Stimuli-responsive plasmonic core-satellite assemblies: i-motif DNA linker enabled intracellular pH sensing

In situ stimulus-responsive self-assembled nanomaterials for drug delivery and disease treatment

The individual motifs that respond to specific stimuli for the self-assembly of nanomaterials play important roles. In situ constructed nanomaterials are formed spontaneously without human intervention and have promising applications in bioscience. However, due to the complex physiological environment of the human body, designing stimulus-responsive self-assembled nanomaterials in vivo is a challenging problem for researchers. In this article, we discuss the self-assembly principles of various nanomaterials in response to the tissue microenvironment, cell membrane, and intracellular stimuli. We propose the applications and advantages of in situ self-assembly in drug delivery and disease diagnosis and treatment, with a focus on in situ self-assembly at the lesion site, especially in cancer. Additionally, we introduce the significance of introducing exogenous stimulation to construct self-assembly in vivo. Based on this foundation, we put forward the prospects and possible challenges in the field of in situ self-assembly. This review uncovers the relationship between the structure and properties of in situ self-assembled nanomaterials and provides new ideas for innovative drug molecular design and development to solve the problems in the targeted delivery and precision medicine.

Analyte Co-localization at Electromagnetic Gap Hot-Spots for Highly Sensitive (Bio)molecular Detection by Plasmon Enhanced Spectroscopies

Electromagnetic hot-spots at ultranarrow plasmonic nanogaps carry immense potential to drive detection limits down to few molecules in sensors based on surface-enhanced Raman or fluorescence spectroscopies. However, leveraging the EM hot-spots requires access to the gaps, which in turn depends on the size of the analyte in relation to gap distances. Herein, we leverage a well-calibrated process based on self-assembly of block copolymer colloids on a full-wafer level to produce high-density plasmonic nanopillar arrays exhibiting a large number (>10¹⁰ cm^-2) of uniform interpillar EM hot-spots. The approach allows convenient handles to systematically vary the interpillar gap distances down to a sub-10 nm regime. The results show compelling trends of the impact of analyte dimensions in relation to the gap distances toward their leverage over interpillar hot-spots and the resulting sensitivity in SERS-based molecular assays. Comparing the detection of labeled proteins in surface-enhanced Raman and metal-enhanced fluorescence configurations further reveal the relative advantage of fluorescence over Raman detection while encountering the spatial limitations imposed by the gaps. Quantitative assays with limits of detection down to picomolar concentrations are realized for both small organic molecules and proteins. The well-defined geometries delivered by a nanofabrication approach are critical to arriving at realistic geometric models to establish meaningful correlation between the structure, optical properties, and sensitivity of nanopillar arrays in plasmonic assays. The findings emphasize the need for the rational design of EM hot-spots that takes into account the analyte dimensions to drive ultrahigh sensitivity in plasmon-enhanced spectroscopies.

Biomacromolecular-Assembled Nanoclusters: Key Aspects for Robust Colloidal SERS Sensing

Superstructures of gold nanospheres offer augmented surface-enhanced Raman scattering (SERS) activities beyond the limits of their individual building blocks. However, for application as reliable and quantitative colloidal SERS probes, some key aspects need to be considered to combine efficiency and robustness with respect to hotspot excitation, analyte adsorption, signal stability, and colloidal stability. For this purpose, we studied core/satellite superstructures with spherical cores as a simple optically isotropic model system. Superstructures of different core sizes were assembled using bovine serum albumin (BSA), which serves as a non-specific biomacromolecular linker and provides electrosteric stabilization. We show that the "noisy" spectral footprint of the protein coating may serve as an internal standard, which allows accurate monitoring of the adsorption kinetics of analytes. The SERS activity was quantified using 4-mercaptobenzoic acid (MBA) as an aromatic low-molecular-weight model analyte. The molar SERS efficiency was studied by variation of the particle (Au⁰) and analyte concentrations with a limit of detection of 10^-7 M MBA. The practical importance of colloidal stability for robust measurement conditions was demonstrated by comparing the superstructures with their citrate-stabilized or protein-coated building blocks. We explain the theoretical background of hotspot formation by a leader/follower relationship of asymmetric control between the core and the satellites and give practical guidelines for robust colloidal SERS sensing probes.

