The detection of DNA hybridization on phosphorus dendrimer multilayer films by surface plasmon field enhanced-fluorescence spectroscopy

Phosphorus-carrying cascade molecules: inner architecture to biomedical applications

Cascade molecules are nearly uniform-sized macromolecules of small molecules or linear polymer cores built around symmetric branching units. A wide range of biological properties can be achieved with phosphorus-containing dendrimers, depending on their terminal functions, ranging from biomaterials to imaging, drug delivery, and acting as a drug by themselves. This feature article presents significant examples of phosphorus-containing dendrimers used to develop biochips, support cell cultures, carry or deliver biomacromolecules and drugs, bioimaging, and combinational benefits. Because of the thermal stability, ferrocene function, and physical and chemical properties of phosphorus, dendrimers show greater rigidity, mobility, and strength. These dendrimers will be discussed as having a favorable effect on cell growths, especially on neuronal cells, as well as human immune cells like natural killer cells and monocytes, which have a crucial part in preventing cancerous and viral infections. Several phosphorus dendrimers are effective as drugs by themselves (drug per se) and show their activity against neurodegenerative diseases, cancer, inflammation, ocular hypertension, and transmissible spongiform encephalopathies (TSEs) in both in vivo and in vitro. The present review discusses the synthetic route, fabrications, and biomedical applications of phosphorus-containing dendrimers. The toxicity of these dendrimers was also reported.

Surface Plasmon-Assisted Fluorescence Enhancing and Quenching: From Theory to Application

The integration of surface plasmon resonance and fluorescence yields a multiaspect improvement in surface fluorescence sensing and imaging, leading to a paradigm shift of surface plasmon-assisted fluorescence techniques, for example, surface plasmon enhanced field fluorescence spectroscopy, surface plasmon coupled emission (SPCE), and SPCE imaging. This Review aims to characterize the unique optical property with a common physical interpretation and diverse surface architecture-based measurements. The fundamental electromagnetic theory is employed to comprehensively unveil the fluorophore-surface plasmon interaction, and the associated surface-modification design is liberally highlighted to balance the surface plasmon-induced fluorescence-enhancement efforts and the surface plasmon-caused fluorescence-quenching effects. In particular, all types of surface structures, for example, silicon, carbon, protein, DNA, polymer, and multilayer, are systematically interrogated in terms of component, thickness, stiffness, and functionality. As a highly interdisciplinary and expanding field in physics, optics, chemistry, and surface chemistry, this Review could be of great interest to a broad readership, in particular, among physical chemists, analytical chemists, and in surface-based sensing and imaging studies.

How Surfaces Affect Hybridization Kinetics

Hybridization between nucleic acid strands immobilized on a solid support with partners in solution is widely practiced in bioanalytical technologies and materials science. An important fundamental aspect of understanding these reactions is the role played by immobilization in the dynamics of duplex formation and disassembly. This report reviews and analyzes literature kinetic data to identify commonly observed trends and to correlate them with probable molecular mechanisms. The analysis reveals that while under certain conditions impacts from immobilization are minimal so that surface and solution hybridization kinetics are comparable, it is more typical to observe pronounced offsets between the two scenarios. In the forward (hybridization) direction, rates at the surface commonly decrease by one to two decades relative to solution, while in the reverse direction rates of strand separation at the surface can exceed those in solution by tens of decades. By recasting the deviations in terms of activation barriers, a consensus of how immobilization impacts nucleation, zipping, and strand separation can be conceived within the classical mechanism in which duplex formation is rate limited by preassembly of a nucleus a few base pairs in length, while dehybridization requires the cumulative breakup of base pairs along the length of a duplex. Evidence is considered for how excess interactions encountered on solid supports impact these processes.

Dendrimer-modified magnetic nanoparticles as a sorbent in dispersive micro-solid phase extraction for preconcentration of metribuzin in a water sample

This study was conducted to synthesize magnetic nanoparticles (MNPs) modified with generation 5 (G₅) polyamidoamine (PAMAM) dendrimer and apply them as a sorbent in the dispersive-micro-solid phase extraction (D-μ-SPE) method for preconcentration of metribuzin in water samples. The characterization of synthesized nanoparticles was performed by Fourier transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), scanning electron microscopy (SEM), dynamic light scattering (DLS), and vibrating sample magnetometry (VSM). The effects of sample solution pH, the terminal group type, dendrimer generation, ionic strength, sorbent dosage, and desorption conditions on the removal efficiency were investigated. The linear range was calculated from 25-1000 μg L^-1 and the LOD was 10 μg L^-1. The recovery percentages for the spiked real samples ranged from 95.3% to 103.5% and relative standard deviations (RSD%) were in the range of 87.2-92.1 and 4.2 to 6.3 (n = 5) respectively. Applying the method developed in this work in water samples revealed good extraction recoveries with a RSD of 5.6-7.3%.

