Distance dependence of single-fluorophore quenching by gold nanoparticles studied on DNA origami

A facile dual-mode SERS/fluorescence aptasensor for AFB1 detection based on gold nanoparticles and magnetic nanoparticles

Aflatoxin B1 (AFB1) is a virulent metabolite secreted by Aspergillus fungi, impacting crop quality and posing health risks to human. Herein, a dual-mode Raman/fluorescence aptasensor was constructed to detect AFB1. The aptasensor was assembled by gold nanoparticles (AuNPs) and magnetic nanoparticles (MNPs), while the surface-enhanced Raman scattering (SERS) and fluorescence resonance energy transfer (FRET) effects were both realized. AuNPs were modified with the Raman signal molecule 4-MBA and the complementary chain of AFB1 aptamer (cDNA). MNPs were modified with the fluorescence signal molecule Cy5 and the AFB1 aptamer (AFB1 apt). Through base pairing, AuNPs aggregated on the surface of MNPs, forming a satellite-like nanocomposite, boosting SERS signal via increased "hot spots" but reducing fluorescence signal due to the proximity of AuNPs to Cy5. Upon exposure to AFB1, AFB1 apt specifically bound to AFB1, causing AuNPs detachment from MNPs, weakening the SERS signal while restoring the fluorescence signal. AFB1 concentration displayed a good linear relationship with SERS/fluorescence signal in the range of 0.01 ng/mL-100 ng/mL, with a detection limit as low as 5.81 pg/mL. The use of aptamer assured the high selectivity toward AFB1. Furthermore, the spiked recovery in peanut samples ranged from 91.4 % to 95.6 %, indicating the applicability of real sample detection. Compared to single-signal sensor, this dual-signal sensor exhibited enhanced accuracy, robust anti-interference capability, and increased flexibility, promising for toxin detection in food safety applications.

Cooperative dynamics of DNA-grafted magnetic nanoparticles optimize magnetic biosensing and coupling to DNA origami

Magnetic nanoparticles (MNPs) provide new opportunities for enzyme-free biosensing of nucleic acid biomarkers and magnetic actuation by patterning on DNA origami, yet how the DNA grafting density affects their dynamics and accessibility remains poorly understood. Here, we performed surface functionalization of MNPs with single-stranded DNA (ssDNA) via click chemistry with a tunable grafting density, which enables the encapsulation of single MNPs inside a functional polymeric layer. We used several complementary methods to show that particle translational and rotational dynamics exhibit a sigmoidal dependence on the ssDNA grafting density. At low densities, ssDNA strands adopt a coiled conformation that results in minor alterations to particle dynamics, while at high densities, they organize into polymer brushes that collectively influence particle dynamics. Intermediate ssDNA densities, where the dynamics are most sensitive to changes, show the highest magnetic biosensing sensitivity for the detection of target nucleic acids. Finally, we demonstrate that MNPs with high ssDNA grafting densities are required to efficiently couple to DNA origami. Our results establish ssDNA grafting density as a critical parameter for the functionalization of MNPs for magnetic biosensing and functionalization of DNA nanostructures.

Thermometries for Single Nanoparticles Heated with Light

The development of efficient nanoscale photon absorbers, such as plasmonic or high-index dielectric nanostructures, allows the remotely controlled release of heat on the nanoscale using light. These photothermal nanomaterials have found applications in various research and technological fields, ranging from materials science to biology. However, measuring the nanoscale thermal fields remains an open challenge, hindering full comprehension and control of nanoscale photothermal phenomena. Here, we review and discuss existent thermometries suitable for single nanoparticles heated under illumination. These methods are classified in four categories according to the region where they assess temperature: (1) the average temperature within a diffraction-limited volume, (2) the average temperature at the immediate vicinity of the nanoparticle surface, (3) the temperature of the nanoparticle itself, and (4) a map of the temperature around the nanoparticle with nanoscale spatial resolution. In the latter, because it is the most challenging and informative type of method, we also envisage new combinations of technologies that could be helpful in retrieving nanoscale temperature maps. Finally, we analyze and provide examples of strategies to validate the results obtained using different thermometry methods.

Large Fluorescence Enhancement via Lossless All-Dielectric Spherical Mesocavities

Nano- and microparticles are popular media to enhance optical signals, including fluorescence from a dye proximal to the particle. Here we show that homogeneous, lossless, all-dielectric spheres with diameters in the mesoscale range, between nano- (≲100 nm) and micro- (≳1 μm) scales, can offer surprisingly large fluorescence enhancements, up to F ∼ 104. With the absence of nonradiative Ohmic losses inherent to plasmonic particles, we show that F can increase, decrease or even stay the same with increasing intrinsic quantum yield q0, for suppressed, enhanced or intact radiative decay rates of a fluorophore, respectively. Further, the fluorophore may be located inside or outside the particle, providing additional flexibility and opportunities to design fit for purpose particles. The presented analysis with simple dielectric spheres should spur further interest in this less-explored scale of particles and experimental investigations to realize their potential for applications in imaging, molecular sensing, light coupling, and quantum information processing.

Lab-on-a-DNA origami: nanoengineered single-molecule platforms

DNA origami nanostructures are self-assembled into almost arbitrary two- and three-dimensional shapes from a long, single-stranded viral scaffold strand and a set of short artificial oligonucleotides. Each DNA strand can be functionalized individually using well-established DNA chemistry, representing addressable sites that allow for the nanometre precise placement of various chemical entities such as proteins, molecular chromophores, nanoparticles, or simply DNA motifs. By means of microscopic and spectroscopic techniques, these entities can be visualized or detected, and either their mutual interaction or their interaction with external stimuli such as radiation can be studied. This gives rise to the Lab-on-a-DNA origami approach, which is introduced in this Feature Article, and the state-of-the-art is summarized with a focus on light-harvesting nanoantennas and DNA platforms for single-molecule analysis either by optical spectroscopy or atomic force microscopy (AFM). Light-harvesting antennas can be generated by the precise arrangement of chromophores to channel and direct excitation energy. At the same time, plasmonic nanoparticles represent a complementary approach to focus light on the nanoscale. Plasmonic nanoantennas also allow for the observation of single molecules either by Raman scattering or fluorescence spectroscopy and DNA origami platforms provide unique opportunities to arrange nanoparticles and molecules to be studied. Finally, the analysis of single DNA motifs by AFM allows for an investigation of radiation-induced processes in DNA with unprecedented detail and accuracy.

