DNA-Driven Nanoparticle Assemblies for Biosensing and Bioimaging

DNA molecules with superior flexibility, affinity and programmability have garnered considerable attention for the controllable assembly of nanoparticles (NPs). By controlling the density, length and sequences of DNA on NPs, the configuration of NP assemblies can be rationally designed. The specific recognition of DNA enables changes to be made to the spatial structures of NP assemblies, resulting in differences in tailorable optical signals. Comprehensive information on the fabrication of DNA-driven NP assemblies would be beneficial for their application in biosensing and bioimaging. This review analyzes the progress of DNA-driven NP assemblies, and discusses the tunable configurations determined by the structural parameters of DNA skeletons. The collective optical properties, such as chirality, fluorescence and surface enhanced Raman resonance (SERS), etc., of DNA-driven NP assemblies are explored, and engineered tailorable optical properties of these spatial structures are achieved. We discuss the development of DNA-directed NP assemblies for the quantification of DNA, toxins, and heavy metal ions, and demonstrate their potential application in the biosensing and bioimaging of tumor markers, RNA, living metal ions and phototherapeutics. We hihghlight possible challenges in the development of DNA-driven NP assemblies, and further direct potential prospects in the practical applications of macroscopical materials and photonic devices.

Multicomponent Plasmonic Nanoparticles: From Heterostructured Nanoparticles to Colloidal Composite Nanostructures

Plasmonic nanostructures possessing unique and versatile optoelectronic properties have been vastly investigated over the past decade. However, the full potential of plasmonic nanostructure has not yet been fully exploited, particularly with single-component homogeneous structures with monotonic properties, and the addition of new components for making multicomponent nanoparticles may lead to new-yet-unexpected or improved properties. Here we define the term "multi-component nanoparticles" as hybrid structures composed of two or more condensed nanoscale domains with distinctive material compositions, shapes, or sizes. We reviewed and discussed the designing principles and synthetic strategies to efficiently combine multiple components to form hybrid nanoparticles with a new or improved plasmonic functionality. In particular, it has been quite challenging to precisely synthesize widely diverse multicomponent plasmonic structures, limiting realization of the full potential of plasmonic heterostructures. To address this challenge, several synthetic approaches have been reported to form a variety of different multicomponent plasmonic nanoparticles, mainly based on heterogeneous nucleation, atomic replacements, adsorption on supports, and biomolecule-mediated assemblies. In addition, the unique and synergistic features of multicomponent plasmonic nanoparticles, such as combination of pristine material properties, finely tuned plasmon resonance and coupling, enhanced light-matter interactions, geometry-induced polarization, and plasmon-induced energy and charge transfer across the heterointerface, were reported. In this review, we comprehensively summarize the latest advances on state-of-art synthetic strategies, unique properties, and promising applications of multicomponent plasmonic nanoparticles. These plasmonic nanoparticles including heterostructured nanoparticles and composite nanostructures are prepared by direct synthesis and physical force- or biomolecule-mediated assembly, which hold tremendous potential for plasmon-mediated energy transfer, magnetic plasmonics, metamolecules, and nanobiotechnology.

Chiral Plasmonic Biosensors

Biosensing requires fast, selective, and highly sensitive real-time detection of biomolecules using efficient simple-to-use techniques. Due to a unique capability to focus light at nanoscale, plasmonic nanostructures provide an excellent platform for label-free detection of molecular adsorption by sensing tiny changes in the local refractive index or by enhancing the light-induced processes in adjacent biomolecules. This review discusses the opportunities provided by surface plasmon resonance in probing the chirality of biomolecules as well as their conformations and orientations. Various types of chiral plasmonic nanostructures and the most recent developments in the field of chiral plasmonics related to biosensing are considered.

Biological Molecules-Governed Plasmonic Nanoparticle Dimers with Tailored Optical Behaviors

Self-assembly opens new avenues to direct the organization of nanoparticles (NPs) into discrete structures with predefined configuration and association numbers. Plasmonic NP dimers provide a well-defined system for investigating the plasmonic coupling and electromagnetic (EM) interaction in arrays of NPs. The programmability and structural plasticity of biomolecules offers a convenient platform for constructing of NP dimers in a controllable way. Plasmonic coupling of NPs enables dimers to exhibit tunable optical properties, such as surface-enhanced Raman scattering (SERS), chirality, photoluminescence, and electrochemiluminescence (ECL) properties, which can be tailored by altering the biomolecules, the building blocks with distinct compositions, sizes and morphology, the interparticle distances, as well as the geometric configuration of the constituent NPs. An overview of recent developments in biological molecules-governed NP dimers, the tailored optical behaviors, and challenges in enhancing optical signals and proposing plasmonic biosensors are discussed in this Perspective.

