Use of plasmon coupling to reveal the dynamics of DNA bending and cleavage by single EcoRV restriction enzymes

Nanoscopic optical rulers beyond the FRET distance limit: fundamentals and applications

In the last few decades, Förster resonance energy transfer (FRET) based spectroscopy rulers have served as a key tool for the understanding of chemical and biochemical processes, even at the single molecule level. Since the FRET process originates from dipole-dipole interactions, the length scale of a FRET ruler is limited to a maximum of 10 nm. Recently, scientists have reported a nanomaterial based long-range optical ruler, where one can overcome the FRET optical ruler distance dependence limit, and which can be very useful for monitoring biological processes that occur across a greater distance than the 10 nm scale. Advancement of nanoscopic long range optical rulers in the last ten years indicate that, in addition to their long-range capability, their brightness, long lifetime, lack of blinking, and chemical stability make nanoparticle based rulers a good choice for long range optical probes. The current review discusses the basic concepts and unique light-focusing properties of plasmonic nanoparticles which are useful in the development of long range one dimensional to three dimensional optical rulers. In addition, to provide the readers with an overview of the exciting opportunities within this field, this review discusses the applications of long range rulers for monitoring biological and chemical processes. At the end, we conclude by speculating on the role of long range optical rulers in future scientific research and discuss possible problems, outlooks and future needs in the use of optical rulers for technological applications.

Probing DNA Stiffness through Optical Fluctuation Analysis of Plasmon Rulers

The distance-dependent plasmon coupling between biopolymer tethered gold or silver nanoparticles forms the foundation for the so-called plasmon rulers. While conventional plasmon ruler applications focus on the detection of singular events in the far-field spectrum, we perform in this Letter a ratiometric analysis of the continuous spectral fluctuations arising from thermal interparticle separation variations in plasmon rulers confined to fluid lipid membranes. We characterized plasmon rulers with different DNA tethers and demonstrate the ability to detect and quantify differences in the plasmon ruler potential and tether stiffness. The influence of the nature of the tether (single-stranded versus double-stranded DNA) and the length of the tether is analyzed. The characterization of the continuous variation of the interparticle separation in individual plasmon rulers through optical fluctuation analysis provides additional information about the conformational flexibility of the tether molecule(s) located in the confinement of the deeply subdiffraction limit interparticle gap and enhances the versatility of plasmon rulers as a tool in Biophysics and Nanotechnology.

Photoluminescence of a Plasmonic Molecule

Photoluminescent Au nanoparticles are appealing for biosensing and bioimaging applications because of their non-photobleaching and non-photoblinking emission. The mechanism of one-photon photoluminescence from plasmonic nanostructures is still heavily debated though. Here, we report on the one-photon photoluminescence of strongly coupled 50 nm Au nanosphere dimers, the simplest plasmonic molecule. We observe emission from coupled plasmonic modes as revealed by single-particle photoluminescence spectra in comparison to correlated dark-field scattering spectroscopy. The photoluminescence quantum yield of the dimers is found to be surprisingly similar to the constituent monomers, suggesting that the increased local electric field of the dimer plays a minor role, in contradiction to several proposed mechanisms. Aided by electromagnetic simulations of scattering and absorption spectra, we conclude that our data are instead consistent with a multistep mechanism that involves the emission due to radiative decay of surface plasmons generated from excited electron-hole pairs following interband absorption.

Reversible Aptamer-Au Plasmon Rulers for Secreted Single Molecules

Plasmon rulers, consisting of pairs of gold nanoparticles, allow single-molecule analysis without photobleaching or blinking; however, current plasmon rulers are irreversible, restricting detection to only single events. Here, we present a reversible plasmon ruler, comprised of coupled gold nanoparticles linked by a single aptamer, capable of binding individual secreted molecules with high specificity. We show that the binding of target secreted molecules to the reversible plasmon ruler is characterized by single-molecule sensitivity, high specificity, and reversibility. Such reversible plasmon rulers should enable dynamic and adaptive live-cell measurement of secreted single molecules in their local microenvironment.

Localized Surface Plasmon Resonance Biosensing: Current Challenges and Approaches

Localized surface plasmon resonance (LSPR) has emerged as a leader among label-free biosensing techniques in that it offers sensitive, robust, and facile detection. Traditional LSPR-based biosensing utilizes the sensitivity of the plasmon frequency to changes in local index of refraction at the nanoparticle surface. Although surface plasmon resonance technologies are now widely used to measure biomolecular interactions, several challenges remain. In this article, we have categorized these challenges into four categories: improving sensitivity and limit of detection, selectivity in complex biological solutions, sensitive detection of membrane-associated species, and the adaptation of sensing elements for point-of-care diagnostic devices. The first section of this article will involve a conceptual discussion of surface plasmon resonance and the factors affecting changes in optical signal detected. The following sections will discuss applications of LSPR biosensing with an emphasis on recent advances and approaches to overcome the four limitations mentioned above. First, improvements in limit of detection through various amplification strategies will be highlighted. The second section will involve advances to improve selectivity in complex media through self-assembled monolayers, “plasmon ruler” devices involving plasmonic coupling, and shape complementarity on the nanoparticle surface. The following section will describe various LSPR platforms designed for the sensitive detection of membrane-associated species. Finally, recent advances towards multiplexed and microfluidic LSPR-based devices for inexpensive, rapid, point-of-care diagnostics will be discussed.

