Selective dsDNA-templated formation of copper nanoparticles in solution

H2O2-mediated fluorescence quenching of double-stranded DNA templated copper nanoparticles for label-free and sensitive detection of glucose

A label-free fluorescent sensor has been developed for glucose detection based on H₂O₂-mediated fluorescence quenching of ds-DNA templated Cu NPs.

Inhibition of double-stranded DNA templated copper nanoparticles as label-free fluorescent sensors for l-histidine detection

A label-free fluorescent sensing strategy was reported for l-histidine detection by the inhibition of double-stranded DNA templated copper nanoparticles.

An electrochemical aptasensor for thrombin detection based on the recycling of exonuclease III and double-stranded DNA-templated copper nanoparticles assisted signal amplification

In this paper, we report an improved electrochemical aptasensor based on exonuclease III and double-stranded DNA (dsDNA)-templated copper nanoparticles (CuNPs) assisted signal amplification. In this sensor, duplex DNA from the hybridization of ligated thrombin-binding aptamer (TBA) subunits and probe DNA can act as an effective template for the formation of CuNPs on the electrode surface, so copper ions released from acid-dissolution of CuNPs may catalyze the oxidation of ο-phenylenediamine to produce an amplified electrochemical response. In the presence of thrombin, a short duplex domain with four complementary base pairs can be stabilized by the binding of TBA subunits with thrombin, in which TBA subunit 2 can be partially digested from 3' terminal with the cycle of exonuclease III, so the ligation of TBA subunits and the subsequent formation of CuNPs can be inhibited. By electrochemical characterization of dsDNA-templated CuNPs on the electrode surface, our aptasensor can display excellent performances for the detection of thrombin in a broad linear range from 100 fM to 1 nM with a low detection limit of 20.3 fM, which can also specially distinguish thrombin in both PBS and serum samples. Therefore, our aptasensor might have great potential for clinical diagnosis of biomarkers in the future.

Sequence-dependent dsDNA-templated formation of fluorescent copper nanoparticles

There are only a few systematic rules about how to selectively control the formation of DNA-templated metal nanoparticles (NPs) by varying sequence combinations of double-stranded DNA (dsDNA), although many attempts have been made. Herein, we develop a facile method for sequence-dependent formation of fluorescent CuNPs by using dsDNA as templates. Compared with random sequences, AT sequences are better templates for highly fluorescent CuNPs. Other specific sequences, for example, GC sequences, do not induce the formation of CuNPs. These results shed light on directed DNA metallization in a sequence-specific manner. Significantly, both the fluorescence intensity and the fluorescence lifetime of CuNPs can be tuned by the length or the sequence of dsDNA. In order to demonstrate the promising practicality of our findings, a sensitive and label-free fluorescence nuclease assay is proposed.

Bio-NCs--the marriage of ultrasmall metal nanoclusters with biomolecules

Ultrasmall metal nanoclusters (NCs) have attracted increasing attention due to their fascinating physicochemical properties. Today, functional metal NCs are finding growing acceptance in biomedical applications. To achieve a better performance in biomedical applications, metal NCs can be interfaced with biomolecules, such as proteins, peptides, and DNA, to form a new class of biomolecule-NC composites (or bio-NCs in short), which typically show synergistic or novel physicochemical and physiological properties. This feature article focuses on the recent studies emerging at the interface of metal NCs and biomolecules, where the interactions could impart unique physicochemical properties to the metal NCs, as well as mutually regulate biological functions of the bio-NCs. In this article, we first provide a broad overview of key concepts and developments in the novel biomolecule-directed synthesis of metal NCs. A special focus is placed on the key roles of biomolecules in metal NC synthesis. In the second part, we describe how the encapsulated metal NCs affect the structure and function of biomolecules. Followed by that, we discuss several unique synergistic effects observed in the bio-NCs, and illustrate them with examples highlighting their potential biomedical applications. Continued interdisciplinary efforts are required to build up in-depth knowledge about the interfacial chemistry and biology of bio-NCs, which could further pave their ways toward biomedical applications.

