Next-Generation DNA-Functionalized Quantum Dots as Biological Sensors

Formation of ZnS quantum dots using green tea extract: applications to protein binding, bio-sensing, anti-bacterial and cell cytotoxicity studies

Biocompatible quantum dots (QDs) have attracted a lot of attention due to their potential biological applications (drug delivery, sensing and diagnosis). Here, we have synthesized 2-4 nm sized biocompatible zinc sulphide (ZnS) QDs using a plant leaf extract as an immobilizing and stabilizing agent via a green route. We have investigated the biological effects of ZnS QDs in a variety of applications, including (1) anti-bacterial activity, (2) cell cytotoxicity, (3) bio-sensing and (4) protein binding. Studies on the anti-bacterial activity of the as-synthesized ZnS QDs against E. coli and E. faecalis inhibited bacterial growth effectively and showed a cytotoxic effect on the HeLa cell line. The biosynthesized ZnS QDs act as a fluorescence probe to detect bilirubin and rifampicin (RFP) with a wide linear range, high sensitivity, good selectivity, and a low limit of detection (LOD), with LOD values of 22.12 ± 0.25 ng mL^-1 and 122.37 ± 0.42 ng mL^-1, respectively. In a biological matrix, the QDs can form a complex with biomacromolecules; therefore, we studied the interaction between a carrier protein (HSA) and the as-synthesized ZnS QDs. The surface functionalized and nano-sized ZnS-GT QDs were observed to form complexes with the human serum albumin (HSA) protein and quenched the intrinsic fluorescence of HSA through static and dynamic quenching modes. The binding affinity was observed to be of the order of 10⁵ M^-1 for the HSA-ZnS-GT QD interactions, which can be considered as a reversible mode of binding. The effect of the ZnS QDs on other ligands and protein interactions was also studied. Enhanced binding affinities for HSA-quercetin ((5.994 ± 0.139) × 10⁵ M^-1) and HSA-luteolin ((3.068 ± 0.127) × 10⁵ M^-1) interactions were also observed in the presence of ZnS-GT QDs.

Quantitative Detection of Gastrointestinal Tumor Markers Using a Machine Learning Algorithm and Multicolor Quantum Dot Biosensor

This work was to explore the application value of gastrointestinal tumor markers based on gene feature selection model of principal component analysis (PCA) algorithm and multicolor quantum dots (QDs) immunobiosensor in the detection of gastrointestinal tumors. Based on the PCA method, the neighborhood rough set algorithm was introduced to improve it, and the tumor gene feature selection model (OPCA) was established to analyze its classification accuracy and accuracy. Four kinds of coupled biosensors were fabricated based on QDs, namely, 525 nm Cd Se/Zn S QDs-carbohydrate antigen 125 (QDs525-CA125 McAb), 605 nm Cd Se/Zn S QDs-cancer antigen 19-9 (QDs605-CA19-9 McAb), 645 nm Cd Se/Zn S QDs-anticancer embryonic antigen (QDs 645-CEA McAb), and 565 nm Cd Se/Zn S QDs-anti-alpha-fetoprotein (QDs565-AFP McAb). The quantum dot-antibody conjugates were identified and quantified by fluorescence spectroscopy and ultraviolet absorption spectroscopy. The results showed that the classification precision of OPCA model in colon tumor and gastric cancer datasets was 99.52% and 99.03%, respectively, and the classification accuracy was 94.86% and 94.2%, respectively, which were significantly higher than those of other algorithms. The fluorescence values of AFP McAb, CEA McAb, CA19-9 McAb, and CA125 McAb reached the maximum when the conjugation concentrations were 25 µg/mL, 20 µg/mL, 30 µg/mL, and 30 µg/m, respectively. The highest recovery rate of AFP was 98.51%, and its fluorescence intensity was 35.78 ± 2.99, which was significantly higher than that of other antigens (P < 0.001). In summary, the OPCA model based on PCA algorithm can obtain fewer feature gene sets and improve the accuracy of sample classification. Intelligent immunobiosensors based on machine learning algorithms and QDs have potential application value in gastrointestinal gene feature selection and tumor marker detection, which provides a new idea for clinical diagnosis of gastrointestinal tumors.

Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami

Control over the copy number and nanoscale positioning of quantum dots (QDs) is critical to their application to functional nanomaterials design. However, the multiple non-specific binding sites intrinsic to the surface of QDs have prevented their fabrication into multi-QD assemblies with programmed spatial positions. To overcome this challenge, we developed a general synthetic framework to selectively attach spatially addressable QDs on 3D wireframe DNA origami scaffolds using interfacial control of the QD surface. Using optical spectroscopy and molecular dynamics simulation, we investigated the fabrication of monovalent QDs of different sizes using chimeric single-stranded DNA to control QD surface chemistry. By understanding the relationship between chimeric single-stranded DNA length and QD size, we integrated single QDs into wireframe DNA origami objects and visualized the resulting QD-DNA assemblies using electron microscopy. Using these advances, we demonstrated the ability to program arbitrary 3D spatial relationships between QDs and dyes on DNA origami objects by fabricating energy-transfer circuits and colloidal molecules. Our design and fabrication approach enables the geometric control and spatial addressing of QDs together with the integration of other materials including dyes to fabricate hybrid materials for functional nanoscale photonic devices.

Quantum Dots for Cancer-Related miRNA Monitoring

Quantum dots (QDs) possess exceptional optoelectronic properties that enable their use in the most diverse applications, namely, in the medical field. The prevalence of cancer has increased and has been considered the major cause of death worldwide. Thus, there has been a great demand for new methodologies for diagnosing and monitoring cancer in cells to provide an earlier prognosis of the disease and contribute to the effectiveness of treatment. Several molecules in the human body can be considered relevant as cancer markers. Studies published over recent years have revealed that micro ribonucleic acids (miRNAs) play a crucial role in this pathology, since they are responsible for some physiological processes of the cell cycle and, most important, they are overexpressed in cancer cells. Thus, the analytical sensing of miRNA has gained importance to provide monitoring during cancer treatment, allowing the evaluation of the disease's evolution. Recent methodologies based on nanochemistry use fluorescent quantum dots for sensing of the miRNA. Combining the unique characteristics of QDs, namely, their fluorescence capacity, and the fact that miRNA presents an aberrant expression in cancer cells, the researchers created diverse strategies for miRNA monitoring. This review aims to present an overview of the recent use of QDs as biosensors in miRNA detection, also highlighting some tutorial descriptions of the synthesis methods of QDs, possible surface modification, and functionalization approaches.

DNA-Modified Liquid Crystal Droplets

In this work, we have combined the advantages of sequence programmability of DNA nanotechnology and optical birefringence of liquid crystals (LCs). Herein, DNA amphiphiles were adsorbed onto LC droplets. A unique phenomenon of LC droplet aggregation was demonstrated, using DNA-modified LC droplets, through complementary DNA hybridization. Further functionalization of DNA-modified LC droplets with a desired DNA sequence was used to detect a wide range of chemicals and biomolecules, such as Hg²⁺, thrombin, and enzymes, through LC droplet aggregation and vice versa, which can be seen through the naked eye. These DNA-modified LC droplets can be printed onto a desired patterned surface with temperature-induced responsiveness and reversibility. Overall, our work is the first to report DNA-modified LC droplet, which provides a general detection platform based on the development of DNA aptamers. Additionally, this work inspires the exploration of surface information visualization combined with microcontact printing.

Shedding Light on DNA-Based Nanoprobes for Live-Cell MicroRNA Imaging

DNA-based nanoprobes integrated with various imaging signals have been employed for fabricating versatile biosensor platforms for the study of intracellular biological process and biomarker detection. The nanoprobes developments also provide opportunities for endogenous microRNA (miRNA) in situ analysis. In this review, the authors are primarily interested in various DNA-based nanoprobes for miRNA biosensors and declare strategies to reveal how to customize the desired nanoplatforms. Initially, various delivery vehicles for nanoprobe architectures transmembrane transport are delineated, and their biosecurity and ability for resisting the complex cellular environment are evaluated. Then, the novel strategies for designing DNA sequences as target miRNA specific recognition and signal amplification modules for miRNA detection are presented. Afterward, recent advances in imaging technologies to accurately respond and produce significant signal output are summarized. Finally, the challenges and future directions in the field are discussed.