Modulation of Interparticle Distance in Discrete Gold Nanoparticle Dimers and Trimers by DNA Single-Base Pairing

Self-assembled structures of metallic nanoparticles with dynamically changeable interparticle distance hold promise for the regulation of collective physical properties. This paper describes gold nanoparticle dimers and trimers that exhibit spontaneous and reversible changes in interparticle distance. To exploit this property, a gold nanoparticle is modified with precisely one long DNA strand and approximately five short DNA strands. The long DNA serves to align the nanoparticles on a template DNA via hybridization, while the short DNAs function to induce the interparticle distance changes. The obtained dimer and trimer are characterized with gel electrophoresis, dynamic light scattering measurements, and transmission electron microscopy (TEM). When the complementary short DNA is added to form the fully matched duplexes on the particle surface in the presence of MgCl2 , spontaneous reduction of the interparticle distance is observed with TEM and cryo-electron microscopy. By contrast, when the terminal-mismatched DNA is added, no structural change occurs under the same conditions. Therefore, the single base pairing/unpairing at the outermost surface of the nanoparticle impacts the interparticle distance. This unique feature could be applied to the regulation of structures and properties of various DNA-functionalized nanoparticle assemblies.

Single Nanoparticle-Based Heteronanojunction as a Plasmon Ruler for Measuring Dielectric Thin Films

Nondestructive, noninvasive and accurate measurement of thin film thicknesses on dielectric substrates is challenging. In this work a ruler for measuring thin film thicknesses utilizes the heteronanojunction construct formed between a plasmonic nanoparticle and a high refractive index nonplasmonic substrate. The high near-field sensitivity in the nanojunction renders it suitable for measuring the thickness of intervening dielectric thin films. We demonstrate this by controlling the thickness of dielectric spacer layers created by overgrowing SiO2 thin films on commercially available silicon substrates. While Rayleigh (using dark-field) scattering measurements show that the spectral response is well correlated to the thickness of SiO2 spacer layers the distance-dependence is much steeper with surface-enhanced Raman scattering (SERS). Good agreement between 3D simulations and experimental results confirm the plasmon ruler construct's sensitivity to the dielectric thin film spacing. Thus, we postulate that this single nanoparticle based heteronanojunction configuration can serve as a convenient and simple ruler in metrology of thin films as well as a platform for SERS-based detection even in cases where plasmonically active films are not a suitable substrate.

Long-range two-photon scattering spectroscopy ruler for screening prostate cancer cells

Optical rulers have served as a key tool for scientists from different disciplines to address a wide range of biological activity. Since the optical window of state of the art FRET rulers is limited to a 10 nm distance, developing long range optical rulers is very important to monitor real life biological processes. Driven by this need, the current manuscript reports for the first time the design of long-range two-photon scattering (TPS) spectroscopy rulers using gold nano-antenna separated by a bifunctional rigid double strand DNA molecule, which controls the spectroscopy ruler length. Reported data demonstrate that the TPS spectroscopy ruler's working window is a within a 25 nm distance, which is more than twice that of well recognized FRET optical ruler. A possible mechanism for the two-photon spectroscopy ruler's long range capability have been discussed using angle-resolved TPS measurement and FDTD simulations. Solution-phase experimental data demonstrated that a long-range TPS ruler using A9 aptamer can be used for the screening of prostate-specific membrane antigen (PSMA) (+) prostate cancer cells even at 5 cells per mL level. Reported result with PSMA (-) normal skin HaCaT cells indicate that TPS ruler based assay has the capability to enable distinction from non-targeted cell lines. Ultimately, the long range TPS ruler can be used towards better understanding of chemical and biological processes.