Recent advances in the field of bionanotechnology: an insight into optoelectric bacteriorhodopsin, quantum dots, and noble metal nanoclusters

Molecular sensors and molecular electronics are a major component of a recent research area known as bionanotechnology, which merges biology with nanotechnology. This new class of biosensors and bioelectronics has been a subject of intense research over the past decade and has found application in a wide variety of fields. The unique characteristics of these biomolecular transduction systems has been utilized in applications ranging from solar cells and single-electron transistors (SETs) to fluorescent sensors capable of sensitive and selective detection of a wide variety of targets, both organic and inorganic. This review will discuss three major systems in the area of molecular sensors and electronics and their application in unique technological innovations. Firstly, the synthesis of optoelectric bacteriorhodopsin (bR) and its application in the field of molecular sensors and electronics will be discussed. Next, this article will discuss recent advances in the synthesis and application of semiconductor quantum dots (QDs). Finally, this article will conclude with a review of the new and exciting field of noble metal nanoclusters and their application in the creation of a new class of fluorescent sensors.

DNA-mediated biomineralization of rare-earth nanoparticles for simultaneous imaging and stimuli-responsive drug delivery

A DNA-guided method for surface engineering of NaGdF4:Ce/Tb hybrid nanoparticle has been proposed. In this study, the DNA molecules that retained after one-pot NaGdF4:Ce/Tb synthesis is directly utilized as biotemplate for CaP heterogeneous nucleation, thus the dual-purpose function of DNA is realized in the current study which could afford a new type of pH-responsive theranostic platform to enhance the therapeutic efficiency while minimizing side effects. The introduction of another layer of aptamer molecules on CaP facilitated cellular uptake of the resulting nanocomposite into specific target cells via receptor-mediated endocytosis. After been taken by the target tumor cells, the NaGdF4:Ce/Tb@CaP was found to be mostly accumulated in lysosome, which facilitated the dissolving of CaP coatings as non-toxic ions to initiate drug release and efficient cancer cell destruction. We envision that the hybrid nanocarrier may serve as practical and multifunctional probe for cancer therapy and the presented synthesis approach here may also benefit the preparation of many other types of multifunctional inorganic-biomolecular hybrid nanostructures based on the DNA nanotechnology.

Concatemeric dsDNA-templated copper nanoparticles strategy with improved sensitivity and stability based on rolling circle replication and its application in microRNA detection

DNA-templated copper nanoparticles (CuNPs) have emerged as promising fluorescent probes for biochemical assays, but the reported monomeric CuNPs remain problematic because of weak fluorescence and poor stability. To solve this problem, a novel concatemeric dsDNA-templated CuNPs (dsDNA-CuNPs) strategy was proposed by introducing the rolling circle replication (RCR) technique into CuNPs synthesis. In this strategy, a short oligonucleotide primer could trigger RCR and be further converted to a long concatemeric dsDNA scaffold through hybridization. After the addition of copper ions and ascorbate, concatemeric dsDNA-CuNPs could effectively form and emit intense fluorescence in the range of 500-650 nm under a 340 nm excitation. In comparison with monomeric dsDNA-CuNPs, the sensitivity of concatemeric dsDNA-CuNPs was greatly improved with ~10,000 folds amplification. And their fluorescence signal was detected to reserve ~60% at 2.5 h after formation, revealing ~2 times enhanced stability. On the basis of these advantages, microRNA let-7d was selected as the model target to testify this strategy as a versatile assay platform. By directly using let-7d as the primer in RCR, the simple, low-cost, and selective microRNA detection was successfully achieved with a good linearity between 10 and 400 pM and a detection limit of 10 pM. The concatemeric dsDNA-CuNPs strategy might be widely adapted to various analytes that can directly or indirectly induce RCR.

