Label-Free Raman Observation of TET1 Protein-Mediated Epigenetic Alterations in DNA.

Epigenetic modifications of DNA are known to modulate gene activity and expression and are believed to result in genetic diseases, such as cancer. Four modified cytosines were discovered in mammalian genomes: 5-methycytoine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC). They are regarded as DNA epigenetic markers and play key roles in the regulation of the dynamic balance between DNA methylation and demethylation. Although detection approaches toward 5mC are ubiquitous, few assays have reported the simultaneous determination of all four modified cytosines as well as monitoring of their dynamic alterations. Here, we developed a label-free surface enhanced Raman spectroscopy (SERS)-based method for directly sensing the four DNA modifications by using a plasmonic gold nanohole array (PGNA) with well-controlled hot spots and an open surface as the substrate. This method is based on identifying SERS spectral features resulting from DNA base modifications. Our study shows that 5mC, 5hmC, 5fC, and 5caC exhibit distinct Raman spectroscopic signatures at 785, 660, 1450, and 1680 cm-1, respectively. Moreover, the developed method can be used for tracking of the dynamic alterations among these four modified cytosines in DNA mediated by the ten-eleven translocation (TET) protein. The dynamic stepwise conversion from 5mC into 5hmC, 5fC, and 5caC is further demonstrated to be a typical three-step consecutive reaction with rate constants of 0.6, 0.25, and 0.15 min-1, respectively, which has not been achieved before via a SERS-based method.

Sensitive Bacterial Detection via Dielectrophoretic-Enhanced Mass Transport Using Surface-Plasmon-Resonance Biosensors.

The performance of surface plasmon resonance (SPR)-based bacterial biosensors is often compromised as a result of diffusion-limited mass transport of bacteria to the sensing surface. In this work, dually functional interdigitated electrodes (IDEs) were developed to sustain SPR and increase bacterial mass transport through external application of dielectrophoresis (DEP). IDEs were defined into 50 nm Au films with fixed electrode gaps ( EG = 5 µm) and varied electrode widths ( EW = 10, 20, and 100 µm),  referred to as interdigitated SPR (iSPR) chips. The iSPR chips with EW = 100 µm effectively supported SPR, with comparable sensitivity to those of conventional SPR chips. The surfaces of iSPR chips ( EW = 100 µm) were modified with mannose to target the FimH adhesin of Escherichia coli and increase cellular adhesion. An LOD of ∼3.0 × 102 CFU/mL E. coli was achieved on mannosylated iSPR chips under positive-DEP conditions, which is about a 5 order of magnitude improvement compared with those of mannosylated conventional SPR chips without DEP. Furthermore, secondary antibody amplification enabled selective enhancement of dilute (103 CFU/mL) E. coli suspensions, whereas no amplification was observed for concentrated (108 CFU/mL) nontarget ( Staphylococcus epidermidis) bacterial suspensions. The results presented here indicate the great potential of the incorporation of DEP into SPR biosensors for rapid, sensitive, and specific detection of bacteria with broad applications in areas of biomedical diagnostics, environmental monitoring, food safety, and homeland security.

Tuning the spectral response of ultraviolet organic-inorganic hybrid photodetectors via charge trapping and charge collection narrowing.

Organic-inorganic hybrid ultraviolet photodetectors with tunable spectral response are desirable for many different applications. In this work, we blended poly[bis(4-phenyl)(2,4,6-trimethylphenyl)amine] (PTAA) with ZnO nanoparticles in weight ratios of 1 : 1 and 2 : 1 to create charge traps within the active layers for devices with the conventional structure ITO/PEDOT : PSS/PTAA : ZnO/BCP/Al. Thin (150-200 nm) and thick (1400-1900 nm) active layers were employed to utilize charge collection narrowing (CCN). Both thickness and composition of the active layer impacted the spectral tunability of the photoresponse. A single narrow response peak centered at 420 nm (the PTAA absorption edge) with a full width at half maximum of 12 nm was achieved from the device with a 1900 nm active layer and PTAA : ZnO weight ratio of 1 : 1. Decreasing the active layer thickness to 150 nm resulted in a broad spectral response between 320-420 nm with an external quantum efficiency (EQE) value of 295% under 350 nm illumination and a -1 V bias, exhibiting photomultiplication via charge trapping and injection even at small reverse biases. Increasing the weight ratio of PTAA : ZnO to 2 : 1 lowered both the dark current and photocurrent, eliminated photomultiplication in the thin device, and diminished the efficacy of CCN to narrow the spectral photoresponse in the thick device. Transfer matrix method (TMM) and 3-dimensional finite-difference time-domain (3D-FDTD) simulations were performed to understand the impact of thickness and composition of the active layer on the spectral response of UV photodetectors in terms of exciton generation rate and electric field distribution within the devices.