Quantifying lipid contents in enveloped virus particles with plasmonic nanoparticles

Phosphatidylserine (PS) and monosialotetrahexosylganglioside (GM1 ) are examples of two host-derived lipids in the membrane of enveloped virus particles that are known to contribute to virus attachment, uptake, and ultimately dissemination. A quantitative characterization of their contribution to the functionality of the virus requires information about their relative concentrations in the viral membrane. Here, a gold nanoparticle (NP) binding assay for probing relative PS and GM1 lipid concentrations in the outer leaflet of different HIV-1 and Ebola virus-like particles (VLPs) using sample sizes of less than 3 × 10(6) particles is introduced. The assay evaluates both scattering intensity and resonance wavelength, and determines relative NP densities through plasmon coupling as a measure for the target lipid concentrations in the NP-labeled VLP membrane. A correlation of the optical observables with absolute lipid contents is achieved by calibration of the plasmon coupling-based methodology with unilamellar liposomes of known PS or GM1 concentration. The performed studies reveal significant differences in the membrane of VLPs that assemble at different intracellular sites and pave the way to an optical quantification of lipid concentration in virus particles at physiological titers.

Probing a label-free local bend in DNA by single molecule tethered particle motion

Being capable of characterizing DNA local bending is essential to understand thoroughly many biological processes because they involve a local bending of the double helix axis, either intrinsic to the sequence or induced by the binding of proteins. Developing a method to measure DNA bend angles that does not perturb the conformation of the DNA itself or the DNA-protein complex is a challenging task. Here, we propose a joint theory-experiment high-throughput approach to rigorously measure such bend angles using the Tethered Particle Motion (TPM) technique. By carefully modeling the TPM geometry, we propose a simple formula based on a kinked Worm-Like Chain model to extract the bend angle from TPM measurements. Using constructs made of 575 base-pair DNAs with in-phase assemblies of one to seven 6A-tracts, we find that the sequence CA6CGG induces a bend angle of 19° ± 4°. Our method is successfully compared to more theoretically complex or experimentally invasive ones such as cyclization, NMR, FRET or AFM. We further apply our procedure to TPM measurements from the literature and demonstrate that the angles of bends induced by proteins, such as Integration Host Factor (IHF) can be reliably evaluated as well.

Single-molecule sensing of caspase activation in live cells via plasmon coupling nanotechnology

Apoptotic caspases execute programmed cell death, where low levels of caspase activity are linked to cancer (Kasibhatla & Tseng, 2003). Chemotherapies utilize induction of apoptosis as a key mechanism for cancer treatment, where caspase-3 is a major player involved in dismantling these aberrant cells. The ability to sensitively measure the initial caspase-3 cleavage events during apoptosis is important for understanding the initiation of this complex cellular process; however, current ensemble methods are not sensitive enough to measure single cleavage events in cells. To overcome this, we describe a procedure to develop peptide-linked gold nanoparticles that have unique optical properties and can serve as beacons to visualize the apoptotic drug response in cancer cells at the single-molecule level. By thorough analyses of their trajectories, one can reveal early-stage caspase-3 activation in live cells continuously and with no ambiguity.

Intracellular synthesis of silver nanoparticle by actinobacteria and its antimicrobial activity

Intracellular synthesis of silver nanoparticles (AgNPs) using Rhodococcus spp. is demonstrated. The synthesized nanoparticles were characterized by UV-Vis spectroscopy, X-ray diffraction, energy dispersive spectroscopy, Fourier trans-form infrared spectroscopy, and transmission electron microscopy. Transmission electron microscopy study of microorganisms' revealed synthesis of nanoparticle was occurring inside the cell, in the cytoplasm. AgNPs ranged from 5 to 50 nm. Formed nanoparticles were stable in the colloidal solution due to presence of proteins on the surface. AgNPs showed excellent bactericidal and bacteriostatic activity against pathogenic microorganisms.

Widefield spectral monitoring of nanometer distance changes in DNA-templated plasmon rulers

The nanometer-scale sensitivity of electromagnetic plasmon coupling allows the translation of minute morphological changes in nanostructures into macroscopic optical signals. We demonstrate here a widefield spectral analysis of 40 nm diameter gold nanoparticle (AuNP) dimers, linked by a short DNA double strand, using a low-cost color CCD camera and allowing a quantitative estimation of interparticle distances in a 3-20 nm range. This analysis can be extended to lower spacings and a parallel monitoring of dimer orientations by performing a simple polarization analysis. Our measurement approach is calibrated against confocal scattering spectroscopy using AuNP dimers that are distorted from a stretched geometry at low ionic strength to touching particles at high salt concentrations. We then apply it to identify dimers featuring two different conformations of the same DNA template and discuss the parallel colorimetric sensing of short sequence-specific DNA single strands using dynamic plasmon rulers.

Electric field induced surface-enhanced Raman spectroscopy for multianalyte detection

This work demonstrates the ability to detect and isolate an analyte from a multianalyte mixture by SERS sensing.

A simple cyanide sensing probe based on Ag/Fe3O4nanoparticles

The first direct approach in ultra-trace cyanide determination through a simple, selective and rapid reaction by simply-synthesized recyclable Ag/Fe₃O₄nanostructures.