Rational Design of Memory-Based Sensors: the Case of Molecular Calorimeters

Thermodynamic characterization is crucial for understanding molecular interactions. However, methodologies for measuring heat changes in small open systems are extremely limited. We document a new approach for designing molecular sensors, that function as calorimeters: sensors based on memory. To design a memory-based sensor, we take advantage of the unique kinetic properties of nucleic acid scaffolds. Particularly, we elaborate on the differences in folding and unfolding rates in nucleic acid quadruplexes. DNA-based i-motifs unfold fast in response to small heats but do not fold back when the system is equilibrated with surroundings. We translated this behavior into a molecular memory function that enables the measurement of heat changes in open environments. The new sensors are biocompatible, operate homogeneously, and measure small heats released over long time periods. As a proof-of-concept, we demonstrate how the molecular calorimeters report heat changes generated in water/propanol mixing and in ligand/protein binding.

Large area Al2O3-Au raspberry-like nanoclusters from iterative block-copolymer self-assembly

In the field of functional nanomaterials, core–satellite nanoclusters have recently elicited great interest due to their unique optoelectronic properties. However, core–satellite synthetic routes to date are hampered by delicate and multistep reaction conditions and no practical method has been reported for the ordering of these structures onto a surface monolayer. Herein we show a reproducible and simplified thin film process to fabricate bimetallic raspberry nanoclusters using block copolymer (BCP) lithography. The fabricated inorganic raspberry nanoclusters consisted of a ∼36 nm alumina core decorated with ∼15 nm Au satellites after infusing multilayer BCP nanopatterns. A series of cylindrical BCPs with different molecular weights allowed us to dial in specific nanodot periodicities (from 30 to 80 nm). Highly ordered BCP nanopatterns were then selectively infiltrated with alumina and Au species to develop multi-level bimetallic raspberry features. Microscopy and X-ray reflectivity analysis were used at each fabrication step to gain further mechanistic insights and understand the infiltration process. Furthermore, grazing-incidence small-angle X-ray scattering studies of infiltrated films confirmed the excellent order and vertical orientation over wafer scale areas of Al₂O₃/Au raspberry nanoclusters. We believe our work demonstrates a robust strategy towards designing hybrid nanoclusters since BCP blocks can be infiltrated with various low cost salt-based precursors. The highly controlled nanocluster strategy disclosed here could have wide ranging uses, in particular for metasurface and optical based sensor applications.

Large area Al₂O₃–Au raspberry-like nanoclusters and other complex structures have been created by iterative block-copolymer self-assembly, paving the way to a new generation of on-demand metallic architectures.

Nucleic-Acid Structures as Intracellular Probes for Live Cells

The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.

Controllable "Clicked-to-Assembled" Plasmonic Core-Satellite Nanostructures and Its Surface-Enhanced Fluorescence in Living Cells

The assembly of noble-metal core-satellite (CS) nanostructures is an appealing means to control their plasmonic properties for their applications such as surface-enhanced fluorescence or Raman scattering. However, till now there is a lack of some rapid or convenient methods to construct stable CS nanostructures. Here, we proposed a "clicked-to-assembly" strategy based on the fast and specific "click chemistry" reaction between trans-cyclooctene (TCO) and 1,2,4,5-tetrazine (Tz). The CS nanostructures were constructed within 8 min by simple mixing of TCO- or Tz-modified nanoparticles (TCO-NPs or Tz-NPs) without any catalysts or heating required. Transmission electron microscopy experiments show that the constructed CS nanostructures are uniform, and particularly the number of "satellite" nanoparticles in the core surface is controllable by simply adjusting the feeding ratio of TCO-NPs or Tz-NPs in the reaction. The strong surface plasmon coupling effect (SPCE) was observed in these CS nanostructures, which was dependent on the coverage degree, size and composition of the satellite, and core NPs. The nanostructures with tuned surface plasmon resonance (SPR) effect were tried for the surface-enhanced fluorescence in living cells. Such well-defined CS nanostructures could potentially serve as efficient SPR-enhanced fluorescent probes as diagnostics or biomedical imaging agents in nanomedicine.

i-Motif DNA: structural features and significance to cell biology

The i-motif represents a paradigmatic example of the wide structural versatility of nucleic acids. In remarkable contrast to duplex DNA, i-motifs are four-stranded DNA structures held together by hemi- protonated and intercalated cytosine base pairs (C:C⁺). First observed 25 years ago, and considered by many as a mere structural oddity, interest in and discussion on the biological role of i-motifs have grown dramatically in recent years. In this review we focus on structural aspects of i-motif formation, the factors leading to its stabilization and recent studies describing the possible role of i-motifs in fundamental biological processes.