Enhancement of Probe Density in DNA Sensing by Tuning the Exponential Growth Regime of Polyelectrolyte Multilayers

Surface-based biosensing devices benefit from a dedicated design of the probe layer present at the transducing interface. The layer architecture, its physicochemical properties, and the embedding of the receptor sites affect the probability of binding the analyte. Here, the enhancement of the probe density at the sensing interface by tuning the exponential growth regime of polyelectrolyte multilayers (PEMs) is presented. PEMs were made of poly-l-lysine (PLL), with appended clickable dibenzocyclooctyne (DBCO) groups and oligo(ethylene glycol) chains, and poly(styrene sulfonate) (PSS). The DNA probe loading and target hybridization efficiencies of the PEMs were evaluated as a function of the PLL layer number and the growth regime by a quartz crystal microbalance (QCM). An amplification factor of 25 in the target DNA detection was found for a 33-layer exponentially grown PEM compared to a monolayer. A Voigt-based model showed that DNA probe binding to the DBCO groups is more efficient in the open, exponentially grown films, while the hybridization efficiencies appeared to be high for all layer architectures. These results show the potential of such engineered gel-like structures to increase the detection of bio-relevant analytes in biosensing systems.

A novel label-free solid-state electrochemiluminescence sensor based on the resonance energy transfer from Ru(bpy)32+ to GO for DNA hybridization detection

Based on electrochemiluminescence resonance energy transfer (ERET) from Ru(bpy)₃²⁺ to graphene oxide (GO), a novel label-free solid-state ECL sensor for sensitive detection of DNA was proposed. First, Ru(bpy)₃²⁺/AuNPs was successfully prepared by using a simple and green method and characterized by transmission electron microscopy (TEM), Energy Dispersive X-ray (EDX), and UV-vis spectroscopy. Then, the Ru(bpy)₃²⁺/AuNPs colloid was assembled on the gold electrode surface for solid-state ECL film which also later could be used to immobilize thiol-derivatized, single-stranded DNA (HS-ssDNA) via Au-S interactions. The stepwise modification procedure was characterized by cyclic voltammetry(CV), electrochemical impedance spectroscopy (EIS), probe approach curves (PAC) and ECL, respectively. The resulting modified electrode was tested as ECL biosensor for DNA detection. Upon addition of GO, the strong noncovalent interaction between HS-ssDNA and GO led to ECL quenching because of ERET. When in the presence of target ssDNA (t-ssDNA), the distance between the HS-ssDNA and GO increased, which significantly hindered the ERET and, thus, resulted in the restoration of ECL. The ECL intensity of the biosensor increased linearly with t-ssDNA concentration in the range of 50-1000pM, and the detection limit is 20pM. To the best of our knowledge, this is the first application of solid-state ERET from Ru(bpy)₃²⁺ to GO and opens new opportunities for sensitive detection of biorecognition events.

Phosphorus dendrimers for nanomedicine

From biomaterials to imaging, and from drug delivery to drugs by themselves, phosphorus-containing dendrimers offer a large palette of biological properties, depending essentially on their types of terminal functions. The most salient examples of phosphorus dendrimers used for the elaboration of bio-chips and of supports for cell cultures, for imaging biological events, and for carrying and delivering drugs or biomacromolecules are presented in this feature article. Several phosphorus dendrimers can be considered also as drugs per se (by themselves) in particular to fight against cancers, neurodegenerative diseases, and inflammation, both in vitro and in vivo. Toxicity assays are also reported.

Bifunctional Phosphorus Dendrimers and Their Properties

Dendrimers are hyperbranched and monodisperse macromolecules, generally considered as a special class of polymers, but synthesized step-by-step. Most dendrimers have a uniform structure, with a single type of terminal function. However, it is often desirable to have at least two different functional groups. This review will discuss the case of bifunctional phosphorus-containing dendrimers, and the consequences for their properties. Besides the terminal functions, dendritic structures may have also a function at the core, or linked off-center to the core, or at the core of dendrons (dendritic wedges). Association of two dendrons having different terminal functions leads to Janus dendrimers (two faces). The internal structure can also possess functional groups on one layer, or linked to one layer, or on several layers. Finally, there are several ways to have two types of terminal functions, besides the case of Janus dendrimers: either each terminal function bears two functions sequentially, or two different functions are linked to each terminal branching point. Examples of each type of structure will be given in this review, as well as practical uses of such sophisticated structures in the fields of fluorescence, catalysis, nanomaterials and biology.