The conquest of middle-earth: combining top-down and bottom-up nanofabrication for constructing nanoparticle based devices

The development of top-down nanofabrication techniques has opened many possibilities for the design and realization of complex devices based on single molecule phenomena such as e.g. single molecule electronic devices. These impressive achievements have been complemented by the fundamental understanding of self-assembly phenomena, leading to bottom-up strategies to obtain hybrid nanomaterials that can be used as building blocks for more complex structures. In this feature article we highlight some relevant published work as well as present new experimental results, illustrating the versatility of self-assembly methods combined with top-down fabrication techniques for solving relevant challenges in modern nanotechnology. We present recent developments on the use of hierarchical self-assembly methods to bridge the gap between sub-nanometer and micrometer length scales. By the use of non-covalent self-assembly methods, we show that we are able to control the positioning of nanoparticles on surfaces, and to address the deterministic assembly of nano-devices with potential applications in plasmonic sensing and single-molecule electronics experiments.

Plasmonic biosensors

The unique optical properties of plasmon resonant nanostructures enable exploration of nanoscale environments using relatively simple optical characterization techniques. For this reason, the field of plasmonics continues to garner the attention of the biosensing community. Biosensors based on propagating surface plasmon resonances (SPRs) in films are the most well-recognized plasmonic biosensors, but there is great potential for the new, developing technologies to surpass the robustness and popularity of film-based SPR sensing. This review surveys the current plasmonic biosensor landscape with emphasis on the basic operating principles of each plasmonic sensing technique and the practical considerations when developing a sensing platform with the various techniques. The 'gold standard' film SPR technique is reviewed briefly, but special emphasis is devoted to the up-and-coming localized surface plasmon resonance and plasmonically coupled sensor technology.

Dark-field-based observation of single-nanoparticle dynamics on a supported lipid bilayer for in situ analysis of interacting molecules and nanoparticles

Observation of single plasmonic nanoparticles in reconstituted biological systems allows us to obtain snapshots of dynamic processes between molecules and nanoparticles with unprecedented spatiotemporal resolution and single-molecule/single-particle-level data acquisition. This Concept is intended to introduce nanoparticle-tethered supported lipid bilayer platforms that allow for the dynamic confinement of nanoparticles on a two-dimensional fluidic surface. The dark-field-based long-term, stable, real-time observation of freely diffusing plasmonic nanoparticles on a lipid bilayer enables one to extract a broad range of information about interparticle and molecular interactions throughout the entire reaction period. Herein, we highlight important developments in this context to provide ideas on how molecular interactions can be interpreted by monitoring dynamic behaviors and optical signals of laterally mobile nanoparticles.

Toward plasmonics-enabled spatiotemporal activity patterns in three-dimensional culture models

Spatiotemporal activity patterns of proteases such as matrix metalloproteinases and cysteine proteases in organs have the potential to provide insight into how organized structural patterns arise during tissue morphogenesis and may suggest therapeutic strategies to repair diseased tissues. Toward imaging spatiotemporal activity patterns, recently increased emphasis has been placed on imaging activity patterns in three-dimensional culture models that resemble tissues in vivo. Here, we briefly review key methods, based on fluorogenic modifications either to the extracellular matrix or to the protease-of-interest, that have allowed for qualitative imaging of activity patterns in three-dimensional culture models. We highlight emerging plasmonic methods that address significant improvements in spatial and temporal resolution and have the potential to enable quantitative measurement of spatiotemporal activity patterns with single-molecule sensitivity.

Nanoparticle-Film Plasmon Ruler Interrogated with Transmission Visible Spectroscopy

The widespread use of plasmonic nanorulers (PNRs) in sensing platforms has been plagued by technical challenges associated with the development of methods to fabricate precisely controlled nanostructures with high yield and characterize them with high throughput. We have previously shown that creating PNRs in a nanoparticle-film (NP-film) format enables the fabrication of an extremely large population of uniform PNRs with 100% yield using a self-assembly approach, which facilitates high-throughput PNR characterization using ensemble spectroscopic measurements and eliminates the need for expensive microscopy systems required by many other PNR platforms. We expand upon this prior work herein, showing that the NP-film PNR can be made compatible with aqueous sensing studies by adapting it for use in a transmission localized surface plasmon resonance spectroscopy format, where the coupled NP-film resonance responsible for the PNR signal is directly probed using an extinction measurement from a standard spectrophotometer. We designed slide holders that fit inside standard spectrophotometer cuvettes and position NP-film samples so that the coupled NP-film resonance can be detected in a collinear optical configuration. Once the NP-film PNR samples are cuvette-compatible, it is straightforward to calibrate the PNR in aqueous solution and use it to characterize dynamic, angstrom-scale distance changes resulting from pH-induced swelling of polyelectrolyte (PE) spacer layers as thin as 1 PE layer and also of a self-assembled monolayer of an amine-terminated alkanethiol. This development is an important step toward making PNR sensors more user-friendly and encouraging their widespread use in various sensing schemes.

