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

Universal Click-Chemistry Approach for the DNA Functionalization of Nanoparticles

Nanotechnology has revolutionized the fabrication of hybrid species with tailored functionalities. A milestone in this field is the deoxyribonucleic acid (DNA) conjugation of nanoparticles, introduced almost 30 years ago, which typically exploits the affinity between thiol groups and metallic surfaces. Over the last decades, developments in colloidal research have enabled the synthesis of an assortment of nonmetallic structures, such as high-index dielectric nanoparticles, with unique properties not previously accessible with traditional metallic nanoparticles. However, to stabilize, integrate, and provide further functionality to nonmetallic nanoparticles, reliable techniques for their functionalization with DNA will be crucial. Here, we combine well-established dibenzylcyclooctyne-azide click-chemistry with a simple freeze-thaw method to achieve the functionalization of silica and silicon nanoparticles, which form exceptionally stable colloids with a high DNA surface density of ∼0.2 molecules/nm2. Furthermore, we demonstrate that these functionalized colloids can be self-assembled into high-index dielectric dimers with a yield of over 50% via the use of DNA origami. Finally, we extend this method to functionalize other important nanomaterials, including oxides, polymers, core-shell, and metal nanostructures. Our results indicate that the method presented herein serves as a crucial complement to conventional thiol functionalization chemistry and thus greatly expands the toolbox of DNA-functionalized nanoparticles currently available.

Freeze-Driven Synthesis of DNA Hairpin-Conjugated Gold Nanoparticle Biosensors for Dual-Mode Detection

Freeze-based immobilization of deoxyribonucleic acid (DNA) oligonucleotides on gold nanoparticles (AuNPs) is highly efficient for single-stranded oligonucleotides but typically does not accommodate structures such as snap-cooled DNA hairpins (Sc-HPs) and snap-cooled molecular beacons (Sc-MBs) frequently used for biorecognition applications. Recognizing this limitation, we have developed a modified, freeze-based technique specifically designed to enable the adsorption of such hairpin oligonucleotides onto AuNP surfaces while ensuring that they retain their biosensing capabilities. Successful hairpin oligonucleotide conjugation of varying lengths to a wide range of AuNP diameters was corroborated by dynamic light scattering, ζ-potential, and UV-vis spectrophotometry. Moreover, we conducted a thorough evaluation of this modified method, confirming the retention of the sensing functions of Sc-HPs and Sc-MBs. This advancement not only offers a more efficient route for DNA hairpin conjugation but also elucidates the underlying biorecognition functions, with implications for broader applications in molecular diagnostics.

Gold Nanoprobes for Detection of a Crucial EGFR Deletion for Early Diagnosis of Non-Small-Cell Lung Cancer

Gold nanoparticles (AuNPs) exhibit improved optical and spectral properties compared to bulk materials, making them suitable for the detection of DNA, RNA, antigens, and antibodies. Here, we describe a simple, selective, and rapid non-cross linking detection assay, using approx. 35 nm spherical Au nanoprobes, for a common mutation occurring in exon 19 of the epidermal growth factor receptor (EGFR), associated with non-small-cell lung cancer cells. AuNPs were synthesized based on the seed-mediated growth method and functionalized with a specific 16 bp thiolated oligonucleotide using a pH-assisted method. Both AuNPs and Au nanoprobes proved to be highly stable and monodisperse through ultraviolet-visible spectrophotometry, dynamic light scattering (DLS), and electrophoretic light scattering (ELS). Our results indicate a detection limit of 1.5 µg mL-1 using a 0.15 nmol dm-3 Au nanoprobe concentration. In conclusion, this work presents an effective possibility for a straightforward, fast, and inexpensive alternative for the detection of DNA sequences related to lung cancer, leading to a potential platform for early diagnosis of lung cancer patients.

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.

Nanosensor Based on the Dual-Entropy-Driven Modulation Strategy for Intracellular Detection of MicroRNA