Gold Nanorod DNA Origami Antennas for 3 Orders of Magnitude Fluorescence Enhancement in NIR

DNA origami has taken a leading position in organizing materials at the nanoscale for various applications such as manipulation of light by exploiting plasmonic nanoparticles. We here present the arrangement of gold nanorods in a plasmonic nanoantenna dimer enabling up to 1600-fold fluorescence enhancement of a conventional near-infrared (NIR) dye positioned at the plasmonic hotspot between the nanorods. Transmission electron microscopy, dark-field spectroscopy, and fluorescence analysis together with numerical simulations give us insights on the heterogeneity of the observed enhancement values. The size of our hotspot region is ∼12 nm, granted by using the recently introduced design of NAnoantenna with Cleared HotSpot (NACHOS), which provides enough space for placing of tailored bioassays. Additionally, the possibility to synthesize nanoantennas in solution might allow for production upscaling.

Broadband single-molecule fluorescence enhancement based on self-assembled Ag@Au dimer plasmonic nanoantennas

Dimer optical antennas (OAs) enable great fluorescence enhancement and excitation volume reduction and hence potentially can be a very useful tool for single-molecule detection. The realization of broadband fluorescence enhancement with a dimer OA remains an essential step for its usage in multi-color single-molecule fluorescence (SMF) detection. Although silver dimer OAs have been shown to be able to yield broadband fluorescence enhancement over the visible spectrum, they are amenable to oxidization, hard to functionalize, and could cause cytotoxicity. To overcome these limitations, in this work, we took advantage of nano-sized silver due to its optical properties and gold due to its chemical properties and developed an ameliorated Ag@Au dimer OA in terms of its overall performance. The Ag@Au nanoparticle in the dimer OA contains a 70 nm silver core and an ultra-thin (∼1-5 nm) gold shell which play a key role in its optical responses. Furthermore, we employed three typical dyes, i.e., FAM, TAMRA and Cy5, representing the blue, yellow and red ranges, respectively, and characterized their single-molecule fluorescence enhancements in the presence of Au or Ag@Au OAs. Our results indicate that, in contrast to its Au counterpart, the Ag@Au dimer OA prepared here can greatly improve its optical response in the blue range and eventually achieve broadband fluorescence enhancement throughout almost the whole visible spectral range. Meanwhile, it also maintains good chemical stability and accessibility to functionalization. Such Ag@Au dimer OAs are thus expected to have many important applications in the future, including single-molecule sequencing and multi-color biosensing.

DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation

An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control, and well-defined orientation. The DNA origami technique has evolved into a highly versatile bottom-up nanofabrication methodology that fulfils almost all of these features. It enables the nanometric positioning of molecules and nanoparticles with stoichiometric control, and even the orientation of asymmetrical nanoparticles along predefined directions. However, orienting individual molecules has been a standing challenge. Here, we show how single molecules, namely, Cy5 and Cy3 fluorophores, can be incorporated in a DNA origami with controlled orientation by doubly linking them to oligonucleotide strands that are hybridized while leaving unpaired bases in the scaffold. Increasing the number of bases unpaired induces a stretching of the fluorophore linkers, reducing its mobility freedom, and leaves more space for the fluorophore to accommodate and find different sites for interaction with the DNA. Particularly, we explore the effects of leaving 0, 2, 4, 6, and 8 bases unpaired and find extreme orientations for 0 and 8 unpaired bases, corresponding to the molecules being perpendicular and parallel to the DNA double-helix, respectively. We foresee that these results will expand the application field of DNA origami toward the fabrication of nanodevices involving a wide range of orientation-dependent molecular interactions, such as energy transfer, intermolecular electron transport, catalysis, exciton delocalization, or the electromagnetic coupling of a molecule to specific resonant nanoantenna modes.

DNA-mediated dynamic plasmonic nanostructures: assembly, actuation, optical properties, and biological applications

Recent advances in DNA technology have made it possible to combine with the plasmonics to fabricate reconfigurable dynamic nanodevices with extraordinary property and function. These DNA-mediated plasmonic nanostructures have been investigated for a variety of unique and beneficial physicochemical properties and their dynamic behavior has been controlled by endogenous or exogenous stimuli for a variety of interesting biological applications. In this perspective, the recent efforts to use the DNA nanostructures as molecular linkers for fabricating dynamic plasmonic nanostructures are reviewed. Next, the actuation media for triggering the dynamic behavior of plasmonic nanostructures and the dynamic response in optical features are summarized. Finally, the applications, remaining challenges and perspectives of the DNA-mediated dynamic plasmonic nanostructures are discussed.

Electromechanical Photophysics of GFP Packed Inside Viral Protein Cages Probed by Force-Fluorescence Hybrid Single-Molecule Microscopy

Packing biomolecules inside virus capsids has opened new avenues for the study of molecular function in confined environments. These systems not only mimic the highly crowded conditions in nature, but also allow their manipulation at the nanoscale for technological applications. Here, green fluorescent proteins are packed in virus-like particles derived from P22 bacteriophage procapsids. The authors explore individual virus cages to monitor their emission signal with total internal reflection fluorescence microscopy while simultaneously changing the microenvironment with the stylus of atomic force microscopy. The mechanical and electronic quenching can be decoupled by ≈10% each using insulator and conductive tips, respectively. While with conductive tips the fluorescence quenches and recovers regardless of the structural integrity of the capsid, with the insulator tips quenching only occurs if the green fluorescent proteins remain organized inside the capsid. The electronic quenching is associated with the coupling of the protein fluorescence emission with the tip surface plasmon resonance. In turn, the mechanical quenching is a consequence of the unfolding of the aggregated proteins during the mechanical disruption of the capsid.