Dynamic Chiral Nanoparticle Assemblies and Specific Chiroplasmonic Analysis of Cancer Cells

Fabricated Ag@Au core-shell nanoparticle (CS NP) assemblies exhibit pronounced and reverse chiral bisignate plasmonic signals spanning 400 to 580 nm, in comparison to Ag NP assemblies. The time-dependent chiro-optical response of assemblies that shift with shell deposition is systematically recorded. Chiral Ag@Au CS NP assemblies first achieve the special discrimination of circulating tumor cells with HER2 overexpression.

Dual amplified electrochemical immunosensor for highly sensitive detection of Pantoea stewartii sbusp. stewartii

Accurate and highly sensitive detection of Pantoea stewartii sbusp. stewartii-NCPPB 449 (PSS) is urgently required for international shipments due to tremendous agricultural economic losses. Herein, a dual amplified electrochemical sandwich immunosensor for PSS detection was developed, utilizing the good specificity and low cost of electrochemical immunoassay, the favorable conductivity and large specific surface area of gold nanoparticles (Au NPs), and the excellent catalytic ability of and horseradish peroxidase (HRP). A linear curve between current response and PSS concentration was established, and the limit of detection (LOD) was 7.8 × 10(3) cfu/mL, which is 20 times lower than that for conventional enzyme-linked immunosorbent assay (ELISA). This strategy is a useful approach for the highly sensitive detection of plant pathogenic bacterium.

Bovine thrombin enhances the efficiency and specificity of polymerase chain reaction

The polymerase chain reaction (PCR) has become one of the central techniques in molecular biology since its invention. However, PCR can be fraught with difficulties in various situations, and it is desirable to find novel PCR enhancers suitable for universal applications. Here we show that bovine thrombin (BT), a well-known coagulation protein, is exceptionally effective at preventing the formation of primer dimers and enhancing the formation of the desired PCR products. The PCR enhancement effects of BT were demonstrated by testing various types of samples, including low-copy synthetic single-stranded DNAs (ssDNAs), synthetic ssDNA pools, human genomic DNA, and hepatitis B virus genomic DNA. In addition, BT was also able to effectively relieve PCR inhibition by nanomaterial inhibitors such as gold nanoparticles (AuNPs) and graphene oxide (GO). Compared with BSA, one of the most popular PCR enhancers, BT was more effective and required concentrations 18-178 times less than that of BSA to achieve a similar level of PCR enhancement.

Pyramidal sensor platform with reversible chiroptical signals for DNA detection

A heterogeneous chiral sensor for DNA detection is demonstrated by post-assembly system reconfiguration for two types of NPs pyramids. In the presence of target DNA, two types of NPs pyramids undergo dynamic reconfiguration or dissociation process which functions as an off-on or on-off switch towards CD signals changes. Under optimized conditions, the detection limit of this approach can reach to 3.4 aM with no involvement of amplification process.

Shell-programmed Au nanoparticle heterodimers with customized chiroptical activity

Chiral plasmonic assemblies with strong and tunable chiroptical activity are emerging materials yet challenging to fabricate. Moreover, shell-programmed chiroptical regulation is really rare. Here, the chiroptical activity of core-shell (CS) nanoparticles (NPs) heterodimers (HDs) with different types and thicknesses of the shell but featuring the same gap was exploited. It was found that the type of shell guided the position of the chiral peaks, and the shell thickness tuned the intensity but also moderately affected the wavelength shift at invariable interparticle distance. Shell deposition intensified the hot-spot chirality, and evidently guided the enantiomorphous chiral configuration, resulting in a startlingly intense, asymmetric, dipolar coupling strength. The magnitude of the chiroptical activity showed an 8-10 fold enhancement with a maximum anisotropy factor (g-factor) of 1.5 × 10(-2) . Shell-driven chiroptical regulation opens new avenues to feasibly fabricate chiroptically active materials with desired chiroptical response for the development of switchable recognition units for sensitive and various target detections.

Shell-engineered chiroplasmonic assemblies of nanoparticles for zeptomolar DNA detection

DNA-bridged pairs of seemingly spherical metallic nanoparticles (NPs) have chiral geometry due to the nonideal oblong shape of the particles and scissor-like conformation. Here we demonstrate that deposition of gold and silver shells around the NP heterodimers enables spectral modulation of their chiroplasmonic bands in 400-600 nm region and results in significantly enhanced optical activity with g-factors reaching 1.21 × 10(-2). The multimetal heterodimers optimized for coupling with the spin angular momentum of incident photons enable polymerase chain reaction (PCR)-based DNA detection at the zeptomolar level. This significant improvement in the sensitivity of detection is attributed to improvement of base pairing in the presence of NPs, low background for chiroplasmonic detection protocol, and enhancement of photon-plasmon coupling for light with helicity matching that of the twisted geometry of the heterodimers.