Sensitive and selective plasmon ruler nanosensors for monitoring the apoptotic drug response in leukemia

Caspases are proteases involved in cell death, where caspase-3 is the chief executioner that produces an irreversible cutting event in downstream protein substrates and whose activity is desired in the management of cancer. To determine such activity in clinically relevant samples with high signal-to-noise, plasmon rulers are ideal because they are sensitively affected by their interparticle separation without ambiguity from photobleaching or blinking effects. A plasmon ruler is a noble metal nanoparticle pair, tethered in close proximity to one another via a biomolecule, that acts through dipole-dipole interactions and results in the light scattering to increase exponentially. In contrast, a sharp decrease in intensity is observed when the pair is confronted by a large interparticle distance. To align the mechanism of protease activity with building a sensor that can report a binary signal in the presence or absence of caspase-3, we present a caspase-3 selective plasmon ruler (C3SPR) composed of a pair of Zn0.4Fe2.6O4@SiO2@Au core-shell nanoparticles connected by a caspase-3 cleavage sequence. The dielectric core (Zn0.4Fe2.6O4@SiO2)-shell (Au) geometry provided a brighter scattering intensity versus solid Au nanoparticles, and the magnetic core additionally acted as a purification handle during the plasmon ruler assembly. By monitoring the decrease in light scattering intensity per plasmon ruler, we detected caspase-3 activity at single molecule resolution across a broad dynamic range. This was observed to be as low as 100 fM of recombinant material or 10 ng of total protein from cellular lysate. By thorough analyses of single molecule trajectories, we show caspase-3 activation in a drug-treated chronic myeloid leukemia (K562) cancer system as early as 4 and 8 h with greater sensitivity (2- and 4-fold, respectively) than conventional reagents. This study provides future implications for monitoring caspase-3 as a biomarker and efficacy of drugs.

Biological Targeting of Plasmonic Nanoparticles Improves Cellular Imaging via the Enhanced Scattering in the Aggregates Formed

Gold nanoparticles (AuNPs) demonstrate great promise in biomedical applications due to their plasmonically enhanced imaging properties. When in close proximity, AuNPs plasmonic fields couple together, increasing their scattering cross-section due to the formation of hot spots, improving their imaging utility. In the present study, we modified the AuNPs surface with different peptides to target the nucleus and/or the cell as a whole, resulting in similar cellular uptake but different scattering intensities. Nuclear-targeted AuNPs showed the greatest scattering due to the formation of denser nanoparticle clusters (i.e., increased localization). We also obtained a dynamic profile of AuNP localization in living cells, indicating that nuclear localization is directly related to the number of nuclear-targeting peptides on the AuNP surface. Increased localization led to increased plasmonic field coupling, resulting in significantly higher scattering intensity. Thus, biochemical targeting of plasmonic nanoparticles to subcellular components is expected to lead to more resolved imaging of cellular processes.

Mapping bright and dark modes in gold nanoparticle chains using electron energy loss spectroscopy

We present a scanning transmission electron microscopy-electron energy loss spectroscopy (STEM-EELS) investigation of gold nanosphere chains with lengths varying from 1 to 5 particles. We show localized EELS signals from the chains and identify energy-loss peaks arising due to l = 1, 2, 3, 4, and 5 plasmon modes through the use of EELS mapping. We also show the evolution of the energy of these modes as the length of a given chain increases, and we find that a chain containing N particles can accommodate at least N experimentally observable modes, in addition to the transverse mode. As the chain length is increased by the addition of one more gold particle to the chain, the new N + 1 mode becomes the highest energy mode, while the existing modes lower their energy and eventually asymptote as they delocalize along the chain. We also show that modes become increasingly difficult to detect with the EELS technique as l approaches N. The data are compared to numerical simulations.

Probing subdiffraction limit separations with plasmon coupling microscopy: concepts and applications

Due to their advantageous material properties, noble metal nanoparticles are versatile tools in biosensing and imaging. A characteristic feature of gold and silver nanoparticles is their ability to sustain localized surface plasmons that provide both large optical cross-sections and extraordinary photophysical stability. Plasmon coupling microscopy takes advantage of the beneficial optical properties and utilizes electromagnetic near-field coupling between individual noble metal nanoparticle labels to resolve subdiffraction limit separations in an all-optical fashion. This Tutorial provides an introduction into the physical concepts underlying distance dependent plasmon coupling, discusses potential experimental implementation of plasmon coupling microscopy, and reviews applications in the area of biosensing and imaging.