Salt-induced conformational switching of a flat rectangular DNA origami structure

A rectangular DNA origami structure is one of the most studied and often used motif for applications in DNA nanotechnology. Here, we present two assays to study structural changes in DNA nanostructures and reveal a reversible rolling-up of the rectangular DNA origami structure induced by bivalent cations such as magnesium or calcium. First, we applied one-color and two-color superresolution DNA-PAINT with protruding strands along the long edges of the DNA origami rectangle. At increasing salt concentration, a single line instead of two lines is observed as a first indicator of rolling-up. Two-color measurements also revealed different conformations with parallel and angled edges. Second, we placed a gold nanoparticle and a dye molecule at different positions on the DNA origami structure. Distance dependent fluorescence quenching by the nanoparticle reports on dynamic transitions as well as it provides evidence that the rolling-up occurs preferentially along the diagonal of the DNA origami rectangle. The results will be helpful to test DNA structural models and the assays presented will be useful to study further structural transitions in DNA nanotechnology.

Centrifugation-induced assembly of dense hotspots based SERS substrate for enhanced Raman scattering and quenched fluorescence

Hanging (aggregation stuck to the centrifugal tube) in the centrifugation process is always regarded as an unwanted condition. In this work, we develop a centrifugation-induced assembly of dense hotspots surface-enhanced Raman scattering (SERS) substrates from the hanging phenomenon. We discovered interesting sintering-resistant behavior (maintain the sharp nanotip features) of star-like Au nanoparticles after centrifugation-induced assembly, which is in stark contrast with the sintering phenomenon of sphere-like nanoparticles. We also found that one side of centrifugal-induced Au assemblies is two-dimensional (2D, root mean square (rms) roughness down to ∼10 nm), while the other is three-dimensional (3D, rms roughness more than 100 nm). The close-packed feature of the Au assemblies makes them candidates as dense hotspots based SERS substrates. Through systematic investigation of SERS performance of centrifugation-induced assemblies with different morphology (star-like and sphere-like, 2D and 3D), it was found that the 3D side of star-like Au nanoparticles assembly exhibits the highest SERS enhancement together with quenched fluorescence. The star-like SERS substrate also displays high detection uniformity (with 10^-7M Rhodamine 6G) and a low detection limit (down to 10^-12M Rhodamine 6G).

Single Molecule Measurements of the Accessibility of Molecular Surfaces

An important measure of the conformation of protein molecules is the degree of surface exposure of its specific segments. However, this is hard to measure at the level of individual molecules. Here, we combine single molecule photobleaching (smPB, which resolves individual photobleaching steps of single molecules) and fluorescence quenching techniques to measure the accessibility of individual fluorescently labeled protein molecules to quencher molecules in solution. A quencher can reduce the time a fluorophore spends in the excited state, increasing its photostability under continuous irradiation. Consequently, the photo-bleaching step length would increase, providing a measure for the accessibility of the fluorophore to the solvent. We demonstrate the method by measuring the bleaching step-length increase in a lipid, and also in a lipid-anchored peptide (both labelled with rhodamine-B and attached to supported lipid bilayers). The fluorophores in both molecules are expected to be solvent-exposed. They show a near two-fold increase in the step length upon incubation with 5 mM tryptophan (a quencher of rhodamine-B), validating our approach. A population distribution plot of step lengths before and after addition of tryptophan show that the increase is not always homogenous. Indeed there are different species present with differential levels of exposure. We then apply this technique to determine the solvent exposure of membrane-attached N-terminus labelled amylin (h-IAPP, an amyloid associated with Type II diabetes) whose interaction with lipid bilayers is poorly understood. hIAPP shows a much smaller increase of the step length, signifying a lower level of solvent exposure of its N-terminus. Analysis of results from individual molecules and step length distribution reveal that there are at least two different conformers of amylin in the lipid bilayer. Our results show that our method (“Q-SLIP”, Quenching-induced Step Length increase in Photobleaching) provides a simple route to probe the conformational states of membrane proteins at a single molecule level.

Concepts and Application of DNA Origami and DNA Self-Assembly: A Systematic Review

With the arrival of the post-Moore Era, the development of traditional silicon-based computers has reached the limit, and it is urgent to develop new computing technology to meet the needs of science and life. DNA computing has become an essential branch and research hotspot of new computer technology because of its powerful parallel computing capability and excellent data storage capability. Due to good biocompatibility and programmability properties, DNA molecules have been widely used to construct novel self-assembled structures. In this review, DNA origami is briefly introduced firstly. Then, the applications of DNA self-assembly in material physics, biogenetics, medicine, and other fields are described in detail, which will aid the development of DNA computational model in the future.

DNA Origami Nanoantennas for Fluorescence Enhancement

The possibility to increase fluorescence by plasmonic effects in the near-field of metal nanostructures was recognized more than half a century ago. A major challenge, however, was to use this effect because placing single quantum emitters in the nanoscale plasmonic hotspot remained unsolved for a long time. This not only presents a chemical problem but also requires the nanostructure itself to be coaligned with the polarization of the excitation light. Additional difficulties arise from the complex distance dependence of fluorescence emission: in contrast to other surface-enhanced spectroscopies (such as Raman spectroscopy), the emitter should not be placed as close as possible to the metallic nanostructure but rather needs to be at an optimal distance on the order of a few nanometers to avoid undesired quenching effects.Our group addressed these challenges almost a decade ago by exploiting the unique positioning ability of DNA nanotechnology and reported the first self-assembled DNA origami nanoantennas. This Account summarizes our work spanning from this first proof-of-principle study to recent advances in utilizing DNA origami nanoantennas for single DNA molecule detection on a portable smartphone microscope.We summarize different aspects of DNA origami nanoantennas that are essential for achieving strong fluorescence enhancement and discuss how single-molecule fluorescence studies helped us to gain a better understanding of the interplay between fluorophores and plasmonic hotspots. Practical aspects of preparing the DNA origami nanoantennas and extending their utility are also discussed.Fluorescence enhancement in DNA origami nanoantennas is especially exciting for signal amplification in molecular diagnostic assays or in single-molecule biophysics, which could strongly benefit from higher time resolution. Additionally, biophysics can greatly profit from the ultrasmall effective detection volumes provided by DNA nanoantennas that allow single-molecule detection at drastically elevated concentrations as is required, e.g., in single-molecule DNA sequencing approaches.Finally, we describe our most recent progress in developing DNA NanoAntennas with Cleared HOtSpots (NACHOS) that are fully compatible with biomolecular assays. The developed DNA origami nanoantennas have proven robustness and remain functional after months of storage. As an example, we demonstrated for the first time the single-molecule detection of DNA specific to antibiotic-resistant bacteria on a portable and battery-driven smartphone microscope enabled by DNA origami nanoantennas. These recent developments mark a perfect moment to summarize the principles and the synthesis of DNA origami nanoantennas and give an outlook of new exciting directions toward using different nanomaterials for the construction of nanoantennas as well as for their emerging applications.