Assessing the Environmental Effects Related to Quantum Dot Structure, Function, Synthesis and Exposure

Quantum dots (QDs) are engineered semiconductor nanocrystals with unique fluorescent, quantum confinement, and quantum yield properties, making them valuable in a range of commercial and consumer imaging, display, and lighting technologies. Production and usage of QDs are increasing, which increases the probability of these nanoparticles entering the environment at various phases of their life cycle. This review discusses the major types and applications of QDs, their potential environmental exposures, fates, and adverse effects on organisms. For most applications, release to the environment is mainly expected to occur during QD synthesis and end-product manufacturing since encapsulation of QDs in these devices prevents release during normal use or landfilling. In natural waters, the fate of QDs is controlled by water chemistry, light intensity, and the physicochemical properties of QDs. Research on the adverse effects of QDs primarily focuses on sublethal endpoints rather than acute toxicity, and the differences in toxicity between pristine and weathered nanoparticles are highlighted. A proposed oxidative stress adverse outcome pathway framework demonstrates the similarities among metallic and carbon-based QDs that induce reactive oxygen species formation leading to DNA damage, reduced growth, and impaired reproduction in several organisms. To accurately evaluate environmental risk, this review identifies critical data gaps in QD exposure and ecological effects, and provides recommendations for future research. Future QD regulation should emphasize exposure and sublethal effects of metal ions released as the nanoparticles weather under environmental conditions. To date, human exposure to QDs from the environment and resulting adverse effects has not been reported.

Recent advances in catalytic hairpin assembly signal amplification-based sensing strategies for microRNA detection

Accumulative evidences have indicated that abnormal expression of microRNAs (miRNAs) is closely associated with many health disorders, making them be regarded as potentialbiomarkers for early clinical diagnosis. Therefore, it is extremely necessary to develop a highly sensitive, specific and reliable approach for miRNA analysis. Catalytic hairpin assembly (CHA) signal amplification is an enzyme-free toehold-mediated strand displacement method, exhibiting significant potential in improving the sensitivity of miRNA detection strategies. In this review, we first describe the potential of miRNAs as disease biomarkers and therapeutics, and summarize the latest advances in CHA signal amplification-based sensing strategies for miRNA monitoring. We describe the characteristics and mechanism of CHA signal amplification and classify the CHA-based miRNA sensing strategies into several categories based on the "signal conversion substance", including fluorophores, enzymes, nanomaterials, and nucleotide sequences. Sensing performance, limit of detection, merits and disadvantages of these miRNA sensing strategies are discussed. Moreover, the current challenges and prospects are also presented.

Optimizing the dynamic and thermodynamic properties of hybridization in DNA-mediated nanoparticle self-assembly

DNA-directed nanoparticle (DNA-NP) systems provide various applications in sensing, medical diagnosis, data storage, plasmonics and photovoltaics. Bonding probability and melting properties are helpful to evaluate the selectivity, thermostability and thermosensitivity of these applications. We investigated the influence of temperature, nanoparticle size, DNA chain length and surface grafting density of DNA on one nanoparticle on the DNA dynamic hybridization percentage and melting properties of DNA-NP assembly systems by molecular dynamics simulation. The high degree of consistency of free energy estimations for DNA hybridization via our theoretical deduction and the nearest-neighbor rule generally used in experiments validates reasonably our DNA model. The melting temperature and thermosensitivity parameter are determined by the sigmoidal melting curves based on hybridization percentage versus temperature. The results indicated that the hybridization percentage presents a downward trend with increasing temperature and nanoparticle size. Applications based on DNA-NP systems with bigger nanoparticle size, such as DNA probes, have better selectivity, thermostability and thermosensitivity. There exist optimal DNA chain length and surface grafting density where the hybridization percentage reaches the maximal value. The melting temperature reaches a maximum at the point of optimal grafting density, while the thermosensitivity parameter presents an upward trend with the increase of grafting density. Several physical quantities consisting of the radial density function, root mean square end-to-end distance, contact distance parameter and effective volume fraction are used to analyse DNA chain conformations and DNA-NP packing in the assembly process. Our findings provide the theoretical basis for the improvement and optimization of applications based on DNA-NP systems.