Quantitative imaging of single mRNA splice variants in living cells

Alternative messenger RNA (mRNA) splicing is a fundamental process of gene regulation, and errors in RNA splicing are known to be associated with a variety of different diseases. However, there is currently a lack of quantitative technologies for monitoring mRNA splice variants in cells. Here, we show that a combination of plasmonic dimer probes and hyperspectral imaging can be used to detect and quantify mRNA splice variants in living cells. The probes are made from gold nanoparticles functionalized with oligonucleotides and can hybridize to specific mRNA sequences, forming nanoparticle dimers that exhibit distinct spectral shifts due to plasmonic coupling. With this approach, we show that the spatial and temporal distribution of three selected splice variants of the breast cancer susceptibility gene, BRCA1, can be monitored at single-copy resolution by measuring the hybridization dynamics of the nanoplasmonic dimers. Our study provides insights into RNA and its transport in living cells, which could improve our understanding of cellular protein complexes, pharmacogenomics, genetic diagnosis and gene therapies.

Gold nanoparticle 3D-DNA building blocks: high purity preparation and use for modular access to nanoparticle assemblies

Using highly functional 'building-blocks' of AuNPs mono-conjugated to three-dimensional DNA 'rung' structures, both discrete and extended linear assemblies are controllably prepared via addition of various templating backbone strands. This unique approach presents a facile alternative to other methods of AuNP organization through DNA, and has potential utility in the fields of nanophotonics and nanoelectronics.

Optical imaging of individual plasmonic nanoparticles in biological samples

Imaging of plasmonic nanoparticles (PNP) with optical microscopy has aroused considerable attention in recent years. The unique localized surface plasmon resonance (LSPR) from metal nanoparticles facilitates the transduction of a chemical or physical stimulus into optical signals in a highly efficient way. It is therefore possible to perform chemical or biological assays at the single object level with the help of standard optical microscopes. Because the source of background noise from different samples is different, distinct imaging modalities have been developed to discern the signals of interest in complex surroundings. With these convenient yet powerful techniques, great improvements in chemical and biological assays have been demonstrated, and many interesting phenomena and dynamic processes have also been elucidated. Further development and application of optical imaging methods for plasmonic probes should lead to many exciting results in chemistry and biology in the future.

Nano-analysis of DNA conformation changes induced by transcription factor complex binding using plasmonic nanodimers

The plasmon resonant wavelength for a pair of gold nanoparticles, or gold nanodimer, increases inversely with the gap distance between the two nanoparticles. Taking advantage of this property, we performed nanoscale measurements of DNA conformation changes induced by transcription factor binding. Gold nanoparticles were bridged by double-stranded DC5 DNA that included binding sequences for the transcription factors SOX2 and PAX6, which interact on the DC5 enhancer sequence and activate transcription. The gold nanodimers bound by SOX2 shifted the plasmon resonant wavelength from 586.8 to 604.1 nm, indicating that SOX2 binding induces DNA bending. When the SOX2 formed a ternary complex with PAX6 on DC5, the plasmon resonant wavelength showed a further shift to 611.6 nm, indicating additional bending in the DC5 sequence. Furthermore, we investigated DNA conformation changes induced by SOX2 and PAX6 on the DC5-con sequence, which is a consensus sequence of DC5 for the PAX6 binding region that strengthens the PAX6 binding but at the same time disrupts SOX2-PAX6-dependent transcriptional activation. When the PAX6 binding sequence in DC5 was altered to DC5-con, the plasmon resonant wavelength shifted much less to 606.5 nm, which is more comparable to the 603.9 nm by SOX2 alone. These results demonstrate that SOX2-PAX6 cobinding induces a large conformation change in DC5 DNA.

Localized surface plasmon resonance: a unique property of plasmonic nanoparticles for nucleic acid detection

Localized surface plasmon resonance (LSPR) of noble metal nanoparticles (a.k.a. plasmonic nanoparticles) opens up a new horizon for advanced biomolecule sensing. However, an effective and practical sensing system still requires meticulous design to achieve good sensitivity and distinctive selectivity for routine use and high-throughput detection. In particular, the detection of DNA and RNA is crucial in biomedical research and clinical diagnostics. This review describes the fundamental aspects of LSPR and provides an overall account of how it is exploited to assist in nucleic acid sensing. The detection efficiency of each LSPR-based approach is assessed with respect to the assay design, the selection of plasmonic nanoparticles, and the choice of nucleic acid probes which influence the duplex hybridization. Judicious comparison is made among various LSPR-based approaches in terms of the assaying time, the sensitivity or lowest sensing concentration (i.e. limit of detection or LOD), and the single-base mismatch (SBM) selectivity.