Gold Nanoparticles as Carriers for Functional RNA Nanostructures

Conjugates of gold nanoparticles and ribonucleic acid are particularly interesting for biological applications to serve as therapeutics or biosensors. In this paper we present, for the first time, a conjugate of gold nanoparticles and structural RNA (tectoRNA), which serves as a tool for gene expression regulation. The tectoRNA trimer was modified to facilitate the introduction of a thiol linker, which aids the formation of stable RNA:AuNP conjugates. We demonstrated that these complexes can penetrate cells, which were observed in TEM analysis and are effective in gene expression regulation evident in GFP expression studies with fluorescence methods. The presented compounds have the potential to become a new generation of therapeutics that utilize the power of self-assembling, biologically active RNAs and gold nanoparticles, with their diagnostically useful optical properties and biocompatibility advantages.

Current Developments in Native Nanometric Discoidal Membrane Bilayer Formed by Amphipathic Polymers

Unlike cytosolic proteins, membrane proteins (MPs) are embedded within the plasma membrane and the lipid bilayer of intracellular organelles. MPs serve in various cellular processes and account for over 65% of the current drug targets. The development of membrane mimetic systems such as bicelles, short synthetic polymers or amphipols, and membrane scaffold proteins (MSP)-based nanodiscs has facilitated the accommodation of synthetic lipids to stabilize MPs, yet the preparation of these membrane mimetics remains detergent-dependent. Bio-inspired synthetic polymers present an invaluable tool for excision and liberation of superstructures of MPs and their surrounding annular lipid bilayer in the nanometric discoidal assemblies. In this article, we discuss the significance of self-assembling process in design of biomimetic systems, review development of multiple series of amphipathic polymers and the significance of these polymeric "belts" in biomedical research in particular in unraveling the structures, dynamics and functions of several high-value membrane protein targets.

Enzyme Activated Gold Nanoparticles for Versatile Site-Selective Bioconjugation

A new enzymatic method is reported for constructing protein- and DNA-AuNP conjugates. The strategy relies on the initial functionalization of AuNPs with phenols, followed by activation with the enzyme tyrosinase. Using an oxidative coupling reaction, the activated phenols are coupled to proteins bearing proline, thiol, or aniline functional groups. Activated phenol-AuNPs are also conjugated to a small molecule biotin and commercially available thiol-DNA. Advantages of this approach for AuNP bioconjugation include: (1) initial formation of highly stable AuNPs that can be selectively activated with an enzyme, (2) the ability to conjugate either proteins or DNA through a diverse set of functional handles, (3) site-specific immobilization, and (4) facile conjugation that is complete within 2 h at room temperature under aqueous conditions. The enzymatic oxidative coupling on AuNPs is applied to the construction of tobacco mosaic virus (TMV)-AuNP conjugates, and energy transfer between the AuNPs and fluorophores on TMV is demonstrated.

Adsorption of bovine serum albumin on gold nanoprisms: interaction and effect of NIR irradiation on protein corona

Because of their photothermal properties, gold nanoparticles (AuNPs) have gained attention regarding their use in drug delivery and therapeutic applications. In this sense, it is interesting to consider their interactions with biologically available proteins, such as serum albumin, as well as the effects of irradiation and photothermal conversion on the protein structure that can lead to a loss of function or generate an immune response. Gold nanoprisms (AuNPrs) have gained interest due to their low toxicity, ease of synthesis, and excellent stability, promoting their use in bioapplications such as surface-enhanced Raman spectroscopy (SERS), drug delivery, and photothermal therapy. The interaction between AuNPrs, with plasmon bands centred in the near-infrared region (NIR), and bovine serum albumin (BSA) has not been explored yet. UV-Vis spectroscopy, dynamic light scattering (DLS) and fluorescence spectroscopy were used to study the interaction between AuNPrs and BSA in addition to estimation of the adsorption rate and kinetic and thermodynamic parameters (K, ΔH°, ΔG°, ΔS°, and Ea) using adsorption isotherms and Langmuir and Freundlich models. The results suggest spontaneous cooperative binding in multilayer adsorption, achieved by the chemisorption of BSA on the AuNPr surface through the S-Au interaction, as confirmed by Raman spectroscopy. On the other hand, the photothermal conversion efficiency (PE) of the coated nanoparticles after NIR irradiation was assessed, resulting in a slight decrease in the PE of BSA coated on AuNPrs in comparison with that of noncapped nanoparticles. The effect of the irradiation on the protein conformation of capped nanoparticles was also assessed; circular dichroism showed BSA unfolding upon interaction with AuNPrs, with a decrease in the α-helix and β-sheet contents, as well as an increase in random coil conformations. Changes in the Raman spectrum suggest a modification of the disposition of the protein residues exposed to the gold surface after NIR irradiation; but at the secondary structure level, no relevant changes were observed. This provides possibilities for the use of NPs-BSA for bioapplications based on the photothermal effect promoted by laser irradiation, since the biological identity of the protein is preserved after NIR irradiation.

Modulated Luminescence of Lanthanide Materials by Local Surface Plasmon Resonance Effect

Lanthanide materials have great applications in optical communication, biological fluorescence imaging, laser, and so on, due to their narrow emission bandwidths, large Stokes' shifts, long emission lifetimes, and excellent photo-stability. However, the photon absorption cross-section of lanthanide ions is generally small, and the luminescence efficiency is relatively low. The effective improvement of the lanthanide-doped materials has been a challenge in the implementation of many applications. The local surface plasmon resonance (LSPR) effect of plasmonic nanoparticles (NPs) can improve the luminescence in different aspects: excitation enhancement induced by enhanced local field, emission enhancement induced by increased radiative decay, and quenching induced by increased non-radiative decay. In addition, plasmonic NPs can also regulate the energy transfer between two close lanthanide ions. In this review, the properties of the nanocomposite systems of lanthanide material and plasmonic NPs are presented, respectively. The mechanism of lanthanide materials regulated by plasmonic NPs and the scientific and technological discoveries of the luminescence technology are elaborated. Due to the large gap between the reported enhancement and the theoretical enhancement, some new strategies applied in lanthanide materials and related development in the plasmonic enhancing luminescence are presented.

