions between ultrathin (electron transparent) membranes has paved the way for studying processes in liquids in real time by electron microscopy at resolution down to the atomic scale. Electrons interact much more strongly with matter than other probes, for example, X-rays. In ordinary inorganic samples, the main effects are atom displacements and defect formation via knock-on and ionization damage. In liquid-cell electron microscopy, the interaction of the beam with both the suspended nanostructures and the solution creates more diverse effects, so the straightforward scenario of imaging unperturbed nanocrystal chemistry in solution is rarely realized.In this Account, we discuss applications of real-time electron microscopy to the analysis of nanocrystal synthesis, transformations, and self-assembly in solution. While in the simplest case the effects of the electron beam are negligible, the interaction with high-energy electrons often provides excitation or stimulus for solution-phase processes or opens up competing chemical pathways. Real-time observations of self-assembly demonstrate particularly clearly the power of in situ microscopy in identifying key nucleation and growth mechanisms and providing information about preferred structural motifs that can be analyzed to quantify the balance of forces and the role of entropy in stabilizing ordered assemblies. Modifications of the solution by the electron beam can provide stimuli for on-demand self-assembly, for example, via an acid spike due to water radiolysis that locally lowers the pH in the imaged area. While in this and other cases (e.g., colloidal synthesis), beam-induced radicals become part of the experimental design, in imaging redox reactions such as galvanic transformations of nanocrystal templates, radicals need to be managed and if possible eliminated by suitable scavengers. Finally, excitation by the imaging electron beam can transfer energy to individual nanocrystals in solution, thus driving nonthermal (e.g., plasmon-mediated) synthesis or other chemistry while following the reaction progress with high resolution. Overall, with validation by ex situ control experiments, the unique ability of observing processes in solution at the nanometer scale should make liquid-cell electron microscopy an integral part of the toolkit for designing novel inorganic nanocrystal architectures.

Stronger Adsorption of Phosphorothioate DNA Oligonucleotides on Graphene Oxide by van der Waals Forces

Finding DNA sequences that can adsorb strongly on nanomaterials is critical for bioconjugate and biointerface chemistry. In most previous work, unmodified DNA with a phosphodiester backbone (PO DNA) were screened or selected for adsorption on inorganic surfaces. In this work, the adsorption of phosphorothioate (PS)-modified DNA (PS DNA) on graphene oxide (GO) is studied. By use of fluorescently labeled oligonucleotides as probes, all the tested PS DNA strands are adsorbed more strongly on GO compared to the PO DNA of the same sequence. The adsorption mechanism is probed by washing the adsorbed DNA with proteins, surfactants, and urea. Molecular dynamics simulations show that van der Waals forces are responsible for the tighter adsorption of PS DNA. Polycytosine (poly-C) DNA, in general, has a high affinity for the GO surface, and PS poly-C DNA can adsorb even stronger, making it an ideal anchoring sequence on GO. With this knowledge, noncovalent functionalization of GO with a diblock DNA is demonstrated, where a PS poly-C block is used to anchor on the surface. This conjugate achieves better hybridization than the PO DNA of the same sequence for hybridization with the complementary DNA.

Interfacing DNA with Gold Nanoparticles for Heavy Metal Detection

The contamination of heavy metals (e.g., Hg, Pb, Cd and As) poses great risks to the environment and human health. Rapid and simple detection of heavy metals of considerable toxicity in low concentration levels is an important task in biological and environmental analysis. Among the many convenient detection methods for heavy metals, DNA-inspired gold nanoparticles (DNA-AuNPs) have become a well-established approach, in which assembly/disassembly of AuNPs is used for colorimetric signaling of the recognition event between DNA and target heavy metals at the AuNP interface. This review focuses on the recent efforts of employing DNA to manipulate the interfacial properties of AuNPs, as well as the major advances in the colorimetric detection of heavy metals. Beginning with the introduction of the fundamental aspects of DNA and AuNPs, three main strategies of constructing DNA-AuNPs with DNA binding-responsive interface are discussed, namely, crosslinking, electrostatic interaction and base pair stacking. Then, recent achievements in colorimetric biosensing of heavy metals based on manipulation of the interface of DNA-AuNPs are surveyed and compared. Finally, perspectives on challenges and opportunities for future research in this field are provided.