Fabrication and characterization of flexible and tunable plasmonic nanostructures

We present a novel method to fabricate flexible and tunable plasmonic nanostructures based on combination of soft lithography and nanosphere lithography, and perform a comprehensive structural and optical characterization of these structures. Spherical latex particles are uniformly deposited on glass slides and used as molds for polydimethylsiloxane to obtain nanovoid structures. The diameter and depth of the nanostructures are controlled by the size of the latex particles. These surfaces are coated with a thin Ag layer for fabrication of uniform plasmonic nanostructures. Structural characterization of these surfaces is performed by SEM and AFM. Optical properties of these plasmonic nanostructures are evaluated via UV/Vis absorption spectroscopy, dark field microscopy, and surface–enhanced Raman spectroscopy (SERS). Position of the surface plasmon absorption depends on the diameter and depth of the nanostructures. SERS enhancement factor (measured up to 1.4 × 10⁶) is dependent on the plasmon absorption wavelength and laser wavelength used in these experiments.

Emerging chirality in nanoscience

Chirality in nanoscience may offer new opportunities for applications beyond the traditional fields of chirality, such as the asymmetric catalysts in the molecular world and the chiral propellers in the macroscopic world. In the last two decades, there has been an amazing array of chiral nanostructures reported in the literature. This review aims to explore and categorize the common mechanisms underlying these systems. We start by analyzing the origin of chirality in simple systems such as the helical spring and hair vortex. Then, the chiral nanostructures in the literature were categorized according to their material composition and underlying mechanism. Special attention is paid to highlight systems with original discoveries, exceptional structural characteristics, or unique mechanisms.

Functional DNA nanostructures for photonic and biomedical applications

DNA nanostructures, especially DNA origami, receive close interest because of the programmable control over their shape and size, precise spatial addressability, easy and high-yield preparation, mechanical flexibility, and biocompatibility. They have been used to organize a variety of nanoscale elements for specific functions, resulting in unprecedented improvements in the field of nanophotonics and nanomedical research. In this review, the discussion focuses on the employment of DNA nanostructures for the precise organization of noble metal nanoparticles to build interesting plasmonic nanoarchitectures, for the fabrication of visualized sensors and for targeted drug delivery. The effects offered by DNA nanostructures are highlighted in the areas of nanoantennas, collective plasmonic behaviors, single-molecule analysis, and cancer-cell targeting or killing. Finally, the challenges in the field of DNA nanotechnology for realistic application are discussed and insights for future directions are provided.

Photolabile plasmonic vesicles assembled from amphiphilic gold nanoparticles for remote-controlled traceable drug delivery

We have developed a new type of photo-responsive plasmonic vesicles that allow for active delivery of anticancer payloads to specific cancer cells and personalized drug release regulated by external photo-irradiation. Our results show that amphiphilic gold nanoparticles carrying hydrophilic poly(ethylene glycol) (PEG) and photo-responsive hydrophobic poly(2-nitrobenzyl acrylate) (PNBA) can assemble into plasmonic vesicles with gold nanoparticles embedded in the hydrophobic shell of PNBA, which can be converted into hydrophilic poly(acrylic acid) upon photo exposure. Benefiting from the interparticle plasmonic coupling of gold nanoparticles in close proximity, the plasmonic vesicles assembled from amphiphilic gold nanoparticles exhibit distinctively different optical properties from single nanoparticle units, which offer the opportunity to track the photo-triggered disassembly of the vesicles and the associated cargo release by plasmonic imaging. We have shown the dense layer of PEG grafts on the vesicles not only endow plasmonic vesicles with excellent colloidal stability, but also serve as flexible spacers for bioconjugation of targeting ligands to facilitate the specific recognition of cancer cells. The targeted delivery of model anticancer drug doxorubicin, investigated by dual-modality plasmonic and fluorescence imaging and toxicity studies, clearly demonstrated the potential of photolabile plasmonic vesicles as multi-functional drug carriers.

Long-range plasmophore rulers

Using on-wire lithography, we studied the emission properties of nanostructures made of a polythiophene disk separated by fixed nanoscopic distances from a plasmonic gold nanorod. The intense plasmonic field generated by the nanorod modifies the shape of the polythiophene emission spectrum, and the strong distance dependence of this modulation forms the basis for a new type of "plasmophore ruler". Simulations using the discrete dipole approximation (DDA) quantitatively support our experimental results. Importantly, this plasmophore ruler is independent of signal intensity and is effective up to 100 nm, which is more than two times larger than any reported value for rulers based on photoluminescence processes.