Copper nanoclusters as a highly sensitive and selective fluorescence sensor for ferric ions in serum and living cells by imaging

A simple, one-step facile route for preparation of water soluble and fluorescent Cu nanoclusters (NCs) stabilized by tannic acid (TA) is described. The as-prepared TA capped Cu NCs (TA-Cu NCs) are characterized by UV-vis spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, luminescence, transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS). The TA-Cu NCs show luminescence properties having excitation and emission maxima at 360 nm and 430 nm, respectively, with a quantum yield of about 14%. The TA-Cu NCs are very stable even in 0.3 M NaCl, and their luminescent properties show pH independent. The fluorescence (FL) of Cu NCs is strongly quenched by Fe(3+) through an electron transfer mechanism, but not by other metal ions. Furthermore, the FL of the TA-Cu NCs shows no changes with the addition of Fe(2+) or H2O2 individually. On this basis, a facile chemosensor was developed for rapid, reliable, sensitive, and selective sensing of Fe(3+) ions with detection limit as low as 10 nM and a dynamic range from 10 nM to 10 μM. The proposed sensor was successfully used for the determination of iron contents in serum samples. Importantly, the Cu NCs-based FL probe showed long-term stability, good biocompatibility and very low cytotoxicity. It was successfully used for imaging ferric ions in living cells, suggesting the potential application of Cu NCs fluorescent probe in clinical analysis and cell imaging.

DNA as a powerful tool for morphology control, spatial positioning, and dynamic assembly of nanoparticles

Several properties of nanomaterials, such as morphologies (e.g., shapes and surface structures) and distance dependent properties (e.g., plasmonic and quantum confinement effects), make nanomaterials uniquely qualified as potential choices for future applications from catalysis to biomedicine. To realize the full potential of these nanomaterials, it is important to demonstrate fine control of the morphology of individual nanoparticles, as well as precise spatial control of the position, orientation, and distances between multiple nanoparticles. In addition, dynamic control of nanomaterial assembly in response to multiple stimuli, with minimal or no error, and the reversibility of the assemblies are also required. In this Account, we summarize recent progress of using DNA as a powerful programmable tool to realize the above goals. First, inspired by the discovery of genetic codes in biology, we have discovered DNA sequence combinations to control different morphologies of nanoparticles during their growth process and have shown that these effects are synergistic or competitive, depending on the sequence combination. The DNA, which guides the growth of the nanomaterial, is stable and retains its biorecognition ability. Second, by taking advantage of different reactivities of phosphorothioate and phosphodiester backbone, we have placed phosphorothioate at selective positions on different DNA nanostructures including DNA tetrahedrons. Bifunctional linkers have been used to conjugate phosphorothioate on one end and bind nanoparticles or proteins on the other end. In doing so, precise control of distances between two or more nanoparticles or proteins with nanometer resolution can be achieved. Furthermore, by developing facile methods to functionalize two hemispheres of Janus nanoparticles with two different DNA sequences regioselectively, we have demonstrated directional control of nanomaterial assembly, where DNA strands with specific hybridization serve as orthogonal linkers. Third, by using functional DNA that includes DNAzyme, aptamer, and aptazyme, dynamic control of assemblies of gold nanoparticles, quantum dots, carbon nanotubes, and iron oxide nanoparticles in response to one or more stimuli cooperatively have been achieved, resulting in colorimetric, fluorescent, electrochemical, and magnetic resonance signals for a wide range of targets, such as metal ions, small molecules, proteins, and intact cells. Fourth, by mimicking biology, we have employed DNAzymes as proofreading units to remove errors in nanoparticle assembly and further used DNAzyme cascade reactions to modify or repair DNA sequences involved in the assembly. Finally, by taking advantage of different affinities of biotin and desthiobiotin toward streptavidin, we have demonstrated reversible assembly of proteins on DNA origami.

DNA-mediated construction of hollow upconversion nanoparticles for protein harvesting and near-infrared light triggered release

A simple DNA-mediated solvothermal method has been developed for the construction of well-defined hollow UNPs that can be used for a new paradigm to realize NIR light-controlled non-invasive protein release. In vitro studies show that the UNPs are capable of the transportation of enzyme into living cells. Intracellular NIR triggers the release of enzymes with high spatial and temporal precision and the released enzyme also retains its biological activity.

dsDNA-templated fluorescent copper nanoparticles: poly(AT-TA)-dependent formation

Poly(AT-TA) DNA is found to be the specific dsDNA sequence which can act as a highly-efficient template for the formation of dsDNA-templated copper nano-fluorophores.

A new mode to light up an adjacent DNA-scaffolded silver probe pair and its application for specific DNA detection

By fluorescence enhancement of a proximity-dependent DNA-scaffolded silver nanocluster probe pair and exonuclease III-mediated signal amplification, we present a new fluorescence turn-on mode and its application for specific DNA detection.

