Design of asymmetric DNAzymes for dynamic control of nanoparticle aggregation states in response to chemical stimuli

2-LED-µSpectrophotometer for Rapid On-Site Detection of Pathogens Using Noble-Metal Nanoparticle-Based Colorimetric Assays

Novel point-of-care compatible methods such as colorimetric assays have become increasingly important in the field of early pathogen detection. A simple and hand-held prototype device for carrying out DNA-amplification assay based on plasmonic nanoparticles in the colorimetric detection is presented. The low-cost device with two channels (sample and reference) consists of two spectrally different light emitting diodes (LEDs) for detection of the plasmon shift. The color change of the gold-nanoparticle-DNA conjugates caused by a salt-induced aggregation test is examined in particular. A specific and sensitive detection of the waterborne human pathogen Legionella pneumophila is demonstrated. This colorimetric assay, with a simple assay design and simple readout device requirements, can be monitored in real-time on-site.

Fully Solid-State Graphene Transistors with Striking Homogeneity and Sensitivity for the Practicalization of Single-Device Electronic Bioassays

To break through a critical barrier in the practical application of graphene biosensors, namely, device-to-device performance inhomogeneity, this work presents a novel scenario employing a fully solid-state (FSS) transistor configuration. Herein, the graphene sensing unit is completely encapsulated by a high-κ solid dielectric material, which isolates the sensing unit from solution contaminants and thus homogeneously maintains the extraordinary carrier mobility of pristine graphene in batch-made devices. To create an interface sensitive to biomolecular interactions based on the FSS configuration, a metallic floating gate functionalized by conductive mercapto-phenyl molecular linkers is defined on the top-layer solid dielectric. As the solid dielectric layer beneath the metal floating gate enables a higher capacitive gating efficiency than the regular graphene-solution electrical double layer (EDL) interface, the overall transistor amplification gain is further enhanced. As a proof of principle, a label-free DNAzymatic bioassay of Pb²⁺ is conducted. Without the traditional one-by-one device normalization, an excellent concentration detection limit of 929.8 fM is achieved, which is almost 2 orders of magnitude lower than that in existing works. The FSS configuration allows enhanced sensitivity and homogeneity, thereby providing new developmental guidelines for graphene biosensors beyond the laboratory investigation stage. Additionally, it has the potential to be universally applicable for cost-efficient single-device bioassays.

Multi-metal-dependent nucleic acid enzymes

Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.

Gold nanoparticle-based colorimetric biosensors

Gold nanoparticles (AuNPs) provide excellent platforms for the development of colorimetric biosensors as they can be easily functionalised, displaying different colours depending on their size, shape and state of aggregation. In the last decade, a variety of biosensors have been developed to exploit the extent of colour changes as nano-particles (NPs) either aggregate or disperse, in the presence of analytes. Of critical importance to the design of these methods is that the behaviour of the systems has to be reproducible and predictable. Much has been accomplished in understanding the interactions between a variety of substrates and AuNPs, and how these interactions can be harnessed as colorimetric reporters in biosensors. However, despite these developments, only a few biosensors have been used in practice for the detection of analytes in biological samples. The transition from proof of concept to market biosensors requires extensive long-term reliability and shelf life testing, and modification of protocols and design features to make them safe and easy to use by the population at large. Developments in the next decade will see the adoption of user friendly biosensors for point-of-care and medical diagnosis as innovations are brought to improve the analytical performances and usability of the current designs. This review discusses the mechanisms, strategies, recent advances and perspectives for the use of AuNPs as colorimetric biosensors.

"Dipstick" Colorimetric Detection of Metal Ions Based on Immobilization of DNAzyme and Gold Nanoparticles onto a Lateral Flow Device

Real-time, on-site detection and quantification of different trace analytes is a challenge that requires both searching a general class of molecules to recognize a broad range of contaminants and translating this recognition to easily detectable signals. Functional nucleic acids, which include DNAzymes (DNA with catalytic activity) and aptamers (nucleic acids that bind an analyte), are ideal candidates for the target recognition. These nucleic acids can be selected by a combinatorial biology method called in vitro selection to interact with a particular analyte with high specificity and sensitivity. Furthermore, they can be incorporated into sensors by attaching signaling molecules. Due to the high extinction coefficients and distance-dependent optical properties, metallic nanoparticles such as the commonly used gold nanoparticles have been shown to be very attractive in converting analyte-specific functional DNA into colorimetric sensors. DNAzyme directed assembly of gold nanoparticles has been used to make colorimetric sensors for metal ions such as lead, uranium, and copper. To make the operation even easier and less vulnerable to operator's errors, dipstick tests have been constructed. Here, we describe protocols for the preparation of DNAzyme-linked gold nanoparticles (AuNP) that are then immobilized on to lateral flow devices to make easy-to-use dipstick tests for metal ions.