Short DNA-catalyzed formation of quantum dot-DNA hydrogel for enzyme-free femtomolar specific DNA assay

Fast, sensitive, specific, and user-friendly DNA assay is a key technique for the next generation point-of-care molecular diagnosis. However, high-cost, time-consuming, and complicated enzyme-based DNA amplification step is essential to achieve high sensitivity. Herein, a short target DNA-catalyzed formation of quantum dot (QD)-DNA hydrogel is proposed as a new DNA assay platform satisfying the above requirements. A single-stranded target DNA catalyzes the opening cycle of DNA hairpin loops, which are quickly self-assembled with DNA-functionalized QDs to generate QD-DNA hydrogel. The three-dimensional hydrogel network allows efficient resonance energy transfer, dramatically lowering the limit of detection down to ~6 fM without enzymatic DNA amplification. The QD-DNA hydrogel also enables a rapid detection (1 h) with high specificity even for a single-base mismatch. The clinical applicability of the QD-DNA hydrogel is demonstrated for the Klebsiella pneumoniae carbapenemase gene, one of the key targets of drug-resistant pathogenic bacteria.

Activity of CdTe Quantum-Dot-Tagged Superoxide Dismutase and Its Analysis in Capillary Electrophoresis

Quantum dots (QDs) have a broad range of applications in cell biolabeling, cancer treatment, metastasis imaging, and therapeutic drug monitoring. Despite their wide use, relatively little is known about their influence on other molecules. Interactions between QDs and proteins can influence the properties of both nanoparticles and proteins. The effect of mercaptosuccinic acid-capped CdTe QDs on intercellular copper–zinc superoxide dismutase (SOD1)—one of the main enzymatic antioxidants—was investigated. Incubation of SOD1 with QDs caused an increase in SOD1 activity, unlike in the case of CdCl₂, which inhibited SOD1. Moreover, this effect on SOD1 increased with the size and potential of QDs, although the effect became clearly visible in higher concentrations of QDs. The intensity of QD-SOD1 fluorescence, analyzed with the use of capillary electrophoresis with laser-induced fluorescence detection, was dependent on SOD1 concentration. In the case of green QDs, the fluorescence signal decreased with increasing SOD1 concentration. In contrast, the signal strength for Y-QD complexes was not dependent on SOD1 dilutions. The migration time of QDs and their complexes with SOD1 varied depending on the type of QD used. The migration time of G-QD complexes with SOD1 differed slightly. However, in the case of Y-QD complexes with SOD1, the differences in the migration time were not dependent on SOD concentration. This research shows that QDs interact with SOD1 and the influence of QDs on SOD activity is size-dependent. With this knowledge, one might be able to control the activation/inhibition of specific enzymes, such as SOD1.

Quantum Dots for Improved Single-Molecule Localization Microscopy

Colloidal semiconductor quantum dots (QDs) have long established their versatility and utility for the visualization of biological interactions. On the single-particle level, QDs have demonstrated superior photophysical properties compared to organic dye molecules or fluorescent proteins, but it remains an open question as to which of these fundamental characteristics are most significant with respect to the performance of QDs for imaging beyond the diffraction limit. Here, we demonstrate significant enhancement in achievable localization precision in QD-labeled neurons compared to neurons labeled with an organic fluorophore. Additionally, we identify key photophysical parameters of QDs responsible for this enhancement and compare these parameters to reported values for commonly used fluorophores for super-resolution imaging.

Applications of DNA-nanozyme-based sensors

Since the discovery of the enzyme-like activities of nanomaterials, the study of nanozymes has become one of the most popular research frontiers of diverse areas including biosensors. DNA also plays a very important role in the construction of biosensors. Thus, the idea of combined applications of nanozymes with DNA (DNA-nanozyme) is very attractive for the development of nanozyme-based biosensors, which has attracted considerable interest of researchers. To date, many sensors based on DNA-functionalized or templated nanozymes have been reported for the detection of various targets and highly accelerated the development of nanozyme-based sensors. In this review, we summarize the main applications and advances of DNA-nanozyme-based sensors. Additionally, perspectives and challenges are also discussed at the end of the review.