DNA Origami-Enabled Plasmonic Sensing

The reliable programmability of DNA origami makes it an extremely attractive tool for bottom-up self-assembly of complex nanostructures. Utilizing this property for the tuned arrangement of plasmonic nanoparticles holds great promise particularly in the field of biosensing. Plasmonic particles are beneficial for sensing in multiple ways, from enhancing fluorescence to enabling a visualization of the nanoscale dynamic actuation via chiral rearrangements. In this Perspective, we discuss the recent developments and possible future directions of DNA origami-enabled plasmonic sensing systems. We start by discussing recent advancements in the area of fluorescence-based plasmonic sensing using DNA origami. We then move on to surface-enhanced Raman spectroscopy sensors followed by chiral sensing, both utilizing DNA origami nanostructures. We conclude by providing our own views on the future prospects for plasmonic biosensors enabled using DNA origami.

Influence of nonlocal dielectric response on the Au tip-enhanced fluorescence effect

Tip-enhanced fluorescence (TEF) with ultra-high detection sensitivity and spatial resolution has been a powerful characterization technique in the study of surface science and life science. Herein, a systematically theoretical investigation in the visible range had been performed to study TEF properties of a single molecule located inside a nanogap formed by Au tip and substrate. In the strong localized surface plasmon coupling effect, the contribution of nonlocal dielectric response to the fluorescence quantum yield as well as radiative and energy dissipated decay rates were calculated. It is found that the nonlocal dielectric effects become comparable to the radiative and energy dissipated decay rates with the increasing of the tip-molecule distance, as a result, the nonlocal dielectric effect significantly suppresses the fluorescence process. The huge excitation enhancement at the shorter tip-molecule distance can efficiently compensate the low quantum yield, leading to the great fluorescence enhancement. The results show that the maximum enhancement obtained from the calculations can reach as high as four orders of magnitude by optimizing the tip-molecule distance. These results are not only helpful to our understanding of the TEF mechanism but also valuable for its further applications.

Scouting for strong light-matter coupling signatures in Raman spectra

Strong coupling between vibrational transitions and a vacuum field of a cavity mode leads to the formation of vibrational polaritons. These hybrid light-matter states have been widely explored because of their potential to control chemical reactivity. However, the possibility of altering Raman scattering through the formation of vibrational polaritons has been rarely reported. Here, we present the Raman scattering properties of different molecules under vibrational strong coupling conditions. The polariton states are clearly observed in the IR transmission spectra of the coupled system for benzonitrile and methyl salicylate in liquid phase and for polyvinyl acetate in a solid polymer film. However, none of the studied systems exhibits a signature of the polariton states in the Raman spectra. For the solid polymer film, we have used cavities with different layer structures to investigate the influence of vibrational strong coupling on the Raman spectra. The only scenario where alterations of the Raman spectra are observed is for a thin Ag layer being in direct contact with the polymer film. This shows that, even though the system is in the vibrational strong coupling regime, changes in the Raman spectra do not necessarily result from the strong coupling, but are caused by the surface enhancement effects.

In Situ, Noncovalent Labeling and Stimulated Emission Depletion-Based Super-Resolution Imaging of Supramolecular Peptide Nanostructures

Supramolecular materials have gained substantial interest for a number biological and nonbiological applications. However, for optimum utilization of these dynamic self-assembled materials, it is important to visualize and understand their structures at the nanoscale, in solution and in real time. Previous approaches for imaging these structures have utilized super-resolution optical imaging methods such as STORM, which has provided important insights, but suffers from drawbacks of complex sample preparation and slow acquisition times, thus limiting real-time in situ imaging of dynamic processes. We demonstrate a noncovalent fluorescent labeling design for STED-based super-resolution imaging of self-assembling peptides. This is achieved by in situ, electrostatic binding of anionic sulfonates of Alexa-488 dye to the cationic sites of lysine (or arginine) residues exposed on the peptide nanostructure surface. A direct, multiscale visualization of static structures reveals hierarchical organization of supramolecular fibers with sub-60 nm resolution. In addition, the degradation of nanofibers upon enzymatic hydrolysis of peptide could be directly imaged in real time, and although resolution was compromised in this dynamic process, it provided mechanistic insights into the enzymatic degradation process. Noncovalent Alexa-488 labeling and subsequent imaging of a range of cationic self-assembling peptides and peptide-functionalized gold nanoparticles demonstrated the versatility of the methodology for the imaging of cationic supramolecular structures. Overall, our approach presents a general and simple method for the electrostatic fluorescent labeling of cationic peptide nanostructures for nanoscale imaging under physiological conditions and probe dynamic processes in real time and in situ.

Controllable Frequency Dependence of Resonance Energy Transfer Coupled with Localized Surface Plasmon Polaritons

We investigate the intrinsic characteristics of resonance energy transfer (RET) coupled with localized surface plasmon polaritons (LSPPs) from the perspective of macroscopic quantum electrodynamics. To quantify the effect of LSPPs, we propose a numerical scheme that allows us to accurately calculate the rate of RET between a donor-acceptor pair near a nanoparticle. Our study shows that LSPPs can be used to enhance the RET rate significantly and control its frequency dependence by modifying a core/shell structure, which indicates the possibility of RET rate optimization. Moreover, we systematically explore the angle (distance) dependence of the RET rate and analyze its origin. According to different frequency regimes, the angle dependence of RET is dominated by different mechanisms, such as LSPPs, surface plasmon polaritons (SPPs), and anti-resonance. For the proposed core/shell structure, the characteristic distance of RET coupled with LSPPs (approximately 0.05 emission wavelength) is shorter than that of RET coupled with SPPs (approximately 0.1 emission wavelength), which may provide promising applications in energy science.

Recent advances of lanthanide-doped upconversion nanoparticles for biological applications

Near infrared (NIR) excited lanthanide-doped upconversion nanoparticles (UCNPs) are emerging as a new type of fluorescent tag for biological applications, which can emit multi-photon ultraviolet, visible or NIR luminescence for imaging or activation of photosensitive molecules. Here, we present a comprehensive review on recent advances of UCNPs for a manifold of biological applications, including upconversion mechanisms, building bright multicolor upconversion nanocrystals, single nanoparticle and super resolution imaging, in vivo optical and multimodal imaging, photodynamic therapy, light-controlled drug release, biosensing, and toxicities. Our perspectives on the future development of UCNPs are also described.