Paper Sensor Coated with a Poly(carboxybetaine)-Multiple DOPA Conjugate via Dip-Coating for Biosensing in Complex Media.

Cellulose paper is an ideal diagnostic platform for low-cost, easily disposable and lightweight implementation, but requires surface modification to achieve detection with high sensitivity and specificity in complex media. In this work, a polymer-catechol conjugate containing a superhydrophilic nonfouling poly(carboxylbetaine) (pCB) and four surface-binding l-3,4-dihydroxyphenylalanine (DOPA) groups, pCB-(DOPA)4, were applied onto a paper-based sensor surface via a simple "graft-to" immersion process to render the surface with both nonfouling and protein functionalizable properties. This dip-coating technique is effective, convenient and robust as compared to the "graft-from" techniques reported previously with similar nonfouling properties. The coated paper sensor showed both increased analyte diffusion rate and improved sensitivity of glucose detection in human blood serum. The capability of pCB-(DOPA)4-modified paper sensor for specific antigen-antibody detection was demonstrated via the covalent immobilization of bovine serum albumin antibody (anti-BSA) and fibrinogen antibody (anti-Fg) onto the pCB-coated surface via simple 1-ethyl-3-(3-(dimethylamino)propyl)-carbodiimide and N-hydroxysuccinimide (EDC/NHS) chemistry.

Design and development of plasmonic nanostructured electrodes for ITO-free organic photovoltaic cells on rigid and highly flexible substrates.

Indium tin oxide (ITO) is the most common transparent electrode used in organic photovoltaics (OPVs), yet limited indium reserves and poor mechanical properties make it non-ideal for large-scale OPV production. To replace ITO, we designed, fabricated, and deployed plasmonic nanostructured electrodes in inverted OPV devices. We found that active layer absorption is significantly impacted by ZnO thickness which affects the optical field distribution inside the resonant cavity formed between the plasmonic nanostructured electrode and top electrode. High quality Cr/Au nanostructured electrodes were fabricated by nanoimprint lithography and deployed in ITO-free inverted devices on glass. Devices with thinner ZnO showed a PCE as high as 5.70% and higher J SC's than devices on thicker ZnO, in agreement with finite-difference time-domain simulations. In addition, as the active layer was made optically thin, ITO-based devices showed diminished J SC while the resonant cavity effect from plasmonic nanostructured electrodes retained J SC. Preliminary ITO-free, flexible devices on PET showed a PCE of 1.82% and those fabricated on ultrathin and conformable Parylene substrates yielded an initial PCE over 1%. The plasmonic electrodes and device designs in this work show promise for developing highly functioning conformable devices that can be applied to numerous needs for lightweight, ubiquitous power generation.

Long-range surface plasmon resonance and surface-enhanced Raman scattering on X-shaped gold plasmonic nanohole arrays.

A multilayered architecture including a thin Au film supporting an X-shaped nanohole array and a thick continuous Au film separated by a Cytop dielectric layer is reported in this work. Long-range surface plasmon resonance (LR-SPR) was generated at the top Au/water interface, which also resulted in a long-range surface-enhanced Raman scattering (LR-SERS) effect. LR-SPR originates from the coupling of surface plasmons (SPs) propagating along the opposite sides of the thin Au film embedded in a symmetric refractive index environment with Cytop (n = 1.34) and water (n = 1.33). The finite-difference time-domain (FDTD) simulation method was used to investigate the optimal dimensions of the substrate by studying the reflectance spectra and electric field profiles. The calculated optimal structure was then fabricated via electron beam lithography, and its LR-SERS performance was demonstrated by detecting rhodamine 6G and 4-mercaptobenzoic acid in the refractive index-matched environment. We believe that this structure as a LR-SPR or LR-SERS substrate can have broad applications in biosensing.

Inverted hybrid CdSe-polymer solar cells adopting PEDOT:PSS/MoO3 as dual hole transport layers.

