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

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

Rapid genetic screening with high quality factor metasurfaces

Genetic analysis methods are foundational to advancing personalized medicine, accelerating disease diagnostics, and monitoring the health of organisms and ecosystems. Current nucleic acid technologies such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) rely on sample amplification and can suffer from inhibition. Here, we introduce a label-free genetic screening platform based on high quality (high-Q) factor silicon nanoantennas functionalized with nucleic acid fragments. Each high-Q nanoantenna exhibits average resonant quality factors of 2,200 in physiological buffer. We quantitatively detect two gene fragments, SARS-CoV-2 envelope (E) and open reading frame 1b (ORF1b), with high-specificity via DNA hybridization. We also demonstrate femtomolar sensitivity in buffer and nanomolar sensitivity in spiked nasopharyngeal eluates within 5 minutes. Nanoantennas are patterned at densities of 160,000 devices per cm2, enabling future work on highly-multiplexed detection. Combined with advances in complex sample processing, our work provides a foundation for rapid, compact, and amplification-free molecular assays.

Acceleration of DNA Hybridization Chain Reactions on 3D Nanointerfaces of Magnetic Particles and Their Direct Application in the Enzyme-Free Amplified Detection of microRNA

Accelerated DNA hybridization chain reactions (HCRs) using DNA origami as a scaffold have received considerable attention in dynamic DNA nanotechnology. However, tailor-made designs are essential for DNA origami scaffolds, hampering the practical application of accelerated HCRs. Here, we constructed the semilocalized HCR and localized HCR systems using magnetic beads (MBs) as a simple scaffold to explore them for the enzyme-free miR-21 detection. The semilocalized HCR system relied on free diffusing one hairpin DNA and MBs immobilized with another hairpin DNA, and the localized HCR system relied on MBs coimmobilized with two hairpin DNAs. We demonstrated that the DNA density on MBs plays a critical role in HCR kinetics and limit of detection (LOD). Among semilocalized HCR systems, MBs with a medium DNA density showed a faster HCR and lower LOD (10 pM) than the diffusive (conventional) HCR system (LOD: 86 pM). In contrast, the HCR further accelerated for the localized HCR systems as the DNA density increased. The localized HCR system with the highest DNA density showed the fastest HCR and the lowest LOD (533 fM). These findings are of great importance for the rational design of accelerated HCRs using simple scaffolds for practical applications.

How Surfaces Affect Hybridization Kinetics

Hybridization between nucleic acid strands immobilized on a solid support with partners in solution is widely practiced in bioanalytical technologies and materials science. An important fundamental aspect of understanding these reactions is the role played by immobilization in the dynamics of duplex formation and disassembly. This report reviews and analyzes literature kinetic data to identify commonly observed trends and to correlate them with probable molecular mechanisms. The analysis reveals that while under certain conditions impacts from immobilization are minimal so that surface and solution hybridization kinetics are comparable, it is more typical to observe pronounced offsets between the two scenarios. In the forward (hybridization) direction, rates at the surface commonly decrease by one to two decades relative to solution, while in the reverse direction rates of strand separation at the surface can exceed those in solution by tens of decades. By recasting the deviations in terms of activation barriers, a consensus of how immobilization impacts nucleation, zipping, and strand separation can be conceived within the classical mechanism in which duplex formation is rate limited by preassembly of a nucleus a few base pairs in length, while dehybridization requires the cumulative breakup of base pairs along the length of a duplex. Evidence is considered for how excess interactions encountered on solid supports impact these processes.

Simple Single-Legged DNA Walkers at Diffusion-Limited Nanointerfaces of Gold Nanoparticles Driven by a DNA Circuit Mechanism

We designed and prepared a single-legged DNA walker that relies on the creation of a simple diffusion-limited nanointerface on a gold nanoparticle (DNA/PEG⁽⁺⁾-GNP) track co-modified with fluorescence-labeled hairpin DNA and poly(ethylene glycol) (PEG) containing a positively charged amino group at one end. The movement of our single-legged DNA walker is driven by an enzyme-free DNA circuit mechanism through cascading toehold mediated DNA displacement reactions (TMDRs) using fuel hairpin DNAs. The acceleration of TMDRs was observed for the DNA/PEG⁽⁺⁾-GNP track through electrostatic interaction between the positively charged track and negatively charged DNAs, resulting in the acceleration of the DNA circuit and amplification of the fluorescence signal. Furthermore, the DNA/PEG⁽⁺⁾-GNP track allowed autonomous and persistent movement of a walker DNA strand on the same GNP track, because the intraparticle DNA circuit occurred preferentially by preventing diffusion of the negatively charged free walker DNA strand from near the positively charged tracks into solution through electrostatic interaction. Based on comparative study of kinetics of TMDRs and DNA walking behaviors, it is to be noted that the DNA/PEG⁽⁺⁾-GNP track showed the fastest DNA circuit reaction (walking rate) and the largest number of steps taken by the walker DNA strand compared to other GNP tracks with varying nanointerfaces that differ in terms of their type of charges (no and negative charges), density of positive charges, and number of hairpin DNAs per GNP track. These facts reveal that the positive charges on the GNP track play an important role in the acceleration of the DNA circuit, as well as the successful walking motion of the single-legged DNA strand. By using the fluorescence signal amplification functions, our single-legged DNA walker could be applied directly and successfully to enzyme-free miRNA-detection systems. The miRNA-detection system provided higher discrimination of other mismatched miRNAs and higher sensitivity (the lowest LOD: 4.0 pM) when compared to other miRNA-detection systems based on other GNP tracks without positive charges. Unlike existing single-legged DNA walkers, our single-legged DNA walkers do not require complex processes, such as immobilization of the walker DNA strand on the tracks and precise adjustment of the sequence of walker DNA. Therefore, our strategy, based on the creation of diffusion-limited nanointerfaces, has enormous potential for the applications of single-legged DNA walkers to biosensors, bioimaging, and computing.