Promoting DNA Adsorption by Acids and Polyvalent Cations: Beyond Charge Screening

Adsorbing DNA oligonucleotides onto nanoparticles is the first step in developing DNA-based biosensors, drug delivery systems, and smart materials. Since DNA is a polyanion, it is repelled by negatively charged nanoparticles, which constitute the majority of commonly used nanomaterials. Adding salt such as NaCl to screen charge repulsion is a standard method of promoting DNA adsorption. However, Na⁺ does not supply additional attractive forces. In addition, adding a high concentration of NaCl can cause the aggregation of nanomaterials. In this feature article, we mainly summarize the methods developed in our laboratory to promote DNA adsorption by lowering the pH and by adding polyvalent metal ions, especially transition-metal ions. Various materials including noble metals (gold, silver, and platinum), 2D materials (graphene oxide, MoS₂, WS₂, and MXene), polydopamine, and several metal oxides are discussed. In general, low pH can protonate DNA bases and nanoparticle surfaces, reducing charge repulsion and even leading to attraction, although DNA folding at low pH can sometimes be detrimental to adsorption. Polyvalent metal ions can bridge additional interactions to achieve otherwise impossible adsorption. On the basis of the current understanding, a few future research directions are proposed to further improve DNA adsorption.

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.

Native MicroRNA Targets Trigger Self-Assembly of Nanozyme-Patterned Hollowed Nanocuboids with Optimal Interparticle Gaps for Plasmonic-Activated Cancer Detection

The modernized use of nucleic acid (NA) sequences to drive nanostructure self-assembly has given rise to a new class of designed nanomaterials with controllable plasmonic functionalities for broad surface-enhanced Raman scattering (SERS)-based bioanalysis applications. Herein, dual usage of microRNAs (miRNAs) as both valuable cancer biomarkers and direct self-assembly triggers is identified and capitalized upon for custom-designed plasmonic nanostructures. Through strict NA hybridization of miRNA targets, Au nanospheres selectively self-assemble onto hollowed Au/Ag alloy nanocuboids with ideal interparticle distances (≈2.3 nm) for optimal SERS signaling. The intrinsic material properties of the self-assembled nanostructures further elevate miRNA detection performance via nanozyme catalytic SERS signaling cascades. This enables fM-level miR-107 detection limit within a clinically-relevant range without any molecular target amplification. The miRNA-triggered nanostructure self-assembly approach is further applied in clinical patient samples, and showcases the potential of miR-107 as a non-invasive prostate cancer diagnostic biomarker. The use of miRNA targets to drive nanostructure self-assembly holds great promise as a practical tool for miRNA detection in disease applications.

Target-Triggered Polymerization of Branched DNA Enables Enzyme-free and Fast Discrimination of Single-Base Changes

Single-base changes lead to important biological and biomedical implications; however, the discrimination of single-base changes from normal DNA always remains a grand challenge. Herein we developed a DNA recognition and amplification system based on artificial branched DNA, namely, target-triggered polymerization (TTP), to realize enzyme-free and fast discrimination of single-base changes. Branched DNA as monomers rapidly polymerized into DNA nanospheres only with the trigger of specific DNA. Our TTP system worked reliably over a wide range of conditions. Remarkably, our TTP system was capable of discriminating base-changing DNA from normal DNA, including distinguishing 1-4 nucleotide changes and positions of single base, which was attributed to the significant amplification of small differences in hybridization thermodynamics and kinetics. We further proposed a theoretical method for calculating the hybridization probability of nucleic acids, which performed highly consistent with experimental results.