DNA as sensors and imaging agents for metal ions

Increasing interest in detecting metal ions in many chemical and biomedical fields has created demands for developing sensors and imaging agents for metal ions with high sensitivity and selectivity. This review covers recent progress in DNA-based sensors and imaging agents for metal ions. Through both combinatorial selection and rational design, a number of metal-ion-dependent DNAzymes and metal-ion-binding DNA structures that can selectively recognize specific metal ions have been obtained. By attachment of these DNA molecules with signal reporters such as fluorophores, chromophores, electrochemical tags, and Raman tags, a number of DNA-based sensors for both diamagnetic and paramagnetic metal ions have been developed for fluorescent, colorimetric, electrochemical, and surface Raman detection. These sensors are highly sensitive (with a detection limit down to 11 ppt) and selective (with selectivity up to millions-fold) toward specific metal ions. In addition, through further development to simplify the operation, such as the use of "dipstick tests", portable fluorometers, computer-readable disks, and widely available glucose meters, these sensors have been applied for on-site and real-time environmental monitoring and point-of-care medical diagnostics. The use of these sensors for in situ cellular imaging has also been reported. The generality of the combinatorial selection to obtain DNAzymes for almost any metal ion in any oxidation state and the ease of modification of the DNA with different signal reporters make DNA an emerging and promising class of molecules for metal-ion sensing and imaging in many fields of applications.

DNAzyme-based magneto-controlled electronic switch for picomolar detection of lead (II) coupling with DNA-based hybridization chain reaction

A novel magneto-controlled electrochemical DNA biosensor is designed for the ultrasensitive detection of lead coupling a lead-specific DNAzyme with DNA-based hybridization chain reaction (HCR). To construct such a magnetic lead sensor, DNAzyme-based molecular beacons, selective to cleavage in the presence of Pb(2+), are initially immobilized onto magnetic beads, which were used as the recognition elements. Upon addition of target lead, catalytic cleavage of substrate DNA segments in the double-stranded DNAzymes results in the capture of the initiator strands via the conjugated catalytic strands on magnetic beads. The captured DNA initiator strands trigger the hybridization chain reaction between two alternating hairpin DNA structures labeled with ferrocene to form a nicked double-helix on the magnetic beads. Numerous ferrocene molecules are formed on the neighboring probes, each of which produces an electrochemical signal within the applied potential. Under optimal conditions, the electrochemical signal of the magnetic lead sensor increases with the increasing lead level in the sample, and exhibits a linear response over a Pb(2+) concentration range of 0.1-75 nM with a detection limit of 37 pM. Quantitative measurement of Pb(2+) in the complex sample demonstrates the selectivity of the sensor scheme and points favorably to the application of such technologies to the analysis of environmental samples. The unique combination of a DNAzyme with hybridization chain reaction makes it possible to change the DNAzyme to select for other compounds of interest. This work represents the initial steps toward the creation of a robust field sensor for lead in groundwater or drinking water.

DNAzyme-functionalized gold nanoparticles for biosensing

Recent progress in using DNAzyme-functionalized gold nanoparticles (AuNPs) for biosensing is summarized in this chapter. A variety of methods, including those for attaching DNA on AuNPs, detecting metal ions and small molecules by DNAzyme-functionalized AuNPs, and intracellular applications of DNAzyme-functionalized AuNPs are discussed. DNAzyme-functionalized AuNPs will increasingly play more important roles in biosensing and many other multidisciplinary applications. This chapter covers the recent advancement in biosensing applications of DNAzyme-functionalized gold nanoparticles, including the detection of metal ions, small molecules, and intracellular imaging.

Metal ion sensors based on DNAzymes and related DNA molecules

Metal ion sensors are an important yet challenging field in analytical chemistry. Despite much effort, only a limited number of metal ion sensors are available for practical use because sensor design is often a trial-and-error-dependent process. DNAzyme-based sensors, in contrast, can be developed through a systematic selection that is generalizable for a wide range of metal ions. Here, we summarize recent progress in the design of DNAzyme-based fluorescent, colorimetric, and electrochemical sensors for metal ions, such as Pb(2+), Cu(2+), Hg(2+), and UO(2)(2+). In addition, we also describe metal ion sensors based on related DNA molecules, including T-T or C-C mismatches and G-quadruplexes.