Reciprocal Control of Hierarchical DNA Origami-Nanoparticle Assemblies

DNA origami mechanisms offer promising tools for precision nanomanipulation of molecules or nanomaterials. Recent advances have extended the function of individual DNA origami devices to material scales via hierarchical assemblies. However, achieving rapid and precise control of large conformational changes in hierarchical assemblies remains a critical challenge. Here, we demonstrate a method for controlling DNA origami-nanoparticle assemblies through a multiscale approach, in which nanoparticles impart control on the conformation of individual DNA origami mechanisms, whereas DNA origami assemblies control the conformation of nanoparticle arrays. Specifically, we show that the angular distributions of DNA origami hinge mechanisms are tunable as a function of nanoparticle size and distance from the hinge vertex. We selectively adjust the affinity of nanoparticle binding sites, resulting in hinge actuation via DNA melting without releasing the nanoparticle, thereby enabling rapid and reversible temperature-based actuation. Finally, we demonstrate this rapid actuation in DNA origami-nanoparticle arrays of length scales extending over a micron. These results provide guiding principles toward the design of dynamic, DNA-origami hierarchical materials capable of storing and releasing mechanical energy.

Automated sequence design of 2D wireframe DNA origami with honeycomb edges

Wireframe DNA origami has emerged as a powerful approach to fabricating nearly arbitrary 2D and 3D geometries at the nanometer-scale. Complex scaffold and staple routing needed to design wireframe DNA origami objects, however, render fully automated, geometry-based sequence design approaches essential for their synthesis. And wireframe DNA origami structural fidelity can be limited by wireframe edges that are composed only of one or two duplexes. Here we introduce a fully automated computational approach that programs 2D wireframe origami assemblies using honeycomb edges composed of six parallel duplexes. These wireframe assemblies show enhanced structural fidelity from electron microscopy-based measurement of programmed angles compared with identical geometries programmed using dual-duplex edges. Molecular dynamics provides additional theoretical support for the enhanced structural fidelity observed. Application of our top-down sequence design procedure to a variety of complex objects demonstrates its broad utility for programmable 2D nanoscale materials.

Wireframe DNA origami is a powerful approach to creating 2D and 3D geometries. Here the authors introduce an automated computational design approach that programs structures with high structural fidelity.

A Programming 20-30nm Rectangular DNA Origami for Loading Doxorubicin to Penetrate Ovarian Cancer Cells

In DNA nanotechnology, the aim in folding DNA origami is to find a good piece of rectangular DNA origami with desired sizes, which could be larger or smaller for different application purposes. In recent three years, the technique of folding smaller ones is paid heavily attentions. In this work, we design a programming rectangular DNA origami in size 20*30nm with M13p18, which is smallest and cheapest to the best acknowledge of the authors. Since it is not hard to prepare with 30 staple strands and short annealing time, the cost of folding our designed rectangular DNA origami is less than 100 dollars. Although the large origami give more space, the smaller ones are cheaper and has the potential applications in penetrating cancer cells. It is obtained by cell penetrating experiments that our designed rectangular DNA origami can penetrate ovarian cancer cells efficiently even loading doxorubicin, but the thermodynamic stability needs further improved. Our designed programming 20 30nm triangular DNA origami shows potential applications in precision control of nanoscale particles and anti-tumor drug delivery in vivo.

DNA-Assembled Multilayer Sliding Nanosystems

DNA nanotechnology allows for the realization of complex nanoarchitectures in which the spatial arrangements of different constituents and most functions can be enabled by DNA. When optically active components are integrated in such systems, the resulting nanoarchitectures not only provide great insights into the self-assembly of nanoscale elements in a systematic way but also impart tailored optical functionality to DNA origami. In this Letter, we demonstrate DNA-assembled multilayer nanosystems, which can carry out coordinated and reversible sliding motion powered by DNA fuels. Gold nanoparticles cross-link DNA origami filaments to define the configurations of the multilayer nanoarchitectures as well as to mediate relative sliding between the neighboring origami filaments. Meanwhile, the gold nanoparticles serve as optical probes to dynamically interact with the fluorophores tethered on the filaments, rendering in situ detection of the stepwise sliding processes possible. This work seeds the basis to implement DNA-assembled complex optical nanoarchitectures with programmability and addressability, advancing the field with new momentum.

Binary control of enzymatic cleavage of DNA origami by structural antideterminants

Controlling DNA nanostructure interaction with protein is essential in developing nanodevices with programmable function, reactivity, and stability for biological and medical applications. Here, we show that the sequence-specific action of restriction endonucleases towards sharp triangular or rectangular DNA origami exhibits a novel, binary ‘on/off’ behaviour, as canonical recognition sites are either essentially fully reactive, or strongly resistant to enzymatic cutting. Moreover, introduction of structural defects in the sharp triangle can activate an otherwise unreactive site, with a site-to-defect distance of ∼50 nm. We argue that site reactivity is dependent upon programmable, mechanical coupling in the two-dimensional DNA origami, with specific structural elements, including DNA nicks and branches proximal to the sites that can function as negative(anti) determinants of reactivity. Empirically modelling the constraints to DNA degrees of freedom associated with each recognition site in the sharp triangle can rationalize the pattern of suppressed reactivity towards nine restriction endonucleases, in substantial agreement with the experimental results. These results provide a basis for a predictive understanding of structure-reactivity correlates of specific DNA nanostructures, which will allow a better understanding of the behaviour of nucleic acids under nanoscale confinement, as well as in the rational design of functional nanodevices based on self-assembling nucleic acids.