Tunable NIR-II emitting silver chalcogenide quantum dots using thio/selenourea precursors: preparation of an MRI/NIR-II multimodal imaging agent

Aqueous-stable, Cd- and Pb-free colloidal quantum dots with fluorescence properties in the second near-infrared region (NIR-II, 1000-1400) are highly desirable for non-invasive deep-tissue optical imaging and biosensing. The low band-gap semiconductor, silver chalcogenide, offers a non-toxic and stable alternative to existing Pd, As, Hg and Cd-based NIR-II colloidal quantum dots (QDs). We report facile access to NIR-II emission windows with Ag2X (X = S, Se) QDs using easy-to-prepare thio/selenourea precursors and their analogues. The aqueous phase transfer of these QDs with a high conservation of fluorescence quantum yield (retention up to ∼90%) and colloidal stability is demonstrated. A bimodal NIR-II/MRI contrast agent with a tunable fluorescence and high T1 relaxivity of 408 mM-1 s-1 per QD (size ∼ 2.2 nm) and 990 mM-1 s-1 per QD (size ∼ 4.2 nm) has been prepared by grafting 50 and 120 monoaqua Gd(iii) complexes respectively to two differently sized Ag2S QDs. The size of the nanocrystals is crucial for tuning the Gd payload and the relaxivity.

Detection of biological mercaptan by DNA functionalized room temperature phosphorescent quantum dot nanocomposites

In this study, green low-toxicity Mn-doped Zns (Mn-Zns) room-temperature phosphorescent (RTP) quantum dots (QDs) (PQDs) nanocomposites (DNA-PQDs) were prepared under the optimal conditions by using single-stranded DNA (PS-C-ssDNA) rich of cytosine C and Thioguanine G (PS) as the template. DNA-PQDs interact with Ag⁺ to form AgN bonds and further produce C-Ag⁺-C conjugates. As a result, DNA-PQDs cluster together and induce the phosphorescent exciton energy transfer (PEET), resulting in quenching of room-temperature phosphorescent of DNA-PQDs. Nevertheless, Ag⁺ tends to form AgS bonds with biological mercaptan when it is added in, so that Ag⁺ falls from C-Ag⁺-C. DNA-PQDs changed from aggregation to looseness and RTP is recovered accordingly. On this basis, RTP detection of biological mercaptan is realized. Since this sensor system has RTP properties based on DNA-PQDs, it is very applicable to detection of mercaptan compounds in biological fluids.

Graphene Quantum Dot-Based Nanocomposites for Diagnosing Cancer Biomarker APE1 in Living Cells

As an essential DNA repair enzyme, apurinic/apyrimidinic endonuclease 1 (APE1) is overexpressed in most human cancers and is identified as a cancer diagnostic and predictive biomarker for cancer risk assessment, diagnosis, prognosis, and prediction of treatment efficacy. Despite its importance in cancer, however, it is still a significant challenge nowadays to sense abundance variation and monitor enzymatic activity of this biomarker in living cells. Here, we report our construction of biocompatible functional nanocomposites, which are a combination of meticulously designed unimolecular DNA and fine-sized graphene quantum dots. Upon utilization of these nanocomposites as diagnostic probes, massive accumulation of fluorescence signal in living cells can be triggered by merely a small amount of cellular APE1 through repeated cycles of enzymatic catalysis. Most critically, our delicate structural designs assure that these graphene quantum dot-based nanocomposites are capable of sensing cancer biomarker APE1 in identical type of cells under different cell conditions and can be applied to multiple cancerous cells in a highly sensitive and specific manners. This work not only brings about new methods for cytology-based cancer screening but also lays down a general principle for fabricating diagnostic probes that target other endogenous biomarkers in living cells.

Facile incorporation of DNA-templated quantum dots for sensitive electrochemical detection of the oral cancer biomarker interleukin-8

Recent studies reveal a great value of interleukin-8 (IL-8), a pro-inflammatory cytokine, as a potent biomarker for early diagnosis of oral cancer. Herein, a new electrochemical method is proposed to detect IL-8 by facilely incorporating DNA-templated quantum dots (QDs). In principle, target IL-8 is first treated with the reducing agent tris(2-carboxyethyl)phosphine (TCEP) to yield active thiols and then captured by antibody-functionalized magnetic beads (MBs). Thereafter, via the Michael addition reaction between the active thiol and maleimide group, a maleimide-modified DNA probe is linked to the surface of MBs, which can initiate a process of rolling circle amplification. In this way, long-range DNA strands are generated on the MB surface, subsequently recruiting DNA-templated CdTe/CdS QDs (DNA-QDs) to act as electrochemical reporters. By tracing the responses of DNA-QDs, the method allows IL-8 detection in a linear range from 5 to 5000 fg/mL with a detection limit of 3.36 fg/mL. The selectivity, reproducibility, and applicability in complex serum samples are also demonstrated to be favorable, indicating that the method may have a great potential in the future. More importantly, the use of TCEP treatment in the method not only provides a facile way to incorporate DNA-QDs, avoiding the complicated and time-consuming preparation process of antibody-DNA conjugates or functional nanomaterials; but also makes the method capable of being extended to detect other protein biomarkers in view of widespread presence of disulfides, which may hold a broad potential to facilitate efficient biosensing designs.