The entropy-driven strategy has been proposed as a milestone work in the development of nucleic acid amplification technology. With the characteristics of an enzyme-free, isothermal, and relatively simple design, it has been widely used in the field of biological analysis. However, it is still a challenge to apply entropy-driven amplification for intracellular target analysis. In this study, a dual-entropy-driven amplification system constructed on the surface of gold nanoparticles (AuNPs) is developed to achieve fluorescence determination and intracellular imaging of microRNA-21 (miRNA-21). The dual-entropy-driven amplification strategy internalizes the fuel chain to avoid the complexity of the extra addition in the traditional entropy-driven amplification strategy. The unique self-locked fuel chain system is established by attaching the three-stranded structure on two groups of AuNPs, where the Cy5 fluorescent label was first quenched by AuNPs. After the target miRNA-21 is identified, the fuel chain will be automatically unlocked, and the cycle reaction will be driven, leading to fluorescence recovery. The self-powered and waste-recycled fuel chain greatly improves the automation and intelligence of the reaction process. Under the optimal conditions, the linear response range of the nanosensor ranges from 5 pM to 25 nM. This nanoreaction system can be used to realize intracellular imaging of miRNA-21, and its good specificity enables it to distinguish tumor cells from healthy cells. The development of the dual-entropy-driven strategy provides an integrated and powerful way for intracellular miRNA analysis and shows great potential in the biomedical field.

The Effect of Nanoparticle Composition on the Surface-Enhanced Raman Scattering Performance of Plasmonic DNA Origami Nanoantennas

A versatile generation of plasmonic nanoparticle dimers for surface-enhanced Raman scattering (SERS) is presented by combining a DNA origami nanofork and spherical and nonspherical Au or Ag nanoparticles. Combining different nanoparticle species with a DNA origami nanofork to form DNA origami nanoantennas (DONAs), the plasmonic nanoparticle dimers can be optimized for a specific excitation wavelength in SERS. The preparation of such nanoparticle dimers is robust enough to enable the characterization of SERS intensities and SERS enhancement factors of dye-modified DONAs on a single dimer level by measuring in total several thousands of dimers from five different dimer designs, each functionalized with three different Raman reporter molecules and measured at four different excitation wavelengths. Based on these data, SERS enhancement factor (EF) distributions have been determined for each dimer design and excitation wavelengths. The structures and measurement conditions with the highest EFs are suitable for single-molecule SERS (SM-SERS), which is realized by placing single dye molecules into hot spots. We demonstrate that the probability of placing single molecules in a strongly enhancing hot spot for SM-SERS can be increased by using anisotropic nanoparticles with several sharp edges, such as nanoflowers. Combining a Ag nanoparticle with a Au particle in one dimer structure allows for a broadband excitation covering almost the whole visible range. The most versatile plasmonic dimer structure for SERS combines a spherical Ag nanoparticle with a Au nanoflower. Employing the discontinuous Galerkin time domain method, we numerically investigate the bare, symmetric dimers with respect to spectral and near-field properties, showing that, indeed, the nanoflowers induce multiple hot spots located at the edges which surpass the intensity of the spherical dimers, indicating the possibility for SM-SERS. The presented DONA structures and SERS data provide a robust basis for applying such designs as versatile SERS tags and as substrates for SM-SERS measurements.

Highly Uniform DNA Monolayers Generated by Freezing-Directed Assembly on Gold Surfaces Enable Robust Electrochemical Sensing in Whole Blood

Assembling DNA on solid surfaces is fundamental to surface-based DNA technology. However, precise control over DNA conformation and organization at solid-liquid interfaces remains a challenge, resulting in limited stability and sensitivity in biosensing applications. We herein communicate a simple and robust method for creating highly uniform DNA monolayers on gold surfaces by a freeze-thawing process. Using Raman spectroscopy, fluorescent imaging, and square wave voltammetry, we demonstrate that thiolated DNA is concentrated and immobilized on gold surfaces with an upright conformation. Moreover, our results reveal that the freezing-induced DNA surfaces are more uniform, leading to improved DNA stability and target recognition. Lastly, we demonstrate the successful detection of a model drug in undiluted whole blood while mitigating the effects of biofouling. Our work not only provides a simple approach to tailor the DNA-gold surface for biosensors but also sheds light on the unique behavior of DNA oligonucleotides upon freezing on the liquid-solid interface.

Hydrogel-based molecular tension fluorescence microscopy for investigating receptor-mediated rigidity sensing

Extracellular matrix (ECM) rigidity serves as a crucial mechanical cue impacting diverse biological processes. However, understanding the molecular mechanisms of rigidity sensing has been limited by the spatial resolution and force sensitivity of current cellular force measurement techniques. Here we developed a method to functionalize DNA tension probes on soft hydrogel surfaces in a controllable and reliable manner, enabling molecular tension fluorescence microscopy for rigidity sensing studies. Our findings showed that fibroblasts respond to substrate rigidity by recruiting more force-bearing integrins and modulating integrin sampling frequency of the ECM, rather than simply overloading the existing integrin-ligand bonds, to promote focal adhesion maturation. We also demonstrated that ECM rigidity positively regulates the pN force of T cell receptor-ligand bond and T cell receptor mechanical sampling frequency, promoting T cell activation. Thus, hydrogel-based molecular tension fluorescence microscopy implemented on a standard confocal microscope provides a simple and effective means to explore detailed molecular force information for rigidity-dependent biological processes.