Polyfunctionalised Nanoparticles Bearing Robust Gadolinium Surface Units for High Relaxivity Performance in MRI

The first example of an octadentate gadolinium unit based on DO3A (hydration number q=1) with a dithiocarbamate tether has been designed and attached to the surface of gold nanoparticles (around 4.4 nm in diameter). In addition to the superior robustness of this attachment, the restricted rotation of the Gd complex on the nanoparticle surface leads to a dramatic increase in relaxivity (r₁ ) from 4.0 mm^-1  s^-1 in unbound form to 34.3 mm^-1  s^-1 (at 10 MHz, 37 °C) and 22±2 mm^-1  s^-1 (at 63.87 MHz, 25 °C) when immobilised on the surface. The one-pot synthetic route provides a straightforward and versatile way of preparing a range of multifunctional gold nanoparticles. The incorporation of additional surface units for biocompatibility (PEG and thioglucose units) and targeting (folic acid) leads to little detrimental effect on the high relaxivity observed for these non-toxic multifunctional materials. In addition to the passive targeting attributed to gold nanoparticles, the inclusion of a unit capable of targeting the folate receptors overexpressed by cancer cells, such as HeLa cells, illustrates the potential of these assemblies.

Distance Dependence of Single-Molecule Energy Transfer to Graphene Measured with DNA Origami Nanopositioners

Despite the thorough investigation of graphene since 2004, altering its surface chemistry and reproducible functionalization remain challenging. This hinders fabrication of more complex hybrid materials with controlled architectures, and as a consequence the development of sensitive and reliable sensors and biological assays. In this contribution, we introduce DNA origami structures as nanopositioners for placing single dye molecules at controlled distances from graphene. The measurements of fluorescence intensity and lifetime of single emitters carried out for distances ranging from 3 to 58 nm confirmed the d^-4 dependence of the excitation energy transfer to graphene. Moreover, we determined the characteristic distance for 50% efficiency of the energy transfer from single dyes to graphene to be 17.7 nm. Using pyrene molecules as a glue to immobilize DNA origami nanostructures of various shape on graphene opens new possibilities to develop graphene-based biophysics and biosensing.

Mapping plasmon-enhanced upconversion fluorescence of Er/Yb-doped nanocrystals near gold nanodisks

Fluorescence enhancement effects have many potential applications in the domain of biochemical sensors and optoelectronic devices. Here, the emission properties of up-converting nanocrystals near nanostructures that support surface plasmon resonances have been investigated. Gold nanodisks of various diameters were illuminated in the near-infrared (λ = 975 nm) and a single fluorescent nanocrystal glued at the end of an atomic force microscope tip was scanned around them. By detecting its visible fluorescence around each structure, it is found that the highest fluorescence enhancement occurs in a zone that forms a two-lobe pattern near the nanodisks and which corresponds to the map of the near-field intensity calculated at the excitation wavelength. In agreement with numerical simulations, it is also observed that the maximum fluorescence enhancement takes place when the disk diameter is around 200 nm. Surprisingly, this disk size is small when compared to that yielding the highest far-field scattering resonance, which occurs for disks with a diameter of 300-350 nm at the same excitation wavelength. This shift between the near and far-field resonances should be taken into account in the design of structures in systems that use plasmon enhanced fluorescence effects.

Gold nanocluster-loaded hybrid albumin nanoparticles with fluorescence-based optical visualization and photothermal conversion for tumor detection/ablation

Gold nanoclusters (AuNCs) are viewed as effective hyperthermal agents for the treatment of tumors. Whereas AuNCs formed by the agglomeration of several to tens of gold atoms (<1-2 nm) possess significant fluorescence, they have a negligible hyperthermal effect, while AuNCs comprised of spherical gold nanoparticles (AuNPs > a few nanometers) have a marked hyperthermic effect but lose their inherent fluorescence and obstruct the intensity of neighboring fluorescent dyes due to Forster resonance energy transfer (FRET). To achieve both hyperthermia and fluorescence-based optical visualization, we generated hybrid albumin nanoparticles containing AuNCs (~88 nm) comprising AuNPs (~4.5 nm). We generated a series of formulated AuNCs and optimized the size, morphology, NIR absorbance (600-900 nm), hyperthermal activity, and fluorescence spectral characters of the resulting hybrid albumin nanoparticles (AuNCs/BSA-NPs) by considering the interparticle distance between the AuNPs and Cy5.5. Among these, AuNCs/BSA-NPs (formula D) had a strong hyperthermic effect and had well-preserved fluorescence intensity (from the attached Cy5.5) due to localized surface plasmon resonance (LSPR) and a reduction in FRET. These AuNCs/BSA-NPs were able to elevate the surface tumor temperature of HCT116-bearing mice to >50 °C following 808 nm laser irradiation (1.5 W/cm², 10 min), which remarkably suppressed tumor growth (17.8 ± 16.9 mm³vs. PBS and AuNCs/BSA-NPs (formula E): ~1850 and ~1250 mm³, respectively). Also, Cy5.5-modified AuNCs/BSA-NPs (formula D) showed good performance in optical fluorescence imaging of target tumors in HCT116 tumor-bearing mice. Together, our results indicate that the interparticle distance between albumin or Cy5.5 and AuNPs/AuNCs can be optimized to achieve both hyperthermia and fluorescence emission by striking a balance between LSPR and FRET effects. We believe that the AuNC/BSA-NPs formulation presented here can serve as a potential platform for both optically visualizing and treating colon cancers.

Plasmon-assisted Förster resonance energy transfer at the single-molecule level in the moderate quenching regime

Metallic nanoparticles were shown to affect Förster energy transfer between fluorophore pairs. However, to date, the net plasmonic effect on FRET is still under dispute, with experiments showing efficiency enhancement and reduction. This controversy is due to the challenges involved in the precise positioning of FRET pairs in the near field of a metallic nanostructure, as well as in the accurate characterization of the plasmonic impact on the FRET mechanism. Here, we use the DNA origami technique to place a FRET pair 10 nm away from the surface of gold nanoparticles with sizes ranging from 5 to 20 nm. In this configuration, the fluorophores experience only moderate plasmonic quenching. We use the acceptor bleaching approach to extract the FRET rate constant and efficiency on immobilized single FRET pairs based solely on the donor lifetime. This technique does not require a posteriori correction factors neither a priori knowledge of the acceptor quantum yield, and importantly, it is performed in a single spectral channel. Our results allow us to conclude that, despite the plasmon-assisted Purcell enhancement experienced by donor and acceptor partners, the gold nanoparticles in our samples have a negligible effect on the FRET rate, which in turns yields a reduction of the transfer efficiency.