Inverted CdSe quantum dots (QDs):poly (3-hexylthiophene) (P3HT) organic/inorganic hybrid solar cells (OIHSCs) with the PEDOT: PSS/MoO3 dual hole transport layers (HTLs) showed superior performance over those with a single HTL of PEDOT: PSS or MoO3. The enhanced electron blocking at the active layer/anode interface as well as the prevention of leakage current accounted for the enhancement in the efficiency of the solar cells with the dual HTLs. By adopting the inverted structure and using the dual HTLs, the resistive losses of the CdSe QDs:P3HT hybrid system at high illumination power were effectively prevented. Further study showed the structure of dual HTLs was applicable to the solar cells with CdSe QDs and nanorods (NRs) blended with poly(thienothiophene-co-benzodithiophenes)7-F20 (PTB7-F20).

Cellulose paper sensors modified with zwitterionic poly(carboxybetaine) for sensing and detection in complex media.

Poly(carboxybetaine) (PCB) functionalized cellulose paper was used as a paper-based microfluidic device. The results showed that the PCB modified paper sensor was able to achieve (a) more rapid and sensitive glucose detection from undiluted human serum compared to bare cellulose and (b) specific antigen detection via covalently immobilized antibodies.

Sensitive and fast detection of fructose in complex media via symmetry breaking and signal amplification using surface-enhanced Raman spectroscopy.

A new strategy is proposed to sensitively and rapidly detect analytes with weak Raman signals in complex media using surface-enhanced Raman spectroscopy (SERS) via detecting the SERS signal changes of the immobilized probe molecules on SERS-active substrates upon binding of the analytes. In this work, 4-mercaptophenylboronic acid (4-MPBA) was selected as the probe molecule which was immobilized on the gold surface of a quasi-three-dimensional plasmonic nanostructure array (Q3D-PNA) SERS substrate to detect fructose. The molecule of 4-MPBA possesses three key functions: molecule recognition and reversible binding of the analyte via the boronic acid group, amplification of SERS signals by the phenyl group and thus shielding of the background noise of complex media, and immobilization on the surface of SERS-active substrates via the thiol group. Most importantly, the symmetry breaking of the 4-MPBA molecule upon fructose binding leads to the change of area ratio between totally symmetric 8a ring mode and nontotally symmetric 8b ring mode, which enables the detection. The detection curves were obtained in phosphate-buffered saline (PBS) and in undiluted artificial urine at clinically relevant concentrations, and the limit of detection of 0.05 mM was achieved.

Cross-linked carboxybetaine SAMs enable nanoparticles with remarkable stability in complex media.

A photo-cross-linkable carboxybetaine (CB)-terminated thiol with only one CB headgroup was introduced to modify gold nanoparticles (GNPs) via self-assembled monolayers (SAMs). This CB-terminated thiol consists of three moieties: (a) an anchoring thiol group, which binds directly to the GNP surface, (b) a CB terminal group, which is highly resistant to protein adsorption, and (c) a diacetylene group in the middle, which is converted to a poly(enyne) structure during UV irradiation via 1,4-topochemical polymerization. Results show that, after cross-linking, CB-modified GNPs are highly resistant to protein adsorption from undiluted human blood serum and cell uptake, and are stable at low pH and high temperature. This cross-linkable CB thiol holds tremendous potentials for biomedical applications where stable and thin coatings are needed.

A robust graft-to strategy to form multifunctional and stealth zwitterionic polymer-coated mesoporous silica nanoparticles.

Mesoporous silica nanoparticles (MSNs) are a new class of carrier materials promising for drug/gene delivery and many other important applications. Stealth coatings are necessary to maintain their stability in complex media. Herein, a biomimetic polymer conjugate containing one ultralow fouling poly(carboxybetaine) (pCBMA) chain and one surface-adhesive catechol (DOPA) residue group was efficiently grafted to the outer surface of SBA-15 type MSNs using a convenient and robust method. The cytotoxicity of SBA-15-DOPA-pCBMAs was evaluated by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Results showed no significant decrease in cell viability at the tested concentration range. Macrophage cell uptake studies revealed that the uptake ratios of SBA-15-DOPA-pCBMAs were much lower than that of parent MSNs. Furthermore, inductively coupled plasma mass spectrometry (ICP-MS) analysis results showed that after SBA-15-DOPA-pCBMAs were conjugated with a targeting cyclo-[Arg-Gly-Asp-d-Tyr-Lys] (cRGD) peptide, uptake by bovine aortic endothelial cells (BAECs) was notably increased. Results indicated that cRGD-functionalized MSNs were able to selectively interact with cells expressing αvß3 integrin. Thus, MSNs with DOPA-pCBMAs are promising as stealth multifunctional biocarriers for targeted drug delivery or diagnostics.