DNA i-Motifs With Guanidino-i-Clamp Residues: The Counterplay Between Kinetics and Thermodynamics and Implications for the Design of pH Sensors

I-motif structures, adopted by cytosine-rich DNA strands, have attracted considerable interest as possible regulatory elements in genomes. Applied science exploits the advantages of i-motif stabilization under acidic conditions: i-motif-based pH sensors and other biocompatible nanodevices are being developed. Two key characteristics of i-motifs as core elements of nanodevices, i.e., their stability under physiological conditions and folding/unfolding rates, still need to be improved. We have previously reported a phenoxazine derivative (i-clamp) that enhances the thermal stability of the i-motif and shifts the pH transition point closer to physiological values. Here, we performed i-clamp guanidinylation to further explore the prospects of clamp-like modifications in i-motif fine-tuning. Based on molecular modeling data, we concluded that clamp guanidinylation facilitated interstrand interactions in an i-motif core and ultimately stabilized the i-motif structure. We tested the effects of guanidino-i-clamp insertions on the thermal stabilities of genomic and model i-motifs. We also investigated the folding/unfolding kinetics of native and modified i-motifs under moderate, physiologically relevant pH alterations. We demonstrated fast folding/unfolding of native genomic and model i-motifs in response to pH stimuli. This finding supports the concept of i-motifs as possible genomic regulatory elements and encourages the future design of rapid-response pH probes based on such structures. Incorporation of guanidino-i-clamp residues at/near the 5′-terminus of i-motifs dramatically decreased the apparent unfolding rates and increased the thermal stabilities of the structures. This counterplay between the effects of modifications on i-motif stability and their effects on kinetics should be taken into account in the design of pH sensors.

Self-Assembly of Polymer-Coated Plasmonic Nanocrystals: From Synthetic Approaches to Practical Applications

Self-assembly of plasmonic nanocrystals (PNCs) and polymers provides access to a variety of functionalized metallic-polymer building blocks and higher-order hybrid plasmonic assemblies, and thus is of considerable fundamental and practical interest. The hybrid assemblies often not only inherit individual characteristics of polymers and PNCs but also exhibit distinct photophysical and catalytic properties compared to that of a single PNC building block. The tailorable plasmonic coupling between PNCs within assemblies enables the precise control over localized surface plasmon resonance, which subsequently affords a series of light-driven or photo-activated applications, such as surface-enhanced Raman scattering detection, photoacoustic imaging, photothermal therapy, and photodynamic therapy. In this review, the synthetic strategies of a library of PNC-polymer hybrid building blocks and corresponding assemblies are summarized along with the mechanisms of polymer-assisted self-assembly of PNCs and the concepts for bridging the intrinsic properties of PNC-polymer assemblies to widespread practical applications.

Probing the conformational switch of I-motif DNA using tunable resistive pulse sensing

I-motif DNA, which can fold and unfold reversibly in various environments, plays a significant role in DNA nanotechnology and biological functions. Thus, it is of fundamental importance to identify the different conformations of i-motif DNA. Here, we demonstrate that distinct structures of i-motif DNA conjugated to polystyrene spheres can be distinguished through tunable resistive pulse sensing technique. When dispersed in acidic buffer, i-motif DNA coating on polystyrene spheres would fold into quadruplex structure and subsequently induce an apparent increase in the translocation duration time upon passing through a nanopore due to the shielding effect of the surface charge of the nanospheres. However, if the DNA strands don't have conformational changes in acidic buffer, little shift can be observed in the translocation duration time of the DNA functionalized polystyrene spheres. A before-and-after assay was also performed to illustrate the fast speed of i-motif DNA folding using this technique. The successful implementation of tunable resistive pulse sensing to monitor the conformational transition of i-motif DNA provides a potential tool to detect the structural changes of DNA and an alternative approach to study the function of DNA structures.