Assembled plasmonic asymmetric heterodimers with tailorable chiroptical response

Directed nanocrystal (NC) heteroassemblies could potentially achieve tailorable multiplex circular dichroism (CD) bands. Here, for the first time, we developed assembly of nanoparticle (NP)-nanorod (NR) chiral heterodimers with chiral molecules to explore their chiroptical activities. The experimental results revealed that plasmonic CD responses were in the region from 520 to 750 nm, which was in agreement with the theoretical simulation. Importantly, the CD band could be regulated by controlling the gaps between adjacent NCs and altering the building blocks of the assemblies. These results show that the plasmonic chiroptical response of NP-NR heterodimers could come from the finger-crossed chiral construction of adjacent NC in the heterodimers and the formation of plasmonic hot-spots in the assemblies could further enhance the plasmonic CD. This work provides a new opportunity to create heterogeneous nanoscale plasmonic objects with tailorable chiroptical response for application in biosensors, in vivo chiral medical carriers and negative refractive index materials.

Asymmetric plasmonic aptasensor for sensitive detection of bisphenol A

A sensitive plasmonic chirality-based aptasensor for the detection of bisphenol A (BPA) was developed. Asymmetric plasmonic nanoparticle dimers were produced by the hybridization of a BPA aptamer and its complementary sequence modified nanoparticles. Under different concentrations of BPA, the intensity of the chiral signal was varied. A low limit of detection of 0.008 ng/mL was obtained in the range 0.02-5 ng/mL.

SERS-active Ag@Au core–shell NP assemblies for DNA detection

SERS-active silver@gold (Ag@Au) core–shell nanoparticles (NPs) assemblies were fabricated by polymerase chain reaction (PCR) for the sensitive DNA detection.

A PCR based magnetic assembled sensor for ultrasensitive DNA detection

An ultrasensitive method for DNA detection based on magnetic assembly induced by polymerase chain reaction (PCR) was developed. The sensor showed a low limit of detection (LOD) of 4.26 aM with a wide range of target DNA from 0.01 fM to 10,000 fM.

Nanoscale superstructures assembled by polymerase chain reaction (PCR): programmable construction, structural diversity, and emerging applications

Polymerase chain reaction (PCR) is an essential tool in biotechnology laboratories and is becoming increasingly important in other areas of research. Extensive data obtained over the last 12 years has shown that the combination of PCR with nanoscale dispersions can resolve issues in the preparation DNA-based materials that include both inorganic and organic nanoscale components. Unlike conventional DNA hybridization and antibody-antigen complexes, PCR provides a new, effective assembly platform that both increases the yield of DNA-based nanomaterials and allows researchers to program and control assembly with predesigned parameters including those assisted and automated by computers. As a result, this method allows researchers to optimize to the combinatorial selection of the DNA strands for their nanoparticle conjugates. We have developed a PCR approach for producing various nanoscale assemblies including organic motifs such as small molecules, macromolecules, and inorganic building blocks, such as nanorods (NRs), metal, semiconductor, and magnetic nanoparticles (NPs). We start with a nanoscale primer and then modify that building block using the automated steps of PCR-based assembly including initialization, denaturation, annealing, extension, final elongation, and final hold. The intermediate steps of denaturation, annealing, and extension are cyclic, and we use computer control so that the assembled superstructures reach their predetermined complexity. The structures assembled using a small number of PCR cycles show a lower polydispersity than similar discrete structures obtained by direct hybridization between the nanoscale building blocks. Using different building blocks, we assembled the following structural motifs by PCR: (1) discrete nanostructures (NP dimers, NP multimers including trimers, pyramids, tetramers or hexamers, etc.), (2) branched NP superstructures and heterochains, (3) NP satellite-like superstructures, (4) Y-shaped nanostructures and DNA networks, (5) protein-DNA co-assembly structures, and (6) DNA block copolymers including trimers and pentamers. These results affirm that this method can produce a variety of chemical structures and in yields that are tunable. Using PCR-based preparation of DNA-bridged nanostructures, we can program the assembly of the nanoscale blocks through the adjustment of the primer intensity on the assembled units, the number of PCR cycles, or both. The resulting structures are highly complex and diverse and have interesting dynamics and collective properties. Potential applications of these materials include chirooptical materials, probe fabrication, and environmental and biomedical sensors.