Effect of DNA density immobilized on gold nanoparticles on nucleic acid detection

Gold nanoparticles (AuNPs) have been utilized as colorimetric biosensors, where target molecule-induced AuNP aggregation can be recognized by a colour change from red to blue. Particularly, single-stranded DNA (ssDNA)-immobilized AuNPs (ssDNA-AuNPs) have been applied to genetic diagnosis due to their rapid and sequence-specific aggregation properties. However, the effect of the density of immobilized ssDNA have not been investigated yet. In this study, we developed a method to control the amount of immobilized ssDNA by use of ethylene glycol, which is expected to control the ice crystal spacing in a freezing-thawing ssDNA-AuNP synthesis method. We also investigated the effect of the DNA density on the sensitivity of the target ssDNA detection, and found that the detection sensitivity was improved at lower DNA densities. To discuss the reason for the improved detection sensitivity, we modified the ssDNA-AuNPs with alkane thiol for better dispersion stability against salt. The results suggest that the DNA density, rather than the dispersion stability, has a significant impact on detection sensitivity.

Recent Advances in DNA Nanomaterials

Applications of DNA-containing nanomaterials (DNA-NMs) in science and technology are currently attracting increasing attention in the fields of medicine, environment, engineering, etc. Such objects have become important for various branches of science and industries due to their outstanding characteristics such as small size, high controllability, clustering actions, and strong permeability. For these reasons, DNA-NMs deserve a review with respect to their recent advancements. On the other hand, precise cluster control, targeted drug distribution in vivo, and cellular micro-nano operation remain as problems. This review summarizes the recent progress in DNA-NMs and their crossover and integration into multiple disciplines (including in vivo/in vitro, microcircles excisions, and plasmid oligomers). We hope that this review will motivate relevant practitioners to generate new research perspectives and boost the advancement of nanomanipulation.

Methods to functionalize gold nanoparticles with tandem-phosphorothioate DNA: role of physicochemical properties of the phosphorothioate backbone in DNA adsorption to gold nanoparticles

Perception of the differences in the physicochemical properties of phosphorothioate DNA (PS-DNA) and phosphodiester DNA (PO-DNA) greatly aids in understanding the AuNP-DNA binding process. Replacing one non-bridging oxygen atom of the anionic phosphodiester backbone with a sulfur atom leads to a major change in the DNA adsorption mechanism of AuNPs. In this work, we investigated and compared salt-aging, low pH-assisted, and freeze-thaw methods for conjugating phosphorothioate-modified oligonucleotides to AuNPs. The results obtained clearly demonstrate that only the pH-assisted method can successfully bind tandem phosphorothioate DNA to gold nanoparticles and sufficiently maintain the colloidal stability of AuNPs. When a phosphate group is converted to a phosphorothioate group, the negative charge of the phosphate group is located on the sulfur atom. Due to the soft nature of sulfur (a very weak H-bond acceptor), the negative charge on the sulfur atom cannot be shielded even with the gradual addition of salt to increase the ionic strength, so, the pH-assisted based method is the best for the functionalization of AuNPs with tandem-PS DNA.

Nanoparticle Spikes Enhance Cellular Uptake via Regulating Myosin IIA Recruitment

Spike-like nanostructures are omnipresent in natural and artificial systems. Although biorecognition of nanostructures to cellular receptors has been indicated as the primary factor for virus infection pathways, how the spiky morphology of DNA-modified nanoparticles affects their cellular uptake and intracellular fate remains to be explored. Here, we design dually emissive gold nanoparticles with varied spikiness (from 0 to 2) to probe the interactions of spiky nanoparticles with cells. We discovered that nanospikes at the nanoparticle regulated myosin IIA recruitment at the cell membrane during cellular uptake, thereby enhancing cellular uptake efficiency, as revealed by dual-modality (plasmonic and fluorescence) imaging. Furthermore, the spiky nanoparticles also exhibited facilitated endocytosis dynamics, as revealed by real-time dark-field microscopy (DFM) imaging and colorimetry-based classification algorithms. These findings highlight the crucial role of the spiky morphology in regulating the intracellular fate of nanoparticles, which may shed light on engineering theranostic nanocarriers.

