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

Preparation of long single-strand DNA concatemers for high-level fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) is a powerful tool to visualize transcripts in fixed cells and tissues. Despite the recent advances in FISH detection methods, it remains challenging to achieve high-level FISH imaging with a simple workflow. Here, we introduce a method to prepare long single-strand DNA concatemers (lssDNAc) through a controllable rolling-circle amplification (CRCA). Prepared lssDNAcs are used to develop AmpFISH workflows. In addition, we present its applications in different scenarios. AmpFISH shows the following advantages: 1) enhanced FISH signal-to-noise ratio (SNR) up to 160-fold compared with single-molecule FISH; 2) simultaneous detection of FISH signals and fluorescent proteins or immunofluorescence (IF) in tissues; 3) simple workflows; and 4) cost-efficiency. In brief, AmpFISH provides convenient and versatile tools for sensitive RNA/DNA detection and to gain useful information on cellular molecules using simple workflows.

Heterodimers of metal nanoparticles: synthesis, properties, and biological applications

Heterodimers of metal nanoparticles consist of two metals, come in many sizes and adopt various shapes. They offer unique properties due to the presence of two metals and have the extraordinary flexibility needed to serve as a multipurpose platform for diverse applications in areas including photonics, sensing, and catalysis. Heterodimer nanoparticles contain different metals that contribute to extraordinary surface plasmon resonance (SPR), surface-enhanced Raman scattering (SERS), and catalytic properties. These properties make them versatile molecules that can be used in intracellular imaging, as antibacterial agents, as photocatalytic and biological macromolecules and for the detection of chemical substances. Moreover, heterodimer nanoparticles are composed of the two metals within larger molecules that provide more choices for modification and application. In this review, we briefly summarize the lesser-known aspects of heterodimers, including some of their properties, and present concrete examples of recent progress in synthesis and applications. This review provides a perspective on achievements and suggests a framework for future research with a focus on the synthesis and application of heterodimers. We also explore the possible applications of heterodimer nanoparticles based on their unique properties.

Present and Future of Surface-Enhanced Raman Scattering

The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article.

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.

Directed Nanoparticle Assembly through Polymer Crystallization

Nanoparticles can be assembled into complex structures and architectures by using a variety of methods. In this review, we discuss recent progress of using polymer crystallization (particularly polymer single crystals, PSCs) to direct nanoparticle assembly. PSCs have been extensively studied since 1957. Mainly appearing as quasi-two-dimensional (2D) lamellae, PSCs are typically used as model systems to determine polymer crystalline structures, or as markers to investigate the crystallization process. Recent research has demonstrated that they can also be used as nanoscale functional materials. Herein, we show that nanoparticles can be directed to assemble into complex shapes by using in situ or ex situ polymer crystal growth. End-functionalized polymers can crystallize into 2D nanosheet PSCs, which are used to conjugate with complementary nanoparticles, leading to a nanosandwich structure. These nanosandwiches can find interesting applications for catalysis, surface-enhanced Raman spectroscopy, and nanomotors. Dissolution of the nanosandwich leads to the formation of Janus nanoparticles, providing a unique method for asymmetric nanoparticle synthesis.

A facile deoxyuridine/biotin-modified molecular beacon for simultaneous detection of proteins and nucleic acids via a label-free and background-eliminated fluorescence assay