A Gold Nanoparticle Bio-Optical Transponder to Dynamically Monitor Intracellular pH

A pH-sensitive bio-optical transponder (pH-BOT) capable of simultaneously reporting the timing of intracellular DNA cargo release from a gold nanoparticle (AuNP) and the evolving intracellular pH (pH i) during endosomal maturation is demonstrated. The pH-BOT is designed with a triple-dye-labeled duplex DNA appended to a 6.6 nm AuNP, utilizing pH-responsive fluorescein paired with DyLight405 as a surface energy transfer (SET) coupled dye pair to ratiometrically report the pH at and after cargo release. A non-SET-coupled dye, DyLight 700, is used to provide dynamic tracking throughout the experiment. The pH-BOT beacon of the cargo uptake, release, and processing was visualized using live-cell confocal fluorescent microscopy in Chinese hamster ovary cells, and it was observed that while maturation of endosomes carrying pH-BOT is slowed significantly, the pH-BOT is distributed throughout the endolysosomal system while remaining at pH ∼6. This observed decoupling of endosomal maturation from acidification lends support to those models that propose that pH alone is not sufficient to explain endosomal maturation and may enable greater insight into our understanding of the fundamental processes of biology.

Thermoresponsive plasmonic core-satellite nanostructures with reversible, temperature sensitive optical properties

Herein is described a facile method for the assembly of plasmonic gold nanoparticles into smart plasmonic core-satellite nanostructures that allow for the dynamic and reversible tuning of the localised surface plasmon resonance using temperature. This smart system takes advantage of the thermoresponsive polymer linker that modulates the gap distance between the core and satellites in response to the temperature, resulting in the tuning of the surface plasmon coupling and resultant optical shift. It permits optical shifts over a wide wavelength range and reversible control of the optical properties by altering the temperature, which may allow these systems to become candidates for temperature sensitive nanosensors.

Au-Protected Ag Core/Satellite Nanoassemblies for Excellent Extra-/Intracellular Surface-Enhanced Raman Scattering Activity

Silver nanoparticles (AgNPs) and their assembled nanostructures such as core/satellite nanoassemblies are quite attractive in plasmonic-based applications. However, one biggest drawback of the AgNPs is the poor chemical stability which also greatly limits their applications. We report fine Au coating on synthesized quasi-spherical silver nanoparticles (AgNSs) with few atomic layers to several nanometers by stoichiometric method. The fine Au coating layer was confirmed by energy-dispersive X-ray spectroscopy elemental mapping and aberration-corrected high-angle annular dark-field scanning transmission electron microscopy. The optimized minimal thickness of Au coating layer on different sized AgNSs (22 nm Ag@0.9 nm Au, 44 nm Ag@1.8 nm Au, 75 nm Ag@2.9 nm Au, and 103 nm Ag@0.9 nm Au) was determined by extreme chemical stability tests using H₂O₂, NaSH, and H₂S gas. The thin Au coating layer on AgNSs did not affect their plasmonic-based applications. The core/satellite assemblies based on Ag@Au NPs showed the comparable SERS intensity and uniformity three times higher than that of noncoated Ag core/satellites. The Ag@Au core/satellites also showed high stability in intracellular SERS imaging for at least two days, while the SERS of the noncoated Ag core/satellites decayed significantly. These spherical Ag@Au NPs can be widely used and have great advantages in plasmon-based applications, intracellular SERS probes, and other biological and analytical studies.

Self-Assembled Raspberry-Like Core/Satellite Nanoparticles for Anti-Inflammatory Protein Delivery

Functional proteins are very promising for protein therapeutics; however, effective delivery of therapeutic proteins remains challenging. Herein, we developed novel core/satellite nanoparticles by tethering therapeutic proteins to the core/shell polymeric particle surface through cucurbit[8]uril (CB[8])-mediated host-guest interactions. The effectiveness of the core/satellite nanoparticles as protein carrier was demonstrated through the intra-articular delivery of interleukin-1 receptor antagonist (IL-1Ra). We showed that IL-1Ra can effectively self-assemble onto the surface of the polymeric nanoparticles and maintained good protein bioactivity by inhibiting IL-1-mediated signaling. More importantly, in vivo results revealed that IL-1Ra-bounded core/satellite nanoparticles could significantly increase the retention time of IL-1Ra in the rat stifle joint compared to soluble IL-1Ra, which could greatly improve the efficacy of IL-1Ra. These results indicate that the facile host-guest self-assembly can be exploited as an effective approach for realizing the therapeutic potential of proteins.