Reactive oxygen species production by catechol stabilized copper nanoparticles

Stable Cu nanoparticles (NPs) prepared using catechol containing dopamine-based linkers could generate reactive oxygen species (ROS) that can activate peroxidase enzymes and catalyze the degradation of fluorescent dye pollutants.

Label-free and turn-on aptamer strategy for cancer cells detection based on a DNA-silver nanocluster fluorescence upon recognition-induced hybridization

We present here a label-free and turn-on aptamer strategy for cancer cell detection based on the recognition-induced conformation alteration of aptamer and hybridization-induced fluorescence enhancement effect of DNA-silver nanoclusters (DNA-Ag NCs) in proximity of guanine-rich DNA sequences. In this strategy, two tailored DNA probes were involved. One is designed as a hairpin-shaped structure consisting of a target specific aptamer sequence at the 3'-end, a guanine-rich DNA sequence, and an arm segment at the 5'-end (denote as recognition probe). The other, serving as a signal probe, contains a sequence for Ag NCs templated synthesis and a link sequence complementary to the arm segment of the recognition probe. Recognizing and binding of the aptamer to cancer cells enforces the recognition probe to undergo a conformational alteration and then initiates hybridization between the arm segment of the recognition probe and the link sequence of the signal probe. The Ag NCs are then close to the guanine-rich DNA, leading to an enhanced fluorescence readout. As proof-of-concept, the CCRF-CEM cancer cell detection were performed by using the specific aptamer, sgc8c. It was demonstrated that this strategy could specially image the CCRF-CEM cells. Determination by flow cytometry allowed for detection of as low as 150 CCRF-CEM cells in 200 μL binding buffer. The general applicability of the strategy is also achieved in the successful detection of Ramos cells. These results implied that this strategy holds considerable potential for simple, sensitive, universal, and specific cancer cell detection with no required washing and separation steps.

Nanomaterials and nanoclusters based on DNA modulation

Besides the inherent chirality, DNA is enriched by nitrogen and oxygen functional groups that are preferential to coordinate with transition metal ions, and its self-assembled structures, including the G-quadruplex, the i-motif, and the conventional Watson-Crick duplex, etc., can be adjusted via different base pairings. Recently biotemplating on the basis of DNA self-assembly has been considered as an attractive method to construct switchable nanomaterials, to direct crystal growth and to design enantioselective selectors/catalysts. This review briefly covers the recent progress relevant to DNA modulated nano/subnano materials. The long-term goal of this area of research is to explore novel promisingly environmental-benign approaches to construct switchable nanomachines, nano/subnano clusters and enantioselective recognition platforms respectively, through DNA-based modulation.

Poly(thymine)-templated fluorescent copper nanoparticles for ultrasensitive label-free nuclease assay and its inhibitors screening

Noble-metal fluorescent nanoparticles have attracted considerable interest on account of their excellent properties and potential applicable importance in many fields. Particularly, we recently found that poly(thymine) (poly T) could template the formation of fluorescent copper nanoparticles (CuNPs), offering admirable potential as novel functional biochemical probes. However, exploration of poly T-templated CuNPs for application is still at a very early stage. We report herein for the first example to develop a novel ultrasensitive label-free method for the nuclease (S1 nuclease as a model system) assay, and its inhibitors screening using the poly T-templated fluorescent CuNPs. In this assay, the signal reporter of poly T of 30 mer (T30) kept the original long state in the absence of nuclease, which could effectively template the formation of fluorescent CuNPs. In the presence of nuclease, poly T was digested to mono- or oligonucleotide fragments with decrease of fluorescence. The proposed method was low-cost and simple in its operation without requirement for complex labeling of probe DNA or sophisticated synthesis of the fluorescent compound. The assay process was very rapid with only 5 min for the formation of fluorescent CuNPs. The capabilities for target detection from complex fluids and screening of nuclease inhibitors were verified. A high sensitivity exhibited with a detectable minimum concentration of 5 × 10(-7) units μL(-1) S1 nuclease, which was about 1-4 orders of magnitude more sensitive than the developed approaches.