Correct spectral conversion between surface-enhanced raman and plasmon resonance scattering from nanoparticle dimers for single-molecule detection

Simultaneous measurement of surface-enhanced Raman scattering (SERS) and localized surface plasmon resonance (LSPR) in nanoparticle dimers presents outstanding opportunities in molecular identification and in the elucidation of physical properties, such as the size, distance, and deformation of target species. SERS-LSPR instrumentation exists and has been used under limited conditions, but the extraction of SERS and LSPR readouts from a single measurement is still a challenge. Herein, the extraction of LSPR spectra from SERS signals is reported and a tool for measuring the interparticle distance from Raman enhancement data by the standardization of the SERS signal is proposed. The SERS nanoruler mechanism incorporates two important aspects (the LSPR scattering peak shift and the Raman shift for measuring interparticle distance), and signifies their exact one-to-one correspondence after spectral correction. The developed methodology is applied to calculate the interparticle distance between nanoparticle dimers from SERS signals, to detect and quantify DNA at the single-molecule level in a base-pair-specific manner. It is also shown that the SERS nanoruler concept can be used in structural analysis for the specific detection of the interaction of immunoglobulin G (IgG) with its target from bianalyte Raman signals with identical shaping at single-molecule resolution. The SERS profile shaping approach not only offers a new detection mechanism for single molecules, but also has excellent potential for studying protein interactions and the intracellular detection of mRNA.

Distance-mediated plasmonic dimers for reusable colorimetric switches: a measurable peak shift of more than 60 nm

The first reconfigurable colorimetric DNA switches based on target DNA binding are reported. This DNA binding actuates a change in the interparticle distance between gold nanoparticle dimers. A significant spectral shift of 68 nm is achievable from on-off switching. The reconfigurability is possible owing to thiol and EDC-imidazole coupling which anchors the DNA linkers to the nanoparticles. The huge spectral shift allows the unaided eye to observe single target biomolecular binding event in real time under a darkfield microscope. The limit-of-detection for target molecules in PBS and human serum are 10(-13) M and 10(-11) M respectively. An improved fabrication strategy via asymmetric functionalization is also described, assisted by solid phase synthesis which minimizes the formation of trimers and multimers.

A plasmon ruler based on nanoscale photothermal effect

The determination of nanoscale distances or distance changes necessitates a nanoscale ruler. In the present paper, distance dependence of particle temperature in an optically heated gold nanoparticle pair is quantitatively investigated to explore the possibility of creating a plasmon ruler based on this effect. The two origins of the distance-dependence, i.e., electromagnetic coupling and thermal accumulative effect, are studied. For the particle temperature, a scaling behavior is found, and it suggests that the decay of particle temperature with the interparticle gap for different particle sizes follows a common exponential decay equation. This scaling behavior is qualitatively explained with a simple dipolar-coupling model combined with a point heat source interaction model. On the basis of this scaling behavior of absorption power, we further establish a plasmon ruler equation relating the particle temperature and the interparticle distance. Our findings can serve as an excellent guideline for designing and optimizing temperature-based plasmon rulers.

Reversible switching of the interparticle distance in DNA-templated gold nanoparticle dimers

We produce gold nanoparticle dimers with a surface-to-surface distance that varies reversibly by a factor of 3 when hybridizing or removing a single target DNA strand. The dimers are built on one DNA template that features a stem-loop enabling the interparticle distance change. Using electrophoresis, we reach 90% sample purities and demonstrate that this chemical process is reversible in solution at room temperature for a low molar excess of the target DNA strand. The kinetics of the reaction is asymmetric due to steric hindrance in the stem-loop opening process. Furthermore, a statistical analysis of cryo-electron microscopy measurements allows us to provide the first quantitative analysis of distance changes in chemically switchable nanoparticle assemblies.

Glycolic acid functionalized chitosan-Au-Fe₃O₄ hybrid nanoparticle based nanohybrid scaffold for drug delivery

The research on biomedical applications of nanoparticles has seen an upsurge in recent years due to their unique capabilities in treatment of ailments. The present paper reports the synthesis of Au-Fe(3)O(4) hybrid nanoparticles. The formation of these nanoparticles was confirmed by transmission electron microscopy (TEM) and physical property measurement system (PPMS). Next step of this paper reveals potential use of novel hybrid of chitosan-g-glycolic acid and Au-Fe(3)O(4) hybrid nanoparticles in controlled drug delivery and tissue engineering applications. Grafting of glycolic acid and drug loading in porous scaffold was characterized by Fourier transform infrared spectroscopy. The nanohybrid scaffolds were found to be stable regardless of pH of the medium and play a key role in cell adhesion, proliferation and migration. Au-Fe(3)O(4) hybrid nanoparticles reinforcement was found to control the drug (cyclophosphamide) release rate in phosphate buffer saline solution (pH 7.4). Therefore, Au-Fe(3)O(4) hybrid nanoparticles are viable additive for formulating sustained drug delivery systems based on glycolic acid grafted chitosan. The cell proliferation profile also shows that prepared nanohybrid is biocompatible providing suitable substrates for tissue engineering.