Nanoparticle Ligand Exchange and Its Effects at the Nanoparticle-Cell Membrane Interface

The nanoparticle (nano)-cell membrane interface is one of the most important interactions determining the fate of nanoparticles (NPs), which can stimulate a series of biological events, allowing theranostic and other biomedical applications. So far, there remains a lack of knowledge about the mechanisms governing the nanoparticle-cell membrane interface, especially the impact of ligand exchange, in which molecules on the nanosurface become replaced with components of the cell membrane, resulting in unique interfacial phenomena. Herein, we describe a family of gold nanoparticles (AuNPs) of the same core size (∼13 nm core), modified with 12 different kinds of surface ligands, and the effects of their exchangeable ligands on both nanoparticle-supported lipid bilayers (SLBs) and nanoparticle-natural cell membrane interfaces. The ligands are categorized according to their molecular weight, charge, and bonding modes (physisorption or chemisorption). Importantly, we found that, depending on the adsorption affinity and size of ligand molecules, physisorbed ligands on the surface of NPs can be exchanged with lipid molecules. At a ligand exchange-dominated interface, the AuNPs typically aggregated into an ordered monolayer in the lipid bilayers, subsequently affecting cell membrane integrity, NP uptake efficiency, and the NP endocytosis pathways. These findings advance our understanding of the underlying mechanisms of the biological effects of nanoparticles from a new point of view and will aid in the design of novel, safe, and effective nanomaterials for biomedicine.

Colloidal semiconductor nanocrystals in energy transfer reactions

Excitonic energy transfer is a versatile mechanism by which colloidal semiconductor nanocrystals can interact with a variety of nanoscale species. This feature article will discuss the latest research on the key scenarios under which semiconductor nanocrystals can engage in energy transfer with other nanoparticles, organic fluorophores, and plasmonic nanostructures, highlighting potential technological benefits to be gained from such processes.

Robust Covalent Coupling Scheme for the Development of FRET Aptasensor based on Amino-Silane-Modified Graphene Oxide

In recent years, numerous aptamers have been physisorbed on graphene oxide (GO) to develop fluorescence resonance energy transfer-based aptasensors using the fluorescence quenching property of GO. However, physisorbed aptasensors show poor signal reversibility and reproducibility as well as nonspecific probe displacement, and thereby are not suitable for many analytical applications. To overcome these problems when working with complex biological samples, we developed a facile and robust covalent surface functionalization technique for GO-based fluorescent aptasensors using a well-studied adenosine triphosphate binding aptamer (ABA). In the scheme, GO is first modified with amino-silane, and further with glutaraldehyde to create available carbonyl groups for the covalent attachment of a fluorophore and an amino dual modified ABA. The surface modification method was characterized by ζ-potential, X-ray photoelectron spectroscopy, and Fourier-transform infrared spectroscopy (FTIR). The linearity, sensitivity, selectivity, and reversibility of the resulting GO-based covalent aptasensor was determined and systematically compared with the physisorbed aptasensor. Although both sensors showed similar performance in terms of sensitivity and linearity, better selectivity and higher resistance to nonspecific probe displacement was achieved with the developed covalent ABA sensor. The surface modification technique developed here is independent of the aptamer sequence, and therefore could be used universally for different analytical applications simply by changing the aptamer sequence for the target biomolecule.

DNA-Assisted Assembly of Gold Nanostructures and Their Induced Optical Properties

Gold nanocrystals have attracted considerable attention due to their excellent physical and chemical properties and their extensive applications in plasmonics, spectroscopy, biological detection, and nanoelectronics. Gold nanoparticles are able to be readily modified and arranged with DNA materials and protein molecules, as well as viruses. Particularly DNA materials with the advantages endowed by programmability, stability, specificity, and the capability to adapt to functionalization, have become the most promising candidates that are widely utilized for building plenty of discrete gold nanoarchitectures. This review highlights recent advances on the DNA-based assembly of gold nanostructures and especially emphasizes their resulted superior optical properties and principles, including plasmonic extinction, plasmonic chirality, surface enhanced fluorescence (SEF), and surface-enhanced Raman scattering (SERS).

Isolation of RNA from a mixture and its detection by utilizing a microgel-based optical device

In this investigation, we show that RNA can be separated from a solution containing DNA and RNA and the isolated RNA can be detected using poly (N-isopropylacrylamide-co-N-(3-aminopropyl) methacrylamide hydrochloride) microgel-based optical devices (etalons). The isolation of RNA was accomplished by using hairpin-functionalized magnetic beads (MMPDNA) and differential melting, based on the fact that the DNA–RNA hybrid duplex is stronger (i.e., high melting temperature) than the DNA–DNA duplex (i.e., low melting temperature). By performing concurrent etalon sensing and fluorescent studies, we found that the MMPDNA combined with differential melting was capable of selectively separating RNA from DNA. This selective separation and simple colorimetric detection of RNA from a mixture will help lead to future RNA-based disease diagnostic devices.

Nanodiamonds and gold nanoparticles to obtain a hybrid nanostructure with potential applications in biomedicine

Using detonation nanodiamonds and fluorescent nitrogen-vacancy center nanodiamonds, linked to gold nanoparticles, we synthesized two hybrid nanostructures (HGDs) that were subsequently conjugated with a fluorophore. An amplification effect induced by the gold nanoparticles increased the emission spectrum of the fluorophore, maximizing the possibilities for imaging applications of these HGDs. The incubation of the nanostructures with HeLa cells produced no alteration of cell viability after 3 h and showed the presence of nanostructures in the cell cytoplasm at 24 h. These observations also indicate the potential biomedical use of the proposed HGDs.

Origin of the Plasmonic Chirality of Gold Nanorod Trimers Templated by DNA Origami

Templated by DNA origami, plasmonic gold nanorods (AuNRs) could be assembled into complex nanostructures with strong chiroptical activities. However, it is still not clear how the plasmonic chirality of a complex nanostructure matters with its daughter structural components. Here, we rationally design and fabricate a series of AuNR trimers and their daughter AuNR dimers. Strikingly, we corroborate by circular dichroism spectroscopy that the plasmonic chirality of asymmetrical AuNR trimers is a nearly perfect summation of the chiroptical response of all their constituent dimeric components. Our results provide fundamental insight into the origin of the plasmonic chirality of complex nanostructures.