Lighting up silica nanotubes transcribed from the submicron structure of a metal-peptide hybrid

Fluorescent silica nanotubes are attracting increasing interest because of their versatile applicability in a range of diverse fields. By using sol-gel transcription of tetraethylorthosilicate (TEOS) from various soft templates, silica nanotubes can be conveniently prepared. Metal-peptide hybrids with well-defined nanostructures and outstanding functionalities are very interesting candidates to serve as templates. Herein, we demonstrate that glutathione (GSH) can act as a building block for a bioinspired structure with dimensions down to the nanoscale, based on specific interactions between metal ions and the peptide. Congo red is able to selectively stain the nanofibres obtained, and appears apple-green in colour, implying that Congo red is promising to serve as an effective and convenient probe for determining the self-assembly of GSH and copper ions. Furthermore, silica nanotubes are synthesized using the nanofibres as a template in a very simple way. The silica nanotubes can be lit up by biomolecule-templated metal nanoparticles or nanoclusters and emit bright fluorescence. This work will certainly open up new opportunities in fabricating a broad range of nanostructured materials with versatile functionalities.

Highly thymine-dependent formation of fluorescent copper nanoparticles templated by ss-DNA

Double-stranded DNAs (ds-DNAs) have been identified as efficient templates favoring the formation of fluorescent copper nanoparticles (Cu NPs). Herein, we have tried to synthesize fluorescent Cu NPs using single-stranded DNAs (ss-DNAs) as templates and to identify the critical DNA sequences. By comparing the results using homopolymer DNAs, hairpin DNAs, and pristine ss-DNAs as templates, we found that DNA thymine base plays a dominant role in producing red-emissive fluorescent Cu NPs on ss-DNA templates. The thymine-dependent growth of the fluorescent Cu NPs is confirmed by Hg2+ mediated T–T base pair in comparison with the other non-specific metal ions, which could be developed into a practical sensor for turn-on fluorescence detection of Hg2+ with a high selectivity. The mechanism is briefly discussed according the DNA sequence-dependent formation of fluorescent Cu NPs. This work demonstrates the sequence role in producing fluorescent Cu NPs that could serve as promising fluorescent nanoprobes in biosensing and DNA-hosted Cu nanomaterials.

Molecular recognition by gold, silver and copper nanoparticles

The intrinsic physical properties of the noble metal nanoparticles, which are highly sensitive to the nature of their local molecular environment, make such systems ideal for the detection of molecular recognition events. The current review describes the state of the art concerning molecular recognition of Noble metal nanoparticles. In the first part the preparation of such nanoparticles is discussed along with methods of capping and stabilization. A brief discussion of the three common methods of functionalization: Electrostatic adsorption; Chemisorption; Affinity-based coordination is given. In the second section a discussion of the optical and electrical properties of nanoparticles is given to aid the reader in understanding the use of such properties in molecular recognition. In the main section the various types of capping agents for molecular recognition; nucleic acid coatings, protein coatings and molecules from the family of supramolecular chemistry are described along with their numerous applications. Emphasis for the nucleic acids is on complementary oligonucleotide and aptamer recognition. For the proteins the recognition properties of antibodies form the core of the section. With respect to the supramolecular systems the cyclodextrins, calix[n]arenes, dendrimers, crown ethers and the cucurbitales are treated in depth. Finally a short section deals with the possible toxicity of the nanoparticles, a concern in public health.

Detection of DNA damage by thiazole orange fluorescence probe assisted with exonuclease III

This work reports a fluorescent dye insertion approach for detection of DNA damage. The capture DNA with overhanging 3'-terminus was immobilized on silicon surface to hybridize with target DNA. The intercalation of cyanine dye of thiazole orange (TO) to the double helix structure of DNA (dsDNA) allowed intense enhancement of fluorescence signal. The DNA damage with chemicals led to poor intercalation of TO into double helix structure, resulting in the decrease of the fluorescence signal. This signal decrease could be further enhanced by exonuclease III (Exo III). With this approach, the target DNA could be detected down to 47 fM. Seven chemicals were chosen as models to monitor DNA damage. The results suggested that the present strategy could be developed to detect DNA damage, to classify the damaging mechanism with chemicals and to estimate the toxic effect of chemicals.