Effects of Small Molecules on DNA Adsorption by Gold Nanoparticles and a Case Study of Tris(2-carboxyethyl)phosphine (TCEP)

DNA-functionalized gold nanoparticles (AuNPs) often encounter various small molecules and ions such as backfilling agents, bifunctional cross-linkers, stabilizers, and molecules from biological fluids both during and after the DNA conjugation process. Small molecules and ions can influence the stability and property of the conjugate, but such interactions are yet to be fully explored. In this work, eight important molecules were studied and compared, including tris(2-carboxyethyl)phosphine hydrochloride (TCEP), 3-(2-pyridyldithio)propionic acid N-hydroxysuccinimide ester (SPDP), 4-maleimidobutyric acid N-hydroxysuccinimide ester (GMBS), 6-hydroxy-1-hexanethiol (MCH), l-glutathione (GSH), bromide (Br^-), bis(p-sulfonatophenyl)phenylphosphine (BSPP), and thiocyanate (SCN^-). Depending on the size, charge, and adsorption affinity on the AuNPs, they can either stabilize or destabilize the AuNPs. Their ability to displace thiolated DNA from AuNPs follows the order of MCH > SPDP > GSH > SCN^- > TCEP > Br^- > BSPP > GMBS. BSPP has the best stabilization effect for the colloidal stability of AuNPs, while it does not displace the adsorbed DNA. TCEP can be adsorbed on AuNPs and enhance the adsorption of A/C rich DNA in low-salt conditions. This work indicates that the effects of small molecules and ions cannot be ignored when studying the DNA-functionalized AuNPs, which ensures optimal applications and correct interpretation of the data.

Freezing-Driven DNA Adsorption on Gold Nanoparticles: Tolerating Extremely Low Salt Concentration but Requiring High DNA Concentration

Attaching thiolated DNA to gold nanoparticles (AuNPs) is a highly important and useful reaction for many applications. Various methods such as adding salts, acids, polymers, and surfactants have been developed to facilitate the reaction. Recently, it was reported that a very high DNA density can be achieved simply by freezing AuNPs with the DNA without any other reagents. DNA oligonucleotides are also known to stretch and align upon freezing. In this work, a set of experiments were performed with a fluorophore and thiol dual-labeled DNA, and the DNA loading density and colloidal stability of AuNPs were measured. The initial salt concentration was unimportant, and even 0.1 mM Na⁺ allowed around 100 DNA attached to each 13 nm AuNPs. On the other hand, a high DNA concentration of 3 μM was needed to achieve the high DNA density and good colloidal stability of AuNPs. When the thiolated DNA was forced in stable secondary structures, the attachment was low, and preadsorbed DNA also inhibited the DNA attachment by the freezing method. Overall, nonstructured thiolated DNA strands need to align by freezing and quickly attached through the ends of the DNA. This work illustrates practical experiment design conditions and offers fundamental surface science insights for the DNA attachment by freezing.

Polyadenine-mediated Immobilization of Aptamers on a Gold Substrate for the Direct Detection of Bacterial Pathogens

Nucleic acid aptamers have been widely used as synthetic probes for bioanalytical applications. Herein, we carried out a detailed study on the immobilization of a series of aptamers ranging from 37 to 88 bases, which are specific to either Escherichia coli (E. coli) or Staphylococcus aureus (S. aureus), on a planar gold substrate via a polyadenine-mediated immobilization method. The resultant surfaces were characterized by both surface plasmon resonance spectroscopy (SPR) and X-ray photoelectron spectroscopy. The results clearly show that the aptamer solution at a lower ionic strength gives rise to a higher lateral density of the aptamer when compared to that at a higher ionic strength. The SPR aptasensors are then employed for detecting their corresponding bacteria (i.e., E. coli and S. aureus, respectively). The data indicate that the SPR aptasensor with a higher density of aptamer exhibits a better capture of target bacteria.

Phosphorothioate DNA Mediated Sequence-Insensitive Etching and Ripening of Silver Nanoparticles

Many DNA-functionalized nanomaterials and biosensors have been reported, but most have ignored the influence of DNA on the stability of nanoparticles. We observed that cytosine-rich DNA oligonucleotides can etch silver nanoparticles (AgNPs). In this work, we showed that phosphorothioate (PS)-modified DNA (PS-DNA) can etch AgNPs independently of DNA sequence, suggesting that the thio-modifications are playing the major role in etching. Compared to unmodified DNA (e.g., poly-cytosine DNA), the concentration of required PS DNA decreases sharply, and the reaction rate increases. Furthermore, etching by PS-DNA occurs quite independent of pH, which is also different from unmodified DNA. The PS-DNA mediated etching could also be controlled well by varying DNA length and conformation, and the number and location of PS modifications. With a higher activity of PS-DNA, the process of etching, ripening, and further etching was taken place sequentially. The etching ability is inhibited by forming duplex DNA and thus etching can be used to measure the concentration of complementary DNA.