Controlling DNA-nanoparticle serum interactions

Understanding the interaction of molecularly assembled nanoparticles with physiological fluids is critical to their use for in vivo delivery of drugs and contrast agents. Here, we systematically investigated the factors and mechanisms that govern the degradation of DNA on the nanoparticle surface in serum. We discovered that a higher DNA density, shorter oligonucleotides, and thicker PEG layer increased protection of DNA against serum degradation. Oligonucleotides on the surface of nanoparticles were highly resistant to DNase I endonucleases, and degradation was carried out exclusively by protein-mediated exonuclease cleavage and full-strand desorption. These results enabled the programming of the degradation rates of the DNA-assembled nanoparticle system from 0.1 to 0.7 h^-1 and the engineering of superstructures that can release two different preloaded dye molecules with distinct kinetics and half-lives ranging from 3.3 to 9.8 h. This study provides a general framework for investigating the serum stability of DNA-containing nanostructures. The results advance our understanding of engineering principles for designing nanoparticle assemblies with controlled in vivo behavior and present a strategy for storage and multistage release of drugs and contrast agents that can facilitate the diagnosis and treatment of cancer and other diseases.

Gold-Planet-Silver-Satellite Nanostructures Using RAFT Star Polymer

The hierarchical self-assembly of distinct nanoelements into precisely ordered nanostructures requires efficient and flexible fabrication strategies. Herein, we report the precise fabrication of bimetallic gold-planet-silver-satellite nanoparticle-arrangements employing RAFT star polymers as particle linker connecting gold nanoparticles (AuNPs) and silver nanoparticles (AgNPs) with judiciously modified surface activity. The strengths of this approach include the adjustability of interparticle distances by tailoring the star polymer molar mass. The prepared nanoassemblies have well-defined structures in which a planet AuNP (∼13 nm) is encompassed by several satellite AgNPs (∼8 nm), thus incorporating the properties of both AuNPs and AgNPs, as confirmed by transmission electron microscopy and UV-vis spectra. Our results highlight the general applicability of RAFT star polymers as a nanosynthesis platform for synthesizing noble metal nanocomposites.

Protein-Assisted Assembly of Modular 3D Plasmonic Raspberry-like Core/Satellite Nanoclusters: Correlation of Structure and Optical Properties

We present a bottom-up assembly route for a large-scale organization of plasmonic nanoparticles (NPs) into three-dimensional (3D) modular assemblies with core/satellite structure. The protein-assisted assembly of small spherical gold or silver NPs with a hydrophilic protein shell (as satellites) onto larger metal NPs (as cores) offers high modularity in sizes and composition at high satellite coverage (close to the jamming limit). The resulting dispersions of metal/metal nanoclusters exhibit high colloidal stability and therefore allow for high concentrations and a precise characterization of the nanocluster architecture in dispersion by small-angle X-ray scattering (SAXS). Strong near-field coupling between the building blocks results in distinct regimes of dominant satellite-to-satellite and core-to-satellite coupling. High robustness against satellite disorder was proved by UV/vis diffuse reflectance (integrating sphere) measurements. Generalized multiparticle Mie theory (GMMT) simulations were employed to describe the electromagnetic coupling within the nanoclusters. The close correlation of structure and optical property allows for the rational design of core/satellite nanoclusters with tailored plasmonics and well-defined near-field enhancement, with perspectives for applications such as surface-enhanced spectroscopies.