Simultaneous detection of different types of cancer biomarkers (nucleic acids and proteins) could facilitate early diagnosis of cancer and clinical treatment. Herein, a simultaneous detection platform of proteins and nucleic acids has been developed using a single substrate probe combining a label-free and background-eliminated fluorescence assay. Telomerase and telomerase RNA (TR) were chosen as the models. The molecular beacon (dU-BIO-HP) that contains deoxyuridine/biotin in its side arm, a TR recognition sequence in the loop and a telomerase substrate primer at the stem end was ingeniously designed. In the presence of telomerase, the stem of dU-BIO-HP is elongated by the addition of telomere repeats complementary to the assistant DNA. Furthermore, the formed dsDNA performed as engaging primers to initiate a SDA reaction, generating abundant G-quadruplex monomers. Similarly, on TR, the hybridization between TR and dU-BIO-HP can open its stem, triggering another SDA reaction, producing abundant short ssDNAs. With the G-quadruplex binding with ZnPPIX and ssDNA binding with SG for specific fluorescence responses, the label-free multiple detection can be achieved. In our strategy, the deoxyuridine of dU-BIO-HP acts as a barrier to block the DNA extension due to its strong inhibitory effects on DNA polymerase activity and to make sure that the two SDA reactions occurred independently. The biotin of dU-BIO-HP enables the reduction of the background from the binding between SG, ZnPPIX and dU-BIO-HP through streptavidin-biotin interaction. This method showed an excellent sensitivity with telomerase and TR detection limit of 2.18 HeLa cells per mL and 0.16 × 10^-12 M, respectively. Furthermore, the telomerase and TR in different cell lines have been evaluated as powerful tools for biomedical research and clinical diagnosis.

Assembling silicon quantum dots into wires, networks and rods via metal ion bridges

Wires and networks of Si quantum dots (QDs) with a length of over 1 μm and a width of ∼30 nm are produced by bridging Si QDs with metal ions in solution. It is shown that the width of the wires is almost independent of the preparation parameters and is always about 30 nm, except for the case when Si QDs larger than 30 nm are used, while the length of the wires depends strongly on the kinds of ions, the amount of ions and the amount of Si QDs in a solution. In addition to the microscopic size assemblies, macroscopic size rods of Si QDs with a width of ∼20 μm are produced by using Zn2+ ions. The XPS analyses reveal that Si QDs are connected to each other via a ZnO layer in the rod. The rods have much higher conductivity and photo-response than Si QD solids produced without metal ions.

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.

A DNA–gold nanoparticle hybrid hydrogel network prepared by enzymatic reaction

We report a DNA–gold nanoparticle (AuNP) hydrogel in which the AuNPs crosslink enzymatically synthesized DNA.

Synthesis of Poly Linear shRNA Expression Cassettes Through Branch-PCR

A facile and universal strategy to construct the poly linear small hairpin RNA (shRNA) expression cassettes with multiple shRNA transcription templates through polymerase chain reaction with flexible branched primers (branch-PCR) is described in this protocol. Double-stranded RNA (dsRNA) is not stable enough for the study of RNA interference (RNAi) delivery in mammalian cells. Therefore, the more stable shRNA transcription template is employed to produce the endogenous transcribed dsRNA. Then, the covalent crosslinked linear shRNA expression cassettes are constructed through the branch-PCR for the long-lasting RNAi effect in this protocol. The branched primer pair is efficiently synthesized through classic click chemistry. In one step of PCR, the much more stable poly linear shRNA expression cassettes can be produced in large scale. This strategy of efficient synthesis of the poly linear gene expression cassettes can also be applied in the field for other target gene delivery. © 2016 by John Wiley & Sons, Inc.

Recent advances in salivary cancer diagnostics enabled by biosensors and bioelectronics

There is a high demand for a non-invasive, rapid, and highly accurate tool for disease diagnostics. Recently, saliva based diagnostics for the detection of specific biomarkers has drawn significant attention since the sample extraction is simple, cost-effective, and precise. Compared to blood, saliva contains a similar variety of DNA, RNA, proteins, metabolites, and microbiota that can be compiled into a multiplex of cancer detection markers. The salivary diagnostic method holds great potential for early-stage cancer diagnostics without any complicated and expensive procedures. Here, we review various cancer biomarkers in saliva and compare the biomarkers efficacy with traditional diagnostics and state-of-the-art bioelectronics. We summarize biomarkers in four major groups: genomics, transcriptomics, proteomics, and metabolomics/microbiota. Representative bioelectronic systems for each group are summarized based on various stages of a cancer. Systematic study of oxidative stress establishes the relationship between macromolecules and cancer biomarkers in saliva. We also introduce the most recent examples of salivary diagnostic electronics based on nanotechnologies that can offer rapid, yet highly accurate detection of biomarkers. A concluding section highlights areas of opportunity in the further development and applications of these technologies.