Development of a Fluorescent Biosensor Based on DNAzyme for Tracing the Release of Zinc in Maize Leaves

A fluorescent biosensor for real-time monitoring the release of Zn²⁺ in plants was constructed through immobilization of DNAzyme-containing hairpin DNA on nanofertilizer ZnO@Au nanoparticles (ZnO@Au NPs). A specially designed hairpin DNA containing both DNAzyme and its substrate sequence, which was also labeled with 5'-FAM and 3'-SH groups, was modified on ZnO@Au NPs through the Au-S bond. The fluorescent signal of FAM was initially quenched by AuNPs. When Zn²⁺ was released from ZnO@Au NPs, DNAzyme was activated and the substrate sequence in hairpin DNA was cleaved. The restored fluorescent signal in Tris-HCl buffer (pH 6.5) was correlated with the concentration of the released Zn²⁺. The performance of the biosensor was first demonstrated in the solution. The linear detection range was from 50 nM to 1.5 μM, with a detection limit of 30 nM. The biosensor system can penetrate into maize leaves with ZnO@Au NPs. With the release of Zn²⁺ in leaves, the restored fluorescence can be imaged by a confocal laser scanning microscope and used for monitoring the release and distribution of Zn²⁺. This work may provide a novel strategy for tracing and understanding the mechanism of nanofertilizers in organisms.

Hybridization-Driven Adsorption of Polyadenine DNA onto Gold Nanoparticles

The attachment of functional DNA to gold nanoparticles via polyadenine adsorption is a well-established technology. This approach was mainly viewed through the lens of changing the DNA charge in order to reduce the electrostatic barrier created by a similarly charged gold surface. However, altering the DNA charge results in the loss of its functionality. This work considers the adsorption process of polyadenines by force that artificially brings them closer to the surface. As a force source, we used the hybridization of a DNA strand carrying polyadenines with a complementary strand already attached to the surface. It was shown that the hybridization forces facilitated the adsorption of polyadenines. We believe that this approach is applicable in various areas where it is essential to preserve the functionality of DNA during conjugation with nanoparticles.

Paper-based LRET sensor for the detection of total heavy rare-earth ions

Based on the mechanism of luminescence resonance energy transfer (LRET) and using a special single strand DNA as the recognition element, a portable paper-based sensor for the accurate detection of total heavy rare-earth ions (mainly Gd3+, Tb3+ and Dy3+) concentration was proposed. The RNA cleaving-DNAzyme should recognize rare-earth ions to cleave RNA on DNA duplexes linking UCNPs and AuNPs, causing UCNPs and AuNPs to approach each other, inducing LRET, which attenuated the green upconversion luminescence (UCL) triggered by the 980 nm laser. UCL was captured by a charge-coupled device (CCD) image sensor and processed with the red-green-blue (RGB) image to quantitatively analyze heavy rare-earth ions in the samples. In the range of 5–50 μmol·L-1, the sensor has good sensitivity, with the limit of detection of 1.26 μmol L−1.

Role of an Ice Surface in the Photoreaction of Coumarins

Ice affects many chemical reactions in nature, which greatly influences the atmosphere, climate, and life. However, the exact mechanism of ice in these chemical reactions remains elusive. For example, it is still an open question as to whether ice can act as a catalyst to greatly enhance the reactivity and selectivity, which is essential for the production of some natural compounds in our planet. Here, we discover that ice can lead to high efficiency and stereoselectivity of the [2 + 2] photodimerization of coumarin and its derivatives. The conversion of the [2 + 2] photodimerization of coumarins enhanced by ice is dozens of times higher than that in the unfrozen saturated solution, and the reaction displays a high syn-head-head stereoselectivity (>95%) in comparison with those in the absence of the ice. Note that almost no reaction occurs in the crystal powder and melt of the coumarins, indicating that the role of ice in the photodimerization reaction is not simply due to the usual mechanisms found in the freezing concentration. We further reveal that the reaction rate is found to be proportional to the total area of the ice surface and follows Michaelis-Menten-like kinetics, indicating that the ice surface catalyzes the reaction. Molecular dynamics simulations demonstrate that ice surfaces can induce reactants to form a two-dimensional liquid-crystal-ordered layer with a suitable intermolecular distance and unique side-by-side packing, facilitating stereoselective photodimerization for syn-head-head dimers. These findings give evidence that ice-surface-induced molecular assembly may play an important role in atmospheric heterogeneous photoreaction processes.