The analytical and biomedical potential of cytosine-rich oligonucleotides: A review

Polycytosine DNA strands are often found among natural sequences, including the ends of telomeres, centromeres, and introns or in the regulatory regions of genes. A characteristic feature of oligonucleotides that are rich in cytosine (C-rich) is their ability to associate under acidic conditions to form a tetraplex i-motif consisting of two parallel stranded cytosine-hemiprotonated cytosine (C·C+) base-paired duplexes that are mutually intercalated in an antiparallel orientation. Nanotechnology has been exploiting the advantages of i-motif pH-dependent formation to fabricate nanomachines, nanoswitches, electrodes and intelligent nanosurfaces or nanomaterials. Although a few reviews regarding the structure, properties and applications of i-motifs have been published, this review focuses on recently developed biosensors (e.g., to detect pH, glucose or silver ions) and drug-delivery biomaterials. Furthermore, we have included examples of sensors based on parallel C-rich triplexes and silver nanoclusters (AgNCs) fabricated on cytosine-rich DNA strands. The potential diagnostic and therapeutic applications of this type of material are discussed.

Nanomanufacturing: A Perspective

Nanomanufacturing, the commercially scalable and economically sustainable mass production of nanoscale materials and devices, represents the tangible outcome of the nanotechnology revolution. In contrast to those used in nanofabrication for research purposes, nanomanufacturing processes must satisfy the additional constraints of cost, throughput, and time to market. Taking silicon integrated circuit manufacturing as a baseline, we consider the factors involved in matching processes with products, examining the characteristics and potential of top-down and bottom-up processes, and their combination. We also discuss how a careful assessment of the way in which function can be made to follow form can enable high-volume manufacturing of nanoscale structures with the desired useful, and exciting, properties.

Regulation of telomeric i-motif stability by 5-methylcytosine and 5-hydroxymethylcytosine modification

The two important epigenetic markers in the human genome, 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC), are involved in gene regulation processes. As a major epigenetic target, cytosines in a C-rich DNA sequence were substituted with mC and hmC to investigate the thermal stability and pH sensitivity of the corresponding i-motifs. Circular Dichroism (CD) studies indicate the formation of i-motifs at acidic pH (<6.5) for mC- and hmC-modified DNA sequences. Thermal denaturation results suggest that DNA i-motifs are stabilized when modified with one or two mCs. However, hypermethylation with mC and single modification with hmC cause destabilization of the structure. A biomimetic crowding agent does not alter the stability effect trends resulting from mC and hmC modifications, though the corresponding i-motifs show elevated melting temperatures without significant changes in pKa values.

Robust Nanoparticle-DNA Conjugates Based on Mussel-Inspired Polydopamine Coating for Cell Imaging and Tailored Self-Assembly

We have demonstrated that mussel-inspired polydopamine can serve as an intermediate coating layer for covalently attaching oligonucleotides on nanostructures of diverse chemical nature, which are made possible by the universal adhesion and spontaneous reactivity of polydopamine. Our results have shown that polydopamine can strongly bond to representative nanoparticles (i.e., Au nanoparticles and magnetic polymer nanobeads) and form a thin layer of coating that allows for attachment of commercially available DNA with thiol or amine end functionality. The resulting DNA-nanoparticle conjugates not only show excellent chemical and thermal stability and high loading density of DNA, but the linked DNA also maintain their biological functions in directing cancer cell targeting and undergo DNA hybridization to form multifunctional magnetic core-plasmonic satellite assemblies. The generally applicable strategy opens new opportunities for easy adoption of DNA-nanoparticle conjugates for broad applications in biosensors and nanomedicine.

In-stem thiazole orange reveals the same triplex intermediate for pH and thermal unfolding of i-motifs

The unfolding pathway of human telomeric i-motifs was monitored by both monomer and exciplex fluorescence of in-stem thiazole orange. A uniform triplex intermediate was determined upon unfolding i-motifs against either pH or thermal denaturation.

A regenerated electrochemical biosensor for label-free detection of glucose and urea based on conformational switch of i-motif oligonucleotide probe

Improving the reproducibility of electrochemical signal remains a great challenge over the past decades. In this work, i-motif oligonucleotide probe-based electrochemical DNA (E-DNA) sensor is introduced for the first time as a regenerated sensing platform, which enhances the reproducibility of electrochemical signal, for label-free detection of glucose and urea. The addition of glucose or urea is able to activate glucose oxidase-catalyzed or urease-catalyzed reaction, inducing or destroying the formation of i-motif oligonucleotide probe. The conformational switch of oligonucleotide probe can be recorded by electrochemical impedance spectroscopy. Thus, the difference of electron transfer resistance is utilized for the quantitative determination of glucose and urea. We further demonstrate that the E-DNA sensor exhibits high selectivity, excellent stability, and remarkable regenerated ability. The human serum analysis indicates that this simple and regenerated strategy holds promising potential in future biosensing applications.