Freezing-directed Stretching and Alignment of DNA Oligonucleotides

Most single-stranded DNA oligonucleotides are random coils with a persistence length of below 1 nm. So far, no good methods are available to stretch oligonucleotides. Herein, it is shown that freezing can stretch DNA, as confirmed using fluorescence resonance energy transfer, thiazole-orange staining, and surface-enhanced Raman spectroscopy. Lateral inter-strand interactions are critical, and the stretched DNA oligonucleotides are aligned. This work also provides a set of methods for studying frozen oligonucleotides. Upon freezing, DNA oligonucleotides are readily adsorbed onto various nanomaterials, including gold nanoparticles, graphene oxide, iron oxide, and WS₂ via the most thermodynamically stable conformation, leading to more stable conjugates.

In situ electron microscopy of the self-assembly of single-stranded DNA-functionalized Au nanoparticles in aqueous solution

Solution-phase self-assembly of DNA-functionalized nanoparticles into mesoscale structures is a promising strategy for creating functional materials from nanocrystal building blocks. The predominant approach has been the use of Watson-Crick base pairing between complementary bases in designated 'sticky ends' to trigger programmable self-assembly into ordered superlattices. Here we demonstrate the ordered self-assembly of Au nanoparticles conjugated with single-stranded (ss) DNA in acidic solutions. Au nanoparticles functionalized with thiolated ssDNA are protected against coalescence and the DNA conformation undergoes significant modifications at low pH, which can be associated with the protonation of adenine bases and the formation of a parallel poly-adenine duplex, which govern the interaction between ssDNA-Au nanoparticle conjugates. In situ liquid cell electron microscopy enables real-time imaging of the self-assembly process and the identification of key characteristics, such as the preferred structural motifs and interparticle separations in the native solution environment. Our results highlight alternatives to conventional base-pairing interactions for building DNA-directed nanoparticle superlattices.

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.

Liquid interfaces with pH-switchable nanoparticle arrays

Stimuli-responsive 2D nanoscale systems offer intriguing opportunities for creating switchable interfaces. At liquid interfaces, such systems can provide control over interfacial energies, surface structure, and rheological and transport characteristics, which is relevant, for example, to bio- and chemical reactors, microfluidic devices, and soft robotics. Here, we explore the formation of a pH-responsive membrane formed from gold nanoparticles grafted with DNA (DNA-NPs) at a liquid-vapor interface. A DNA-NP 2D hexagonal lattice can be reversibly switched by pH modulation between an expanded state of non-connected nanoparticles at neutral pH and a contracted state of linked nanoparticles at acidic pH due to the AH+-H+A base pairing between A-motifs. Our in situ surface X-ray scattering studies reveal that the reversible lattice contraction can be tuned by the length of pH-activated linkers, with up to ∼71% change in surface area.

Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds

A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emission of ThT. The introduction of reverse Watson–Crick T-A base pairs into these dimeric parallel-stranded DNA systems remarkably favors the binding of ThT into the pocket between G•G and A•A base pairs, where ThT is encapsulated thereby restricting its two rotary aromatic rings in the excited state. A similar mechanism is also demonstrated in antiparallel DNA duplexes where several motifs of two consecutive G•G wobble base pairs are incorporated and serve as the active pockets for ThT binding. The insight into the interactions of ThT with non-G-quadruplex DNAs allows us to introduce a new concept for constructing DNA-based sensors and devices. As proof-of-concept experiments, we design a DNA triplex containing GA motifs in its Hoogsteen hydrogen-bonded two parallel strands as a pH-driven nanoswitch and two GA-containing parallel duplexes as novel metal sensing platforms where C–C and T–T mismatches are included. This work may find further applications in biological systems (e.g. disease gene detection) where parallel duplex or triplex stretches are involved.