An ultrasensitive fluorescence detection template of pathogenic bacteria based on dual catalytic hairpin DNA Walker@Gold nanoparticles enzyme-free amplification

Integrating the advantages of catalytic hairpin components and multi-foot DNA walker, we designed a 16S rRNA detection probe template for pathogen bacteria, which utilizes DNA ligation quencher and dual catalytic hairpin@DNA walker to induce signal recovery. The dual catalytic hairpin@DNA walker uses the walking position of the target on the AuNP as a foothold to promote the reaction, so that the biosensing of the low-abundance target sequence can induce signal recovery. During the entire experiment, no enzyme is required, which can avoid the limitation of enzyme degradation under unfavorable conditions and the inability to detect the target. Most importantly, the detection template has the advantages of high sensitivity, and its detection limit is significantly better than that of single hairpin DNA walker probe. As the detection system can sensitively and rapidly detect its targeted bacteria and not rely on any enzyme and sophisticated instrumentation, it has great potential for sensitive and specific pathogenic bacteria detection.

Single-Stranded DNA Recognition over Fluorescent Gold-Aryl Nanoparticles

Fluorescence labeling of gold-aryl nanoparticles, AuNPs-COOH, was achieved by the covalent derivatization with dansyl chloride (DNS-Cl) reagent (5-naphthalene-1-sulfonyl chloride) for potential ssDNA recognition. The fluorescent gold nanoparticles of AuNPs-C6H4-4-COO-dansyl (AuNPs-DNS) of spherical shape and a size of 19.3 ± 8.3 nm were synthesized in a carbonate-bicarbonate buffer (pH = 10.6) at 37 °C. The fluorescence emission at 475 nm was acquired using fluorescence spectroscopy and investigated using time-resolved photoluminescence. The conjugation of ssDNA to AuNPs-DNS using the freeze-thaw and salt-aging methods was confirmed by fluorescence emission quenching, gel electrophoresis separation, and lifetime decrease. Conjugated ssDNA to AuNPs-DNS using the freeze-thaw method was more efficient than the salt-aging method. The purity of ssDNA upon conjugation was measured with optical density, and the obtained A260/A280 ratio was in the range of 1.7–2.0. This research can be applied to other nucleotide recognition and theranostics.

Visible wavelength spectral tuning of absorption and circular dichroism of DNA-assembled Au/Ag core-shell nanorod assemblies

Plasmonic nanoparticles have unique properties which can be harnessed to manipulate light at the nanoscale. With recent advances in synthesis protocols that increase their stability, gold-silver core-shell nanoparticles have become suitable building blocks for plasmonic nanostructures to expand the range of attainable optical properties. Here we tune the plasmonic response of gold-silver core-shell nanorods over the visible spectrum by varying the thickness of the silver shell. Through the chiral arrangement of the nanorods with the help of various DNA origami designs, the spectral tunability of the plasmon resonance frequencies is transferred into circular dichroism signals covering the spectrum from 400 nm to 700 nm. Our approach could aid in the construction of better sensors as well as metamaterials with a tunable optical response in the visible region.

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.

A facile visualized solid-phase detection of virus-specific nucleic acid sequences through an upconversion activated linear luminescence recovery process

Based on the LRET between UCNPs and AuNPs, a solid-phase biosensor was developed for detection of virus-specific nucleic acid sequences by the naked eye, and is expected to become a fast, facile, efficient and reliable POCT platform.

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.

Magnetically Enhanced Liquid SERS for Ultrasensitive Analysis of Bacterial and SARS-CoV-2 Biomarkers

In this work, it is shown that surface-enhanced Raman scattering (SERS) measurements can be performed using liquid platforms to perform bioanalysis at sub-pM concentrations. Using magnetic enrichment with gold-coated magnetic nanoparticles, the high sensitivity was verified with nucleic acid and protein targets. The former was performed with a DNA fragment associated with the bacteria Staphylococcus aureus, and the latter using IgG antibody, a biomarker for COVID-19 screening. It is anticipated that this work will inspire studies on ultrasensitive SERS analyzers suitable for large-scale applications, which is particularly important for in vitro diagnostics and environmental studies.