DNA-templated quantum dots and their applications in biosensors, bioimaging, and therapy

Over the past 10 years, DNA functionalized quantum dots (QDs) have attracted considerable attention in sensing and imaging of disease-relevant biological targets, as well as cancer therapy. Considerable efforts have been devoted to obtaining DNA functionalized QDs with enhanced stability and quantum yield. Here, we focus on a one-pot method, in which phosphorothioate-modified DNA is used as the co-ligand on the basis of the strong binding of sulfur and Cd²⁺. After a short summary of the preparation of DNA-templated QDs, versatile bioapplications based on the constructed ratiometric fluorescent probes, nanobeacons and multiple bottom-up assemblies will be discussed. A substantial part of the review will focus on these applications, ranging from small molecule, biological macromolecule, cancer cell and pathogen sensing to in vitro and in vivo imaging. Besides, drug or siRNA delivery based on DNA-templated QD assemblies will also be briefly discussed here.

Sensitive Oligodeoxynucleotide Synthesis Using Dim and Dmoc as Protecting Groups

In traditional oligodeoxynucleotide (ODN) synthesis, phosphate groups are protected with the 2-cyanoethyl group, and amino groups are protected with acyl groups. At the end of ODN synthesis, deprotection is achieved with strong bases and nucleophiles. Therefore, traditional technologies are not suitable for the synthesis of ODNs containing sensitive functionalities. To address the problem, we report the use of Dim and Dmoc groups, which are based on the 1,3-dithian-2-yl-methyl function, for phosphate and amine protection for the solid phase ODN synthesis. Using the new Dim-Dmoc protection, deprotection was achieved under mild oxidative conditions without using any strong bases and nucleophiles. As a result, the new technology is suitable for the synthesis of ODNs containing sensitive functions. To demonstrate feasibility, seven 20-mer ODNs including four that contain sensitive ester and alkyl chloride groups were synthesized, purified with RP HPLC, and characterized with MALDI-TOF MS and enzyme digestion essays. High purity ODNs were obtained.

Compact quantum dot surface modification to enable emergent behaviors in quantum dot-DNA composites

Quantum dot (QD) biological imaging and sensing applications often require surface modification with single-stranded deoxyribonucleic acid (ssDNA) oligonucleotides. Furthermore, ssDNA conjugation can be leveraged for precision QD templating via higher-order DNA nanostructures to exploit emergent behaviors in photonic applications. Use of ssDNA-QDs across these platforms requires compact, controlled conjugation that engenders QD stability over a wide pH range and in solutions of high ionic strength. However, current ssDNA-QD conjugation approaches suffer from limitations, such as the requirement for thick coatings, low control over ssDNA labeling density, requirement of large amounts of ssDNA, or low colloidal or photostability, restraining implementation in many applications. Here, we combine thin, multidentate, phytochelatin-3 (PC3) QD passivation techniques with strain-promoted copper-free alkyne-azide click chemistry to yield functional ssDNA-QDs with high stability. This process was broadly applicable across QD sizes (i.e., λ_em = 540, 560, 600 nm), ssDNA lengths (i.e., 10-16 base pairs, bps), and sequences (poly thymine, mixed bps). The resulting compact ssDNA-QDs displayed a fluorescence quenching efficiency of up to 89% by hybridization with complementary ssDNA-AuNPs. Furthermore, ssDNA-QDs were successfully incorporated with higher-order DNA origami nanostructure templates. Thus, this approach, combining PC3 passivation with click chemistry, generates ssDNA-PC3-QDs that enable emergent QD properties in DNA-based devices and applications.