A Sensitive DNAzyme-Based Chiral Sensor for Lead Detection

A DNAzyme-based sensor for the determination and quantification of lead ions (Pb²⁺) has been established, which combines the recognition and catalysis of DNAzyme with the optical properties of nanomaterials. Circular dichroism (CD) signals were obtained by a DNAzyme-based assembly of asymmetric silver nanoparticle (AgNPs) dimers. A good linear relationship between CD signals and Pb²⁺ concentration was obtained ranging from 0.05 ng∙mL⁻¹ to 10 ng∙mL⁻¹ with a limit of detection (LOD) of 0.02 ng∙mL⁻¹. The specificity of this sensor in lead ion detection was excellent, and a satisfactory recovery was obtained in the analysis of tap water samples. The proposed technique possesses both high sensitivity and good specificity, giving it great potential for the analysis of Pb²⁺ in water.

Plasmonic Core-Satellites Nanostructures with High Chirality and Bioproperty

In this Letter, gold nanorods (Au NRs) and gold nanoparticles (Au NPs) were assembled into core-satellites (Au NR-NPs) nanostructures using DNA as the linkers. Circular dichroism (CD) measurements of the nanoassemblies displayed two plasmonic CD (PCD) peaks in the vicinity of the surface plasmon resonance (SPR). Interestingly, the number of Au NPs in the assemblies had a significant influence on the shape and intensity of the CD line. The assemblies were enzymatically disassembled by deoxyribonuclease I (DNase I), and the CD responses were simultaneously reversed. With the proof-of-concept design, the PCD response was no change by addding enzyme inhibitor. These experiments suggested that the chirality depended upon the structure of core-satellites nanoassemblies, and the results clarify that the possible origin of the optical activity comes from chiral arrangement of building blocks and Coulomb dipole-dipole interactions. This research also illuminated that the assemblies can be used to develop a new sensor for the sensitive screening of the enzyme inhibitors.

Alternating Plasmonic Nanoparticle Heterochains Made by Polymerase Chain Reaction and Their Optical Properties

Organization of nanoparticles (NPs) of different materials into superstructures of higher complexity represents a key challenge in nanotechnology. Polymerase chain reaction (PCR) was used in this study to fabricate chains consisting of plasmonic NPs of different sizes, thus denoted heterochains. The NPs in such chains are connected by DNA oligomers, alternating in a sequence big-small-big-small-... and spanning lengths in the range of 40-300 nm by varying the number of PCR cycles. They display strong plasmonic chirality at 500-600 nm, the chiral activity revealing nonmonotonous dependence on the length of heterochains. We find the strength of surface-enhanced Raman scattering (SERS) to increase with chain length, while the chiral response initially increased and then decreased with the number of PCR cycles. The relationship between the optical properties of the heterochains and their structure/length is discussed. The length-dependent intense optical response of the plasmonic NP heterochains holds great potential for biosensing applications.

Design and fabrication of three-dimensional chiral nanostructures based on stepwise glancing angle deposition technology

The chiral structures have displayed some inevitable and fascinating properties in many research fields, such as chemistry, biology, mathematics, and physics. In this Article, we report the use of stepwise glancing angle deposition technology to produce the 3D chiral nanostructures. Through the optimization of deposition parameters (such as the orientation angle of poly styrene spheres (PSs) array, the deposition angle, thickness, and number), a great number of chiral structures have been achieved, and their size depends on the diameter of PS spheres. These chiral structures all can be simulated and predesigned through the use of a 3D geometrical model, which greatly improves the efficiency of this method. In addition, the circular dichroism spectrum shows that these chiral structures own an obvious Cotton effect, indicating their potential application as 3D chiral metamaterials.

Self-assembly of chiral nanoparticle pyramids with strong R/S optical activity

Chirality at the nanometer scale represents one of the most rapidly developing areas of research. Self-assembly of DNA-nanoparticle (NP) hybrids enables geometrically precise assembly of chiral isomers. The concept of a discrete chiral nanostructure of tetrahedral shape and topology fabricated from four different NPs located in the corners of the pyramid is fundamental to the field. While the first observations of optical activity of mixed pyramidal assemblies were made in 2009 (Chen, W.; Nano Lett. 2009, 9, 2153-2159), further studies are difficult without finely resolved optical data for precisely organized NP pyramidal enantiomers. Here we describe the preparation of a family of self-assembled chiral pyramids made from multiple metal and/or semiconductor NPs with a yield as high as 80%. Purposefully made R- and S-enantiomers of chiral pyramids with four different NPs from three different materials displayed strong chiroptical activity, with anisotropy g-factors as high as 1.9 × 10(-2) in the visible spectral range. Importantly, all NP constituents contribute to the chiroptical activity of the R/S pyramids. We were able to observe three different circular dichroism signals in the range of 350-550 nm simultaneously. They correspond to the plasmonic oscillations of gold, silver, and bandgap transitions of quantum dots. Tunability of chiroptical bands related to these transitions is essential from fundamental and practical points of view. The predictability of optical properties of pyramids, the simplicity of their self-assembly in comparison with lithography, and the possibility for polymerase chain reaction-based automation of their synthesis are expected to facilitate their future applications.