Dual-stimuli responsive i-motif/nanoflares for sensing ATP in lysosomes

A dual-stimuli responsive i-motif/nanoflare for molecule detection in lysosomes was designed. By combining the structure-switchable i-motif sequence and high recognition ability of an adenosine triphosphate (ATP) aptamer, subcellular sensing and visualization sensing of ATP in lysosomes at the subcellular level can be achieved. This general sensing technique can be applied for a broad range of cellular communication studies to improve our understanding of subcellular signaling and function.

Bio-Enabled Gold Superstructures with Built-In and Accessible Electromagnetic Hotspots

The bio-enabled synthesis of a novel class of surface enhanced Raman scattering probes is presented for functional imaging with built-in and accessible electromagnetic hotspots formed between densely packed satellites grown on a plasmonic core. The superstructures serve as nanoscale sensors to spatiotemporally map intravesicular pH changes along endocytic pathways inside live cells.

Remote Giant Multispectral Plasmonic Shifts of Labile Hinged Nanorod Array via Magnetic Field

We report a remotely mediated and fast responsive plasmonic-magnetic nanorod array with extremely large variability in optical appearance (up to 100 nm shifts in scattering maxima) and concurrently for multiple wavelengths in a broad range from UV-vis to near-infrared (at 450, 550, and 670 nm) with an external magnetic field with variable direction. The observed phenomenon demonstrates a rapid, wide-range response controlled via a noninvasive remote stimulus. The remotely controlled system suggested here is a magnetic field-directed assembly of an ordered monolayer array of unipolar oriented magnetic-plasmonic nickel-gold nanorods flexibly hinged to a sticky substrate. The unique geometry of the mobile nanorod array allows for the instant alteration of the surface plasmon polariton modes in the gold segment of the controllably tilting nanorods. This design demonstrates the utility of hybrid bimetallic nanoparticles and gives a novel approach to the design of fast-acting, remotely controlled color-changing nanomaterials for sensing and interfacial transport.

Effect of interior loop length on the thermal stability and pK(a) of i-motif DNA

The four-stranded i-motif (iM) conformation of cytosine-rich DNA is important in a wide variety of biochemical systems ranging from its use in nanomaterials to a potential role in oncogene regulation. An iM is stabilized by acidic pH that allows hemiprotonated cytidines to form a C·C(+) base pair. Fundamental studies that aim to understand how the lengths of loops connecting the protonated C·C(+) pairs affect intramolecular iM physical properties are described here. We characterized both the thermal stability and the pK(a) of intramolecular iMs with differing loop lengths, in both dilute solutions and solutions containing molecular crowding agents. Our results showed that intramolecular iMs with longer central loops form at pHs and temperatures higher than those of iMs with longer outer loops. Our studies also showed that increases in thermal stability of iMs when molecular crowding agents are present are dependent on the loop that is lengthened. However, the increase in pK(a) for iMs when molecular crowding agents are present is insensitive to loop length. Importantly, we also determined the proton activity of solutions containing high concentrations of molecular crowding agents to ascertain whether the increase in pK(a) of an iM is caused by alteration of this activity in buffered solutions. We determined that crowding agents alone increase the apparent pK(a) of a number of small molecules as well as iMs but that increases to iM pK(a) were greater than that expected from a shift in proton activity.

A sensitive assay of mercury using fluorescence correlation spectroscopy of gold nanoparticles

We described a new and sensitive method for the determination of mercury ions (Hg(2+) ) on the basis of fluorescence correlation spectroscopy (FCS) and recognition of oligonucleotides. In this assay, 30-nm gold nanoparticles (GNPs) were modified with oligonucleotides containing thymine bases (T) as fluorescent probes, and the principle of this assay was based on the specific binding of Hg(2+) by two DNA thymine bases. When two GNPs labelled with different oligonucleotides were mixed with a sample containing Hg(2+), the T-Hg(2+)-T binding reaction should cause GNPs to form dimers (or oligomers), which would lead to a significant increase in the characteristic diffusion time of GNPs in the detection volume. The FCS method is a single molecule detection method and can sensitively detect the change in the characteristic diffusion time of GNPs before and after binding reactions. The quantitative analysis was performed according to the relation between the change in the characteristic diffusion time of GNPs and the concentration of Hg(2+). Under optimal conditions, the linear range of this method was from 0.3 nM to 100 nM, and the detection limit was 0.14 nM for Hg(2+). This new method was successfully applied for direct determination of Hg(2+) levels in water and cosmetics samples.