Advances in aptamer screening and small molecule aptasensors

It has been 20 years since aptamer and SELEX (systematic evolution of ligands by exponential enrichment) were described independently by Andrew Ellington and Larry Gold. Based on the great advantages of aptamers, there have been numerous isolated aptamers for various targets that have actively been applied as therapeutic and analytical tools. Over 2,000 papers related to aptamers or SELEX have been published, attesting to their wide usefulness and the applicability of aptamers. SELEX methods have been modified or re-created over the years to enable aptamer isolation with higher affinity and selectivity in more labor- and time-efficient manners, including automation. Initially, most of the studies about aptamers have focused on the protein targets, which have physiological functions in the body, and their applications as therapeutic agents or receptors for diagnostics. However, aptamers for small molecules such as organic or inorganic compounds, drugs, antibiotics, or metabolites have not been studied sufficiently, despite the ever-increasing need for rapid and simple analytical methods for various chemical targets in the fields of medical diagnostics, environmental monitoring, food safety, and national defense against targets including chemical warfare. This review focuses on not only recent advances in aptamer screening methods but also its analytical application for small molecules.

Phototriggered growth of crystalline Au structures in the presence of a DNA-surfactant complex

A method for the preparation of complex anisotropic gold structures with potential uses in catalysis and photonics is presented based on the use of salmon sperm DNA and a photosensitizer to enable light triggered gold salt reduction.

Nucleic acid-mediated gold oxidation: novel biolithography for surface microfabrication and new insight into gold-based biomaterials

In Nature, certain organisms can perform microbial corrosion on base metals by oxidation of neutral metallic atoms (H. L. Ehrlich, Appl. Microbiol. Biotechnol., 1997). Herein we describe the first discovery of biological nucleic acids able to catalyze and mediate gold oxidation from neutral Au(0) to trivalent Au(III) under certain oxidative environments provided by mild oxidizing reagent N-bromosuccinimide or amino acids. A new biolithography technique for gold patterning is further developed.

Toward site-specific, homogeneous and highly stable fluorescent silver nanoclusters fabrication on triplex DNA scaffolds

A new strategy to create site-specific, homogeneous, and bright silver nanoclusters (AgNCs) with high-stability was demonstrated by triplex DNA as template. By reasonable design of DNA sequence, homogeneous Ag₂ cluster was obtained in the predefined position of CG.C⁺ site of triplex DNA. This strategy was also explored for controlled alignment of AgNCs on the DNA nanoscaffold. To the best of our knowledge, this was the first example to simultaneously answer the challenges of excellent site-specific nucleation and growth, homogeneity and stability against salt of DNA-templated AgNCs.

DNA-hosted copper nanoclusters for fluorescent identification of single nucleotide polymorphisms

Metal nanoclusters have received considerable interest due to their unique properties and potential applications in numerous fields. Particularly, newly emerging Cu nanoclusters offer excellent potential as functional biological probes. In this work, we for the first time report that the fluorescence of DNA-hosted Cu nanoclusters is very sensitive to base type located in the major groove. This intriguing finding provides a sensitive fluorimetric diagnostic of the mismatch type in a specific DNA sequence, which is difficult to achieve by traditional methods. Furthermore, the research results have shed some light on the luminescent mechanism of Cu nanoclusters. Owing to its high specificity and easy operation without rigorously controlled temperature and arduous probe DNA design, it is expected that the proposed procedure can provide a tool for early diagnosis and risk assessment of malignancy.

Aptamer-based fluorescent biosensors

Selected from random pools of DNA or RNA molecules through systematic evolution of ligands by exponential enrichment (SELEX), aptamers can bind to target molecules with high affinity and specificity, which makes them ideal recognition elements in the development of biosensors. To date, aptamer-based biosensors have used a wide variety of detection techniques, which are briefly summarized in this article. The focus of this review is on the development of aptamer-based fluorescent biosensors, with emphasis on their design as well as properties such as sensitivity and specificity. These biosensors can be broadly divided into two categories: those using fluorescently-labeled aptamers and others that employ label-free aptamers. Within each category, they can be further divided into "signal-on" and "signal-off" sensors. A number of these aptamer-based fluorescent biosensors have shown promising results in biological samples such as urine and serum, suggesting their potential applications in biomedical research and disease diagnostics.