Noble Metal Nanoparticles-Based Colorimetric Biosensor for Visual Quantification: A Mini Review

Nobel metal can be used to form a category of nanoparticles, termed noble metal nanoparticles (NMNPs), which are inert (resistant to oxidation/corrosion) and have unique physical and optical properties. NMNPs, particularly gold and silver nanoparticles (AuNPs and AgNPs), are highly accurate and sensitive visual biosensors for the analytical detection of a wide range of inorganic and organic compounds. The interaction between noble metal nanoparticles (NMNPs) and inorganic/organic molecules produces colorimetric shifts that enable the accurate and sensitive detection of toxins, heavy metal ions, nucleic acids, lipids, proteins, antibodies, and other molecules. Hydrogen bonding, electrostatic interactions, and steric effects of inorganic/organic molecules with NMNPs surface can react or displacing capping agents, inducing crosslinking and non-crosslinking, broadening, or shifting local surface plasmon resonance absorption. NMNPs-based biosensors have been widely applied to a series of simple, rapid, and low-cost diagnostic products using colorimetric readout or simple visual assessment. In this mini review, we introduce the concepts and properties of NMNPs with chemical reduction synthesis, tunable optical property, and surface modification technique that benefit the development of NMNPs-based colorimetric biosensors, especially for the visual quantification. The “aggregation strategy” based detection principle of NMNPs colorimetric biosensors with the mechanism of crosslinking and non-crosslinking have been discussed, particularly, the critical coagulation concentration-based salt titration methodology have been exhibited by derived equations to explain non-crosslinking strategy be applied to NMNPs based visual quantification. Among the broad categories of NMNPs based biosensor detection analyses, we typically focused on four types of molecules (melamine, single/double strand DNA, mercury ions, and proteins) with discussion from the standpoint of the interaction between NMNPs surface with molecules, and DNA engineered NMNPs-based biosensor applications. Taken together, NMNPs-based colorimetric biosensors have the potential to serve as a simple yet reliable technique to enable visual quantification.

SERS-based cascade amplification bioassay protocol of miRNA-21 by using sandwich structure with biotin-streptavidin system

In our bioassay protocol, the Ag@4MBA@DNA-biotin probes were synthesized by linking biotin-modified DNA and 4-mercaptobenzoic acid-covered Ag nanoparticles, and the Si@Ag@anti-digoxin/digoxin-DNA substrate was fabricated by immune linking of digoxin-DNA and anti-digoxin immobilized on a Ag-coated wafer. Then, the probes, miRNA-21 and the substrate were constructed into a "sandwich structure" to detect the variation in the SERS signals with respect to miRNA-21 concentrations. Next, streptavidin and extra probes were alternately introduced to implement the cascade amplification of the SERS signal to increase the detection sensitivity. The results show that the limit of detection (LOD) with cascade amplification is remarkably improved from 97.81 pM to 38.02 fM, which is three orders of magnitude higher than the original data without cascade amplification. Furthermore, the SERS-based cascade amplification mechanism was analyzed and is attributed to the "hot spots effect" of the noble metal nanostructure. The biotin-streptavidin (B-S) system was introduced into the SERS detection platform, and the novel SERS-based cascade amplification bioassay protocol has significant creativity for the detection of nucleic acids.

Cost effective surface functionalization of gold nanoparticles with a mixed DNA and PEG monolayer for nanotechnology applications

We report a cost effective and generally applicable method for co-functionalization of gold nanoparticles with a mixed DNA and PEG polymer layer.

An Efficient Particle-Based DNA Circuit System: Catalytic Disassembly of DNA/PEG-Modified Gold Nanoparticle-Magnetic Bead Composites for Colorimetric Detection of miRNA

An efficient particle-based DNA circuit system for a new colorimetric miRNA assay is designed and devised based on a catalytic disassembly strategy through a target miRNA-triggered DNA circuit mechanism. The new particle-based DNA circuit system shows a rapid color change as well as significant improvement of sensitivity without need for other enzymes or instruments.