SERS-encoded nanogapped plasmonic nanoparticles: growth of metallic nanoshell by templating redox-active polymer brushes

We report a new strategy to synthesize core-shell metal nanoparticles with an interior, Raman tag-encoded nanogap by taking advantage of nanoparticle-templated self-assembly of amphiphilic block copolymers and localized metal precursor reduction by redox-active polymer brushes. Of particular interest for surface-enhanced Raman scattering (SERS) is that the nanogap size can be tailored flexibly, with the sub-2 nm nanogap leading to the highest SERS enhancement. Our results have further demonstrated that surface functionalization of the nanogapped Au nanoparticles with aptamer targeting ligands allows for specific recognition and ultrasensitive detection of cancer cells. The general applicability of this new synthetic strategy, coupled with recent advances in controlled wet-chemical synthesis of functional nanocrystals, opens new avenues to multifunctional core-shell nanoparticles with integrated optical, electronic, and magnetic properties.

Functional DNA nanomaterials for sensing and imaging in living cells

Recent developments in integrating high selectivity of functional DNA, such as DNAzymes and aptamers, with efficient DNA delivery into cells by gold nanoparticles or superior near-infrared optical properties of upconversion nanoparticles are reviewed. Their applications in sensing and imaging small organic metabolites, toxins, metal ions, pH, DNA, RNA, proteins, and pathogens are summarized. The advantages and future directions of these functional DNA materials are discussed.

Self assembly of plasmonic core–satellite nano-assemblies mediated by hyperbranched polymer linkers

The morphology of plasmonic nano-assemblies has a direct influence on optical properties, such as localised surface plasmon resonance (LSPR) and surface enhanced Raman scattering (SERS) intensity.

Biodegradable theranostic plasmonic vesicles of amphiphilic gold nanorods

We have developed surface-initiated organocatalytic ring-opening polymerization on functional nanocrystals and synthesized amphiphilic gold nanorods carrying well-defined mixed polymer brushes of poly(ethylene glycol) and polylactide. Self-assembly of the amphiphilic gold nanorods affords biodegradable plasmonic vesicles that can be destructed by both enzymatic degradation and near-infrared photothermal heating. When tagged with Raman probes, strongly coupled gold nanorods in the self-assembled vesicles give rise to highly active SERS signals. The biodegradable plasmonic vesicles exhibit a unique combination of optical and structural properties that are of particular interest for theranostic applications. We have demonstrated that bioconjugated SERS-active plasmonic vesicles can specifically target EpCAM-positive cancer cells, leading to ultrasensitive spectroscopic detection of cancer cells. Furthermore, integration of photothermal effect of gold nanorods and large loading capacity of the vesicles provides opportunities for localized synergistic photothermal ablation and photoactivated chemotherapy, which have shown higher efficiency in killing targeted cancer cells than either single therapeutic modality. The versatile chemistry of organocatalytic ring-opening polymerization, in conjugation with recent development in synthesizing functional nanocrystals with tailored optical, electronic, and magnetic properties opens the possibilities for constructing multifunctional biodegradable platforms for clinical translation.

pH-Induced conformational change and dimerization of DNA chains investigated by analytical ultracentrifugation

pH-induced conformational change of i-motif DNA has been studied by analytical ultracentrifugation. As pH increases, the hydrodynamic radius of individual DNA chains in aqueous solutions prepared by being heat-treated suddenly increases while the molar mass is constant, indicating that the conformation changes from an i-motif to a random coil. When DNA concentrations are higher than 1.0 μM, relatively stable dimers are formed as pH sharply decreases from 7.5 to 4.5. Moreover, the weight percentage of the dimers increases with the initial DNA concentration. The study can help to understand the functions of the telomeres containing repeated cytosine-rich sequences and to develop DNA-based devices.