Gold nanoparticles in nanomedicine: preparations, imaging, diagnostics, therapies and toxicity

This critical review provides an overall survey of the basic concepts and up-to-date literature results concerning the very promising use of gold nanoparticles (AuNPs) for medicinal applications. It includes AuNP synthesis, assembly and conjugation with biological and biocompatible ligands, plasmon-based labeling and imaging, optical and electrochemical sensing, diagnostics, therapy (drug vectorization and DNA/gene delivery) for various diseases, in particular cancer (also Alzheimer, HIV, hepatitis, tuberculosis, arthritis, diabetes) and the essential in vitro and in vivo toxicity. It will interest the medicine, chemistry, spectroscopy, biochemistry, biophysics and nanoscience communities (211 references).

Enzymatic cleavage of nucleic acids on gold nanoparticles: a generic platform for facile colorimetric biosensors

The enzymatic cleavage of nucleic acids (DNA or DNA with a single RNA linkage) on well-dispersed gold nanoparticles (AuNPs) is exploited in the design of facile colorimetric biosensors. The assays are performed at salt concentrations such that DNA-modified AuNPs are barely stabilized by the electrostatic and steric stabilization. Enzymatic cleavage of DNA chains on the AuNP surface destabilizes the AuNPs, resulting in a rapid aggregation driven by van der Waals attraction, and a red-to-purple color change. Two different systems are chosen, DNase I (a DNA endonuclease) and 8-17 (a Pb(2+)-depedent RNA-cleaving DNAzyme), to demonstrate the utility of our assay for the detection of metal ions and sensing enzyme activities. Compared with previous studies in which AuNP aggregates are converted into dispersed AuNPs by enzymatic cleavage of DNA crosslinkers, the present assay is technically simpler. Moreover, the accessibility of DNA to biomolecular recognition elements (e.g. enzymes) on well-dispersed AuNPs in our assay appears to be higher than that embedded inside aggregates. This biosensing system should be readily adaptable to other enzymes or substrates for detection of analytes such as small molecules, proteases and their inhibitors.

Chemical sensing and imaging with metallic nanorods

In this Feature Article, we examine recent advances in chemical analyte detection and optical imaging applications using gold and silver nanoparticles, with a primary focus on our own work. Noble metal nanoparticles have exciting physical and chemical properties that are entirely different from the bulk. For chemical sensing and imaging, the optical properties of metallic nanoparticles provide a wide range of opportunities, all of which ultimately arise from the collective oscillations of conduction band electrons ("plasmons") in response to external electromagnetic radiation. Nanorods have multiple plasmon bands compared to nanospheres. We identify four optical sensing and imaging modalities for metallic nanoparticles: (1) aggregation-dependent shifts in plasmon frequency; (2) local refractive index-dependent shifts in plasmon frequency; (3) inelastic (surface-enhanced Raman) light scattering; and (4) elastic (Rayleigh) light scattering. The surface chemistry of the nanoparticles must be tunable to create chemical specificity, and is a key requirement for successful sensing and imaging platforms.

Smart nanomaterials inspired by biology: dynamic assembly of error-free nanomaterials in response to multiple chemical and biological stimuli

Three-dimensional functional nanoscale assembly requires not only self-assembly of individual nanomaterials responsive to external stimuli, such as temperature, light, and concentrations, but also directed assembly of many different nanomaterials in one-pot responsive to multiple internal stimuli signaling the needs for such materials at a specific location and a particular time. The use of functional DNA (DNAzymes, aptamers, and aptazymes) to meet these challenges is reviewed. In addition, a biology-inspired proof-reading and error correction method is introduced to cope with errors in nanomaterials assembly.

Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers

In the past 25 years, DNA molecules have been utilized both as powerful synthetic building blocks to create nanoscale architectures and as versatile programmable templates for assembly of nanomaterials. In parallel, the functions of DNA molecules have been expanded from pure genetic information storage to catalytic functions like those of protein enzymes (DNAzymes) and specific binding functions like antibodies (aptamers). In the past few years, a new interdisciplinary field has emerged that aims to combine functional DNA biology with nanotechnology to generate more dynamic and controllable DNA-based nanostructures or DNA-templated nanomaterials that are responsive to chemical stimuli.