Efficient construction of stable gene nanoparticles through polymerase chain reaction with flexible branched primers for gene delivery

Flexible branched primers were designed to construct stable gene nanoparticles with multiple target gene copies through polymerase chain reaction, which can be used as an efficient transcription template in eukaryotic cells for gene delivery.

Orientational nanoparticle assemblies and biosensors

Assemblies of nanoparticles (NPs) have regional correlated properties with new features compared to individual NPs or random aggregates. The orientational NP assembly contributes greatly to the collective interaction of individual NPs with geometrical dependence. Therefore, orientational NPs assembly techniques have emerged as promising tools for controlling inorganic NPs spatial structures with enhanced interesting properties. The research fields of orientational NP assembly have developed rapidly with characteristics related to the different methods used, including chemical, physical and biological techniques. The current and potential applications, important challenges remain to be investigated. An overview of recent developments in orientational NPs assemblies, the multiple strategies, biosensors and challenges will be discussed in this review.

Triplex DNA: A new platform for polymerase chain reaction-based biosensor

Non - specific PCR amplification and DNA contamination usually accompany with PCR process, to overcome these problems, here we establish a sensor for thrombin by sequence - specific recognition of the PCR product with molecular beacon through triplex formation. Probe A and probe B were designed for the sensor, upon addition of thrombin, two probes hybridized to each other and the probe B was extended in the presence of Klenow Fragment polymerase and dNTPs. The PCR amplification occurred with further addition of Taq DNA Polymerase and two primers, the PCR product was recognized by molecular beacon through triplex formation. The fluorescence intensity increased with the logarithm of the concentration of thrombin over the range from 1.0 × 10⁻¹² M to 1.0 × 10⁻⁷ M, with a detection limit of 261 fM. Moreover, the effect of DNA contamination and non - specific amplification could be ignored completely in the proposed strategy.

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.

Emerging double helical nanostructures

As one of the most important and land-mark structures found in nature, a double helix consists of two congruent single helices with the same axis or a translation along the axis. This double helical structure renders the deoxyribonucleic acid (DNA) the crucial biomolecule in evolution and metabolism. DNA-like double helical nanostructures are probably the most fantastic yet ubiquitous geometry at the nanoscale level, which are expected to exhibit exceptional and even rather different properties due to the unique organization of the two single helices and their synergistic effect. The organization of nanomaterials into double helical structures is an emerging hot topic for nanomaterials science due to their promising exceptional unique properties and applications. This review focuses on the state-of-the-art research progress for the fabrication of double-helical nanostructures based on 'bottom-up' and 'top-down' strategies. The relevant nanoscale, mesoscale, and macroscopic scale fabrication methods, as well as the properties of the double helical nanostructures are included. Critical perspectives are devoted to the synthesis principles and potential applications in this emerging research area. A multidisciplinary approach from the scope of nanoscience, physics, chemistry, materials, engineering, and other application areas is still required to the well-controlled and large-scale synthesis, mechanism, property, and application exploration of double helical nanostructures.

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.

Colloidal polymers from dipolar assembly of cobalt-tipped CdSe@CdS nanorods

The synthesis of a modular colloidal polymer system based on the dipolar assembly of CdSe@CdS nanorods functionalized with a single cobalt nanoparticle "tip" (CoNP-tip) is reported. These heterostructured nanorods spontaneously self-assembled via magnetic dipolar associations of the cobalt domains. In these assemblies, CdSe@CdS nanorods were carried as densely grafted side chain groups along the dipolar NP chain to form bottlebrush-type colloidal polymers. Nanorod side chains strongly affected the conformation of individual colloidal polymer bottlebrush chains and the morphology of thin films. Dipolar CoNP-tipped nanorods were then used as "colloidal monomers" to form mesoscopic assemblies reminiscent of traditional copolymers possessing segmented and statistical compositions. Investigation of the phase behavior of colloidal polymer blends revealed the formation of mesoscopic phase separated morphologies from segmented colloidal copolymers. These studies demonstrated the ability to control colloidal polymer composition and morphology in a manner observed for classical polymer systems by synthetic control of heterostructured nanorod structure and harnessing interparticle dipolar associations.

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.