Immunoassays for Extracellular Vesicle Detection via Transmembrane Proteins Using Surface Plasmon Resonance Biosensors.

Extracellular vesicles (EVs) are preeminent carriers of biomarkers and have become the subject of intense biomedical research for medical diagnostics using biosensors. To create effective EV-based immunoassays, it is imperative to develop surface chemistry approaches with optimal EV detection targeting transmembrane protein biomarkers that are not affected by cell-to-cell variability. Here, we developed a series of immunoassays for the detection of EVs derived from mouse monocyte cells using surface plasmon resonance (SPR) biosensors. We chemically immobilized antibodies onto mixed self-assembled monolayers of oligo ethylene glycol (OEG) alkanethiolates with carboxylic and hydroxylic terminal groups. The effects of antibody clonality (monoclonal vs polyclonal) and antibody surface coverage in targeting EVs via CD81 tetraspanins were investigated. We determined binding kinetic parameters, establishing trends from steric hindrance effects and epitope recognition properties of antibodies. Our results indicate that a 40% surface coverage of polyclonal antibodies covalently linked onto a mixed SAM with 10% of terminated -COOH groups yields a promising approach for EV detection with a linear range of 1.9 × 108-1.9 × 109 EVs/mL and a limit of detection of 5.9 × 106 EVs/mL. This optimal immunoassay exhibits a 1.92 nM equilibrium dissociation constant for bound EVs, suggesting a high binding affinity when CD81 is targeted. Our study provides important insights into surface chemistry development for EV detection targeted via transmembrane protein biomarkers using antibodies, which has promising applications for disease diagnostics.

Self-Powered Circularly Polarized Light Detection Enabled by Chiral Two-Dimensional Perovskites with Mixed Chiral-Achiral Organic Cations.

Direct detection of circularly polarized light (CPL) holds great promise for the development of various optical technologies. Chiral 2D organic-inorganic halide perovskites make it possible to fabricate CPL-sensitive photodetectors. However, selectively detecting left-handed circularly polarized (LCP) and right-handed circularly polarized (RCP) light remains a significant challenge. Herein, we demonstrate a greatly enhanced distinguishability of photodiode-type CPL photodetectors based on chiral 2D perovskites with mixed chiral aryl (R)-(+),(S)-(-)-α-methylbenzylammonium (R,S-MBA) and achiral alkyl n-butylammonium (nBA) cations. The (R,S-MBA0.5nBA0.5)2PbI4 perovskites exhibit a 10-fold increase in circular dichroism signals compared to (R,S-MBA)2PbI4 perovskites. The CPL photodetectors based on the mixed-cation perovskites exhibit self-powered capabilities with a specific detectivity of 2.45 × 1012 Jones at a 0 V bias. Notably, these devices show high distinguishability (gres) factors of -0.58 and +0.54 based on (R,S-MBA0.5nBA0.5)2PbI4 perovskites, respectively, surpassing the performance of (R-MBA)2PbI4-based devices by over 3-fold and setting a record for CPL detectors based on chiral 2D n = 1 perovskites.

Extracellular vesicles incorporating retrovirus-like capsids for the enhanced packaging and systemic delivery of mRNA into neurons.

The blood-brain barrier (BBB) restricts the systemic delivery of messenger RNAs (mRNAs) into diseased neurons. Although leucocyte-derived extracellular vesicles (EVs) can cross the BBB at inflammatory sites, it is difficult to efficiently load long mRNAs into the EVs and to enhance their neuronal uptake. Here we show that the packaging of mRNA into leucocyte-derived EVs and the endocytosis of the EVs by neurons can be enhanced by engineering leucocytes to produce EVs that incorporate retrovirus-like mRNA-packaging capsids. We transfected immortalized and primary bone-marrow-derived leucocytes with DNA or RNA encoding the capsid-forming activity-regulated cytoskeleton-associated (Arc) protein as well as capsid-stabilizing Arc 5'-untranslated-region RNA elements. These engineered EVs inherit endothelial adhesion molecules from donor leukocytes, recruit endogenous enveloping proteins to their surface, cross the BBB, and enter the neurons in neuro-inflammatory sites. Produced from self-derived donor leukocytes, the EVs are immunologically inert, and enhanced the neuronal uptake of the packaged mRNA in a mouse model of low-grade chronic neuro-inflammation.

Directly functionalizable surface platform for protein arrays in undiluted human blood plasma.