Subnanomolar FRET-Based DNA Assay Using Thermally Stable Phosphorothioated DNA-Functionalized Quantum Dots

Quantum dots (QDs) can serve as an attractive Förster resonance energy transfer (FRET) donor for DNA assay due to their excellent optical properties. However, the specificity and sensitivity of QD-based FRET analysis are prominently reduced by nonspecific DNA adsorption and poor colloidal stability during DNA hybridization, which hinders the practical applications of QDs as a biosensing platform. Here, we report subnanomolar FRET assay of DNA through the stabilization of DNA/QD interface using DNA-functionalized QDs with phosphorothioated single-stranded DNA (pt-ssDNA) as a multivalent ligand in an aqueous solution. In situ DNA functionalization was achieved during the aqueous synthesis of CdTe/CdS QDs, resulting in the maximum photoluminescence quantum yields of 76.9% at an emission wavelength of 732 nm. Conventional monothiolated ssDNA-capped QDs exhibited particle aggregation and photoluminescence (PL) quenching during DNA hybridization at 70 °C due to the dissociation of surface ligands. Such colloidal instability induced the nonspecific adsorption of DNA, resulting in false-positive signal and decreased sensitivity with the limit of detection (LOD) of 16.1 nM. In contrast, the pt-ssDNA-functionalized QDs maintained their colloidal stability and PL properties at elevated temperatures. The LOD of the pt-ssDNA-functionalized QDs was >30 times lower (0.47 nM) while maintaining the high specificity to a target sequence because the strong multivalent binding of pt-ssDNA to the surface of QDs prevents the detachment of pt-ssDNA and nonspecific adsorption of DNA. The study suggests that the ligand design to stabilize the surface of QDs in an aqueous milieu is critically important for the high performance of QDs for specific DNA assay.

Biocomputing with Nanostructures on Lipid Bilayers

Biocomputation is the algorithmic manipulation of biomolecules. Nanostructures, most notably DNA nanostructures and nanoparticles, become active substrates for biocomputation when modified with stimuli-responsive, programmable biomolecular ligands. This approach-biocomputing with nanostructures ("nano-bio computing")-allows autonomous control of matter and information at the nanoscale; their dynamic assemblies and beneficial properties can be directed without human intervention. Recently, lipid bilayers interfaced with nanostructures have emerged as a new biocomputing platform. This new nano-bio interface, which exploits lipid bilayers as a chemical circuit board for information processing, offers a unique reaction space for realizing nanostructure-based computation at a previously unexplored dimension. In this Concept, recent advances in nano-bio computing are briefly reviewed and the newly emerging concept of biocomputing with nanostructures on lipid bilayers is introduced.

Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter

The emergence of high-throughput DNA sequencing technologies sparked a revolution in the field of genomics that has rippled into many branches of the life and physical sciences. The remarkable sensitivity, specificity, throughput, and multiplexing capacity that are inherent to parallel DNA sequencing have since motivated its use as a broad-spectrum molecular counter. A key aspect of extrapolating DNA sequencing to non-traditional applications is the need to append nucleic-acid barcodes to entities of interest. In this review, we describe the chemical and biochemical approaches that have enabled nucleic-acid barcoding of proteinaceous and non-proteinaceous materials and provide examples of downstream technologies that have been made possible by DNA-encoded molecules. As commercially available high-throughput sequencers were first released less than 15 years ago, we believe related applications will continue to mature and close by proposing new frontiers to support this assertion.

Logic Sensing of MicroRNA in Living Cells Using DNA-Programmed Nanoparticle Network with High Signal Gain

Molecular circuits capable of implementing Boolean logic in cellular environments have emerged as an important tool for in situ sensing, elucidating, and modulating cell functions. The performance of existing molecular computation devices in living cells is limited because of the low level of biomolecular inputs and moderate signal gain. Herein, we devised a new class of DNA-programmed nanoparticle network with integrated molecular computation and signal amplification functions for logic sensing of dual microRNA (miRNA) molecules in living cells. The nanoparticle network, which is composed of DNA-bridged gold nanoparticles and quantum dots (QDs), could simultaneously interface with two miRNA molecules, amplify the molecular inputs, perform a calculation through AND logic gate, and generate QD photoluminescence (PL) as an output signal. Significant improvement in imaging sensitivity is achieved by integrating the signal amplifier into the molecular computation device. It allows discrimination of specific cancer cell types via intelligent sensing of miRNA patterns in living cells.