Modulation of DNAzyme Activity via Butanol Dehydration

Understanding the activity of biomolecules in cosolvent systems is important for catalysis, separation and developing biosensors. The majority of previously studied solvents are either phase separated with water or miscible with water. Butanol was recently used to extract water for the conjugation of DNA to gold nanoparticles. In this work, the effect of butanol on the activity of a few RNA-cleaving DNAzymes was studied. A 130-fold improvement in sensitivity for the Na⁺ -specific EtNa DNAzyme was observed, and butanol also improved the activity of another Na⁺ -specific DNAzyme, NaA43T by a few folds. However, when divalent metal ions were used for both EtNa and 17E DNAzymes, the activity was inhibited. A main driven force for enhanced DNAzyme activity is the concentration effect due to butanol dehydration. This study provides insights into the interplay between DNA, metal ions and organic solvents, and such an understanding might be useful for developing sensitive biosensors.

Factors and methods to modulate DNA hybridization kinetics

DNA oligonucleotides are widely used in a diverse range of research fields from analytical chemistry, molecular biology, nanotechnology to drug delivery. In these applications, DNA hybridization is often the most important enabling reaction. Achieving control over hybridization kinetics and a high yield of hybridized products is needed to ensure high-quality and reproducible results. Since DNA strands are highly negatively charged and can also fold upon itself to form various intramolecular structures, DNA hybridization needs to overcome these barriers. Nucleation and diffusion are two main kinetic limiting steps although their relative importance differs in different conditions. The effects of length and sequence, temperature, pH, salt concentration, cationic polymers, organic solvents, freezing and crowding agents are summarized in the context of overcoming these barriers. This article will help researchers in the biotechnology-related fields to better understand and control DNA hybridization, as well as provide a landscape for future work in simulation and experiment to optimize DNA hybridization systems.

Attachment of Single-Stranded DNA to Certain SERS-Active Gold and Silver Substrates: Selected Practical Tips

Layers formed from single-stranded DNA on nanostructured plasmonic metals can be applied as “working elements” in surface–enhanced Raman scattering (SERS) sensors used to sensitively and accurately identify specific DNA fragments in various biological samples (for example, in samples of blood). Therefore, the proper formation of the desired DNA layers on SERS substrates is of great practical importance, and many research groups are working to improve the process in forming such structures. In this work, we propose two modifications of a standard method used for depositing DNA with an attached linking thiol moiety on certain SERS-active structures; the modifications yield DNA layers that generate a stronger SERS signal. We propose: (i) freezing the sample when forming DNA layers on the nanoparticles, and (ii) when forming DNA layers on SERS-active macroscopic silver substrates, using ω-substituted alkanethiols with very short alkane chains (such as cysteamine or mercaptopropionic acid) to backfill the empty spaces on the metal surface unoccupied by DNA. When 6-mercapto-1-hexanol is used to fill the unoccupied places on a silver surface (as in experiments on standard gold substrates), a quick detachment of chemisorbed DNA from the silver surface is observed. Whereas, using ω-substituted alkanethiols with a shorter alkane chain makes it possible to easily form mixed DNA/backfilling thiol monolayers. Probably, the significantly lower desorption rate of the thiolated DNA induced by alkanethiols with shorter chains is due to the lower stabilization energy in monolayers formed from such compounds.

Nucleic Acid Amplification Techniques in Immunoassay: An Integrated Approach with Hybrid Performance

An immunoassay is mostly employed for the direct detection of food contaminants, and a molecular assay for targeting nucleic acids employs amplification techniques for distinguishing genes. The integration of an immunoassay with nucleic acid amplification techniques inherits the direct and rapid performance of an immunoassay and the ultrasensitive merit of a molecular assay. Enthusiastic attention has been attracted in recent years on the utilization of isothermal amplification techniques in an immunoassay, as well as the employment of a lateral flow immunoassay in a molecular assay. Thus, this Review discussed these kinds of approaches from two categories: immuno-nucleic acid amplification (I-NAA) and nucleic acid amplification-immunoassay (NAA-I). The advantages, drawbacks, and future developments were discussed for a comprehensive understanding.

DNA Gold Nanoparticle Motors Demonstrate Processive Motion with Bursts of Speed Up to 50 nm Per Second