Plasmon-Enhanced Fluorescence Biosensors: a Review

Surfaces of metallic films and metallic nanoparticles can strongly confine electromagnetic field through its coupling to propagating or localized surface plasmons. This interaction is associated with large enhancement of the field intensity and local optical density of states which provides means to increase excitation rate, raise quantum yield, and control far field angular distribution of fluorescence light emitted by organic dyes and quantum dots. Such emitters are commonly used as labels in assays for detection of chemical and biological species. Their interaction with surface plasmons allows amplifying fluorescence signal (brightness) that accompanies molecular binding events by several orders of magnitude. In conjunction with interfacial architectures for the specific capture of target analyte on a metallic surface, plasmon-enhanced fluorescence (PEF) that is also referred to as metal-enhanced fluorescence (MEF) represents an attractive method for shortening detection times and increasing sensitivity of various fluorescence-based analytical technologies. This review provides an introduction to fundamentals of PEF, illustrates current developments in design of metallic nanostructures for efficient fluorescence signal amplification that utilizes propagating and localized surface plasmons, and summarizes current implementations to biosensors for detection of trace amounts of biomarkers, toxins, and pathogens that are relevant to medical diagnostics and food control.

Highly sensitive and selective detection of the pyrophosphate anion biomarker under physiological conditions

Self-assembled monolayers on gold of a multidentate adsorbate bearing a bis(carbazolyl)urea unit are prepared and used as a surface resonance plasmon sensor for the detection of hydrogen pyrophosphate anions under physiological conditions.

Surface plasmon resonance sensing of nucleic acids: a review

Biosensors based on surface plasmon resonance (SPR) have become a central tool for the investigation and quantification of biomolecules and their interactions. Nucleic acids (NAs) play a vital role in numerous biological processes and therefore have been one of the major groups of biomolecules targeted by the SPR biosensors. This paper discusses the advances of NA SPR biosensor technology and reviews its applications both in the research of molecular interactions involving NAs (NA-NA, NA-protein, NA-small molecule), as well as for the field of bioanalytics in the areas of food safety, medical diagnosis and environmental monitoring.

Sensitive detection of unlabeled oligonucleotides using a paired surface plasma waves biosensor

Detection of unlabeled oligonucleotides using surface plasmon resonance (SPR) is difficult because of the oligonucleotides' relatively lower molecular weight compared with proteins. In this paper, we describe a method for detecting unlabeled oligonucleotides at low concentration using a paired surface plasma waves biosensor (PSPWB). The biosensor uses a sensor chip with an immobilized probe to detect a target oligonucleotide via sequence-specific hybridization. PSPWB measures the demodulated amplitude of the heterodyne signal in real time. In the meantime, the ratio of the amplitudes between the detected output signal and reference can reduce the excess noise from the laser intensity fluctuation. Also, the common-path propagation of p and s waves cancels the common phase noise induced by temperature variation. Thus, a high signal-to-noise ratio (SNR) of the heterodyne signal is detected. The sequence specificity of oligonucleotide hybridization ensures that the platform is precisely discriminating between target and non-target oligonucleotides. Under optimized experimental conditions, the detected heterodyne signal increases linearly with the logarithm of the concentration of target oligonucleotide over the range 0.5-500 pM. The detection limit is 0.5 pM in this experiment. In addition, the non-target oligonucleotide at concentrations of 10 pM and 10nM generated signals only slightly higher than background, indicating the high selectivity and specificity of this method. Different length of perfectly matched oligonucleotide targets at 10-mer, 15-mer and 20-mer were identified at the concentration of 150 pM.