Sensing with photoluminescent semiconductor quantum dots

Fluorescent sensors benefit from high signal-to-noise and multiple measurement modalities, enabling a multitude of applications and flexibility of design. Semiconductor nanocrystal quantum dots (QDs) are excellent fluorophores for sensors because of their extraordinary optical properties. They have high thermal and photochemical stability compared to organic dyes or fluorescent proteins and are extremely bright due to their large molar cross-sections. In contrast to organic dyes, QD emission profiles are symmetric, with relatively narrow bandwidths. In addition, the size tunability of their emission color, which is a result of quantum confinement, make QDs exceptional emitters with high color purity from the ultra-violet to near infrared wavelength range. The role of QDs in sensors ranges from simple fluorescent tags, as used in immunoassays, to intrinsic sensors that utilize the inherent photophysical response of QDs to fluctuations in temperature, electric field, or ion concentration. In more complex configurations, QDs and biomolecular recognition moieties like antibodies are combined with a third component to modulate the optical signal via energy transfer. QDs can act as donors, acceptors, or both in energy transfer-based sensors using Förster resonance energy transfer (FRET), nanometal surface energy transfer (NSET), or charge or electron transfer. The changes in both spectral response and photoluminescent lifetimes have been successfully harnessed to produce sensitive sensors and multiplexed devices. While technical challenges related to biofunctionalization and the high cost of laboratory-grade fluorimeters have thus far prevented broad implementation of QD-based sensing in clinical or commercial settings, improvements in bioconjugation methods and detection schemes, including using simple consumer devices like cell phone cameras, are lowering the barrier to broad use of more sensitive QD-based devices.

Conformational Details of Quantum Dot-DNA Resolved by Förster Resonance Energy Transfer Lifetime Nanoruler

DNA-nanoparticle conjugates are important tools in nanobiotechnology. Knowing the orientation, function, and length of DNA on nanoparticle surfaces at low nanomolar concentrations under physiological conditions is therefore of great interest. Here, we investigate the conformation of a 31 nucleotides (nt) long DNA attached to a semiconductor quantum dot (QD) via Förster resonance energy transfer (FRET) from Tb-DNA probes hybridized to different positions on the QD-DNA. Precise Tb-to-QD distance determination from 7 to 14 nm along 26 nt of the peptide-appended QD-DNA was realized by time-resolved FRET spectroscopy. The FRET nanoruler measured linear single-stranded (ssDNA) and double-stranded (dsDNA) extensions of ∼0.15 and ∼0.31 nm per base, reflecting the different conformations. Comparison with biomolecular modeling confirmed the denser conformation of ssDNA and a possibly more flexible orientation on the QD surface, whereas the dsDNA was fully extended with radial orientation. The temporally distinct photoluminescence decays of the different DNA-FRET configurations were used for prototypical DNA hybridization assays that demonstrated the large potential for extended temporal multiplexing. The extensive experimental and theoretical analysis of 11 different distances/configurations of the same QD-DNA conjugate provided important information on DNA conformation on nanoparticle surfaces and will be an important benchmark for the development and optimization of DNA-nanobiosensors.

Programmable Metal/Semiconductor Nanostructures for mRNA-Modulated Molecular Delivery

Cytotoxic chemotherapeutics are important tools for the clinical treatment of a variety of solid tumors. However, their use is often complicated by multidrug resistance that can develop in patients, limiting the potencies of these agents. New strategies are needed to provide versatile systems that can respond to and disable resistance mechanisms. We demonstrate the use of a new family of materials, programmable metal/semiconductor nanostructures, for drug delivery and mRNA sensing in drug-resistant cells. These materials are composed of a central core gold nanoparticle surrounded by a layer of DNA-capped quantum dots. The modularity of these "core-satellite" assemblies allows for the construction of superstructures with controlled size and the incorporation of multiple functionalities for drug delivery. The DNA sequence within the nanoparticle specifically binds to an mRNA encoding an important drug resistance factor, MRP1, inside cancer cells, releasing a potent anticancer drug doxorubicin. This event triggers a turn-on fluorescence emission along with a downregulation of the MRP1 drug efflux pump, a main resistance factor for doxorubicin, yielding a remarkable improvement in therapeutic efficacy against drug-resistant cancer cells. This work paves the way for the development of programmable materials with multiple synergistic functionalities for biomedical applications.