Synthetic motors that consume chemical energy to produce mechanical work offer potential applications in many fields that span from computing to drug delivery and diagnostics. Among the various synthetic motors studied thus far, DNA-based machines offer the greatest programmability and have shown the ability to translocate micrometer-distances in an autonomous manner. DNA motors move by employing a burnt-bridge Brownian ratchet mechanism, where the DNA "legs" hybridize and then destroy complementary nucleic acids immobilized on a surface. We have previously shown that highly multivalent DNA motors that roll offer improved performance compared to bipedal walkers. Here, we use DNA-gold nanoparticle conjugates to investigate and enhance DNA nanomotor performance. Specifically, we tune structural parameters such as DNA leg density, leg span, and nanoparticle anisotropy as well as buffer conditions to enhance motor performance. Both modeling and experiments demonstrate that increasing DNA leg density boosts the speed and processivity of motors, whereas DNA leg span increases processivity and directionality. By taking advantage of label-free imaging of nanomotors, we also uncover Lévy-type motion where motors exhibit bursts of translocation that are punctuated with transient stalling. Dimerized particles also demonstrate more ballistic trajectories confirming a rolling mechanism. Our work shows the fundamental properties that control DNA motor performance and demonstrates optimized motors that can travel multiple micrometers within minutes with speeds of up to 50 nm/s. The performance of these nanoscale motors approaches that of motor proteins that travel at speeds of 100-1000 nm/s, and hence this work can be important in developing protocellular systems as well next generation sensors and diagnostics.

Enzyme Activated Gold Nanoparticles for Versatile Site-Selective Bioconjugation

A new enzymatic method is reported for constructing protein- and DNA-AuNP conjugates. The strategy relies on the initial functionalization of AuNPs with phenols, followed by activation with the enzyme tyrosinase. Using an oxidative coupling reaction, the activated phenols are coupled to proteins bearing proline, thiol, or aniline functional groups. Activated phenol-AuNPs are also conjugated to a small molecule biotin and commercially available thiol-DNA. Advantages of this approach for AuNP bioconjugation include: (1) initial formation of highly stable AuNPs that can be selectively activated with an enzyme, (2) the ability to conjugate either proteins or DNA through a diverse set of functional handles, (3) site-specific immobilization, and (4) facile conjugation that is complete within 2 h at room temperature under aqueous conditions. The enzymatic oxidative coupling on AuNPs is applied to the construction of tobacco mosaic virus (TMV)-AuNP conjugates, and energy transfer between the AuNPs and fluorophores on TMV is demonstrated.

DNA Origami-Enabled Plasmonic Sensing

The reliable programmability of DNA origami makes it an extremely attractive tool for bottom-up self-assembly of complex nanostructures. Utilizing this property for the tuned arrangement of plasmonic nanoparticles holds great promise particularly in the field of biosensing. Plasmonic particles are beneficial for sensing in multiple ways, from enhancing fluorescence to enabling a visualization of the nanoscale dynamic actuation via chiral rearrangements. In this Perspective, we discuss the recent developments and possible future directions of DNA origami-enabled plasmonic sensing systems. We start by discussing recent advancements in the area of fluorescence-based plasmonic sensing using DNA origami. We then move on to surface-enhanced Raman spectroscopy sensors followed by chiral sensing, both utilizing DNA origami nanostructures. We conclude by providing our own views on the future prospects for plasmonic biosensors enabled using DNA origami.

DNAzyme Walker for Homogeneous Detection of Enterovirus EV71 and CVB3

When dealing with infectious pathogens, the risk of contamination or infection in the process of detecting them is nonnegligible. Separation-free detection will be beneficial in operation and safety. In this work, we proposed a DNAzyme walker for homogeneous and isothermal detection of enterovirus. The DNAzyme is divided into two inactivate subunits. When the subunit-conjugated antibody binds to the target virus, the activity of the DNAzyme recovers as a result of spatial proximity. The walker propels, and the fluorescence recovers. The final fluorescence intensity of the reaction mixture is related to the concentration of the target virus. The detection limit of this proposed method is 6.6 × 10⁴ copies/mL for EV71 and 4.3 × 10⁴ copies/mL for CVB3, respectively. Besides, this method was applied in detection of EV71 in clinical samples with a satisfactory result. The entire experiment is easy to operate, and the proposed method has great potential for practical use.

Tuning DNA-nanoparticle conjugate properties allows modulation of nuclease activity

Enzyme-nanoparticle interactions can give rise to a range of new phenomena, most notably significant enzymatic rate enhancement. Accordingly, the careful study and optimization of such systems is likely to give rise to advanced biosensing applications. Herein, we report a systematic study of the interactions between nuclease enzymes and oligonucleotide-coated gold nanoparticles (spherical nucleic acids, SNAs), with the aim of revealing phenomena worthy of evolution into functional nanosystems. Specifically, we study two nucleases, an exonuclease (ExoIII) and an endonuclease (Nt.BspQI), via fluorescence-based kinetic experiments, varying parameters including enzyme and substrate concentrations, and nanoparticle size and surface coverage in non-recycling and a recycling formats. We demonstrate the tuning of nuclease activity by SNA characteristics and show that the modular units of SNAs can be leveraged to either accelerate or suppress nuclease kinetics. Additionally, we observe that the enzymes are capable of cleaving restriction sites buried deep in the oligonucleotide surface layer and that enzymatic rate enhancement occurs in the target recycling format but not in the non-recycling format. Furthermore, we demonstrate a new SNA phenomenon, we term 'target stacking', whereby nucleic acid hybridization efficiency increases as enzyme cleavage proceeds during the beginning of a reaction. This investigation provides important data to guide the design of novel SNAs in biosensing and in vitro diagnostic applications.