Kinetic mechanisms in morpholino-DNA surface hybridization

Morpholinos (MOs) are DNA analogues whose uncharged nature can bring fundamental advantages to surface hybridization technologies such as DNA microarrays, by using MOs as the immobilized, or "probe", species. Advancement of MO-based diagnostics, however, is challenged by limited understanding of the surface organization of MO molecules and of how this organization impacts hybridization kinetics and thermodynamics. The present study focuses on hybridization kinetics between monolayers of MO probes and DNA targets as a function of the instantaneous extent of hybridization (i.e., duplex coverage), total probe coverage, and ionic strength. Intriguingly, these experiments reveal distinct kinetic stages, none of which are consistent with Langmuir kinetics. The initial stage, in which duplex coverage remains relatively sparse, indicates confluence of two effects: blockage of target access to unhybridized probes by previously formed duplexes and deactivation of the solid support due to consumption of probe molecules. This interpretation is consistent with a surface organization in which unhybridized MO probes localize near the solid support, underneath a layer of MO-DNA duplexes. As duplex coverage builds, provided saturation is not reached first, the initial stage can transition to an unusual regime characterized by near independence of hybridization rate on duplex coverage, followed by a prolonged approach to equilibrium. The possible origins of these more complex latter behaviors are discussed. Comparison with published data for DNA and peptide nucleic acid (PNA) probes is carried out to look for universal trends in kinetics. This comparison reveals qualitative similarities when comparable surface organization of probes is expected. In addition, MO monolayers are found capable of a broad range of reactivities that span reported values for PNA and DNA probes.

Layer-by-Layer Assemblies in Nanoporous Templates: Nano-Organized Design and Applications of Soft Nanotechnology

The synergistic combination of layer-by-layer (LbL) assembly and nanoporous membrane templating has greatly facilitated the creation of complex and functional nanotubular structures. The approach takes advantage of both the new properties conferred by assembling diverse LbL building blocks and the tight dimensional control offered by nanotemplating to enable new functionalities that arise from the highly anisotropic "one-dimensional" LbL-nanotube format. In this review, we aim to convey the key developments and provide a current snap-shot of such templated LbL nanoarchitectures. We survey recent developments that have enabled the assembly of polymers, biomolecules and inorganic nanoparticles "à la carte", via electrostatic, covalent and specific (bio)recognition interactions. We also discuss the emerging mechanistic understanding of the LbL assembly process within the nanopore environment. Finally, we present a diverse range of LbL nanotube "devices" to illustrate the versatility of the nanotemplated LbL toolbox for generating functional soft nanotechnology.

Effects of lateral spacing on enzymatic on-chip DNA polymerization

Enzymatic on-chip DNA polymerization can be utilized to elongate surface-bound primers with DNA polymerase and to enhance the signal in the detection of target DNAs on the solid support. In order to investigate the steric effect of the enzymatic reaction on the solid support, we compared the efficiency of on-chip DNA polymerization on a high-density surface with that on a spacing-controlled surface. The spacing-controlled, 9-acid dendron-coated surface exhibited approximately 8-fold higher efficiency of on-chip DNA polymerization compared with the high-density surface. The increase in fluorescence intensity during the on-chip DNA polymerization could be fit to an exponential equation, and the saturation level of the 9-acid dendron slide was 7 times higher than that of the high-density slide. The on-chip DNA polymerization was employed to measure the transcription level of nine genes related to epithelial-to-mesenchymal transition in hepatocellular carcinoma cells. Compared to the high-density surface, the dendron-coated surface exhibited a lower detection limit in the on-chip DNA polymerization and higher correlation with transcription levels as determined by quantitative real-time PCR. Our results suggest that control of the lateral spacing of DNA strands on the solid support should significantly enhance the accessibility of DNA polymerase and the efficiency of the on-chip DNA polymerization.

Polyelectrolyte layer-by-layer deposition in cylindrical nanopores

Layer-by-layer (LbL) deposition of polyelectrolytes within nanopores in terms of the pore size and the ionic strength was experimentally studied. Anodic aluminum oxide (AAO) membranes, which have aligned, cylindrical, nonintersecting pores, were used as a model nanoporous system. Furthermore, the AAO membranes were also employed as planar optical waveguides to enable in situ monitoring of the LbL process within the nanopores by optical waveguide spectroscopy (OWS). Structurally well-defined N,N-disubstituted hydrazine phosphorus-containing dendrimers of the fourth generation, with peripherally charged groups and diameters of approximately 7 nm, were used as the model polyelectrolytes. The pore diameter of the AAO was varied between 30-116 nm and the ionic strength was varied over 3 orders of magnitude. The dependence of the deposited layer thickness on ionic strength within the nanopores is found to be significantly stronger than LbL deposition on a planar surface. Furthermore, deposition within the nanopores can become inhibited even if the pore diameter is much larger than the diameter of the G4-polyelectrolyte, or if the screening length is insignificant relative to the dendrimer diameter at high ionic strengths. Our results will aid in the template preparation of polyelectrolyte multilayer nanotubes, and our experimental approach may be useful for investigating theories regarding the partitioning of nano-objects within nanopores where electrostatic interactions are dominant. Furthermore, we show that the enhanced ionic strength dependence of polyelectrolyte transport within the nanopores can be used to selectively deposit a LbL multilayer atop a nanoporous substrate.