Enhancing the peroxidase-like activity and stability of gold nanoparticles by coating a partial iron phosphate shell

Using citrate-capped gold nanoparticles (AuNPs) as peroxidase-mimicking enzymes to design biosensors is hindered by their low catalytic activity and poor colloidal stability, resulting in limited sensitivity and large variations. Herein, the growth of a partial iron phosphate (FeP) shell with Fe²⁺ ions on citrate-capped AuNPs boosted the activity of the AuNPs by up to 20-fold. The FeP-enhanced activity was demonstrated on AuNPs of different sizes, and gold nanostars. When the FeP layer is thick enough to block the access to the Au/FeP interface, the activity was inhibited. Capping the remaining Au surface by thiol also inhibited the activity, suggesting that faster reactions occurred at the interfaces of Au/FeP. Moreover, a FeP shell can stabilize AuNPs against freezing and a high NaCl concentration of 1 M. Sensitive detection of Fe²⁺ was achieved with a detection limit of 0.41 μM, while no other tested transition metal phosphates enhanced the peroxidase-like activity of AuNPs.

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.

DNA-Biofunctionalization of CTAC-Capped Gold Nanocubes

Clinical diagnostics and disease control are fields that strongly depend on technologies for rapid, sensitive, and selective detection of biological or chemical analytes. Nanoparticles have become an integral part in various biomedical detection devices and nanotherapeutics. An increasing focus is laid on gold nanoparticles as they express less cytotoxicity, high stability, and hold unique optical properties with the ability of signal transduction of biological recognition events with enhanced analytical performance. Strong electromagnetic field enhancements can be found in close proximity to the nanoparticle that can be exploited to enhance signals for e.g., metal-enhanced fluorescence or Raman spectroscopy. Even stronger field enhancements can be achieved with sharp-edged nanoparticles, which are synthesized with the help of facet blocking agents, such as cetyltrimethylammonium bromide/chloride (CTAB/CTAC). However, chemical modification of the nanoparticle surface is necessary to reduce the particle’s cytotoxicity, stabilize it against aggregation, and to bioconjugate it with biomolecules to increase its biocompatibility and/or specificity for analytical applications. Here, a reliable two-step protocol following a ligand exchange with bis (p-sulfonatophenyl) phenyl phosphine (BSPP) as the intermediate capping-agent is demonstrated, which results in the reliable biofunctionalization of CTAC-capped gold nanocubes with thiol-modified DNA. The functionalized nanocubes have been characterized regarding their electric potential, plasmonic properties, and stability against high concentrations of NaCl and MgCl₂.

Thermophoretic Detection of Exosomal microRNAs by Nanoflares

Exosomal microRNAs (miRNAs) are reliable and noninvasive biomarkers for the early diagnosis of cancer. Yet, accurate and feasible detection of exosomal miRNAs is often hampered by the low abundance of miRNAs in exosomes and the requirement for RNA extraction in large sample volumes. Here we show a thermophoretic sensor implemented with nanoflares for in situ detection of exosomal miRNAs, without resorting to either RNA extraction or target amplification. Thermophoretic accumulation of nanoflare-treated exosomes leads to an amplified fluorescence signal upon the binding of exosomal miRNAs to nanoflares, allowing for direct and quantitative measurement of exosomal miRNAs down to 0.36 fM in 0.5 μL serum samples. One of the best markers, exosomal miR-375, showed an accuracy of 85% for detection of estrogen receptor-positive breast cancer at early stages (stages I, II). This work provides a feasible tool to improve the diagnosis of cancer.

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.

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 promoted hybridization of very short DNA oligonucleotides

Shorter DNA probes provide better specificity for hybridization, but they may not form stable duplexes at room temperature. In this study, we used thiazole orange to follow DNA hybridization upon freezing and achieved stable 5-mer duplex DNA. Using multiple short probes in tandem, long DNA could also be studied. This study provides insights into DNA hybridization in the frozen state and expands the application of freezing for nucleic acid chemistry.