Protein arrays are a high-throughput approach for proteomic profiling, vital for achieving a greater understanding of biological systems, in addition to disease diagnostics and monitoring therapeutic treatments. In this work, zwitterionic carboxybetaine polymer (pCB) coated substrates were investigated as an array surface platform to enable convenient amino-coupling chemistry on a single directly functionalizable and unblocked film for the sensitive detection of target analytes from undiluted human blood plasma. Using a surface plasmon resonance (SPR) imaging sensor, the antibody immobilization conditions which provided excellent spot morphology and the largest antigen response were determined. It was found that pCB functionalization and the corresponding antigen detection both increased with pH and antibody concentration. Additionally, immobilization only required an aqueous buffer without the need for additives to improve spot quality. The nonspecific protein adsorption to undiluted human plasma on both the antibody immobilized pCB spots and the background were found to be about 9 and 6 ng/cm(2), respectively. A subsequent array consisting of three antibodies spotted onto pCB revealed little cross-reactivity for antigens spiked into the undiluted plasma. The low postfunctionalized nonfouling properties combined with antibody amplification showed similar sensitivities achievable with conventional spectroscopic SPR sensors and the same pCB films, but now with high-throughput capabilities. This represents the first demonstration of low fouling properties following antibody functionalization on protein arrays from undiluted human plasma and indicates the great potential of the pCB platform for high-throughput protein analysis.

In situ strain-level detection and identification of Vibrio parahaemolyticus using surface-enhanced Raman spectroscopy.

The outer membrane of a bacterium is composed of chemical and biological components that carry specific molecular information related to strains, growth stages, expressions to stimulation, and maybe even geographic differences. In this work, we demonstrate that the biochemical information embedded in the outer membrane can be used for rapid detection and identification of pathogenic bacteria using surface-enhanced Raman spectroscopy (SERS). We used seven different strains of the marine pathogen Vibrio parahaemolyticus as a model system. The strains represent four genetically distinct clades isolated from clinical and environmental sources in Washington, U.S.A. The unique quasi-3D (Q3D) plasmonic nanostructure arrays, optimized using finite-difference time-domain (FDTD) calculations, were used as SERS-active substrates for sensitive and reproducible detection of these bacteria. SERS barcodes were generated on the basis of SERS spectra and were used to successfully detect individual strains in both blind samples and mixtures. The sensing and detection methods developed in this work could have broad applications in the areas of environmental monitoring, biomedical diagnostics, and homeland security.

Tunable and highly reproducible surface-enhanced Raman scattering substrates made from large-scale nanoparticle arrays based on periodically poled LiNbO3 templates.

This work describes novel surface-enhanced Raman scattering (SERS) substrates based on ferroelectric periodically poled LiNbO3 templates. The templates comprise silver nanoparticles (AgNPs), the size and position of which are tailored by ferroelectric lithography. The substrate has uniform and large sampling areas that show SERS effective with excellent signal reproducibility, for which the fabrication protocol is advantageous in its simplicity. We demonstrate ferroelectric-based SERS substrates with particle sizes ranging from 30 to 70 nm and present tunable SERS effect from Raman active 4-mercaptopyridine molecules attached to AgNPs when excited by a laser source at 514 nm.

Small to Large Polaron Behavior Induced by Controlled Interactions in Perovskite Quantum Dot Solids.

The polaron is an essential photoexcitation that governs the unique optoelectronic properties of organic-inorganic hybrid halide perovskites, and it has been subject to extensive spectroscopic and theoretical investigation over the past decade. A crucial but underexplored question is how the nature of the photogenerated polarons is impacted by the microscopic perovskite structure and what functional properties this affects. To tackle this question, we chemically tuned the interactions between perovskite quantum dots (QDs) to rationally manipulate the polaron properties. Through a suite of time-resolved spectroscopies, we find that inter-QD interactions open an excited-state channel to form large polaron species, which exhibit enhanced spatial diffusion, slower hot polaron cooling, and a longer intrinsic lifetime. At the same time, polaronic excitons are formed in competition via localized band-edge states, exhibiting strong photoluminescence but are limited by shorter intrinsic lifetimes. This control of polaron type and function through tunable inter-QD interactions not only provides design principles for QD-based materials but also experimentally disentangles polaronic species in hybrid perovskite materials.

Simple physical approach to reducing frictional and adhesive forces on a TiO2 surface via creating heterogeneous nanopores.

A simple physical strategy to reduce the frictional and adhesive forces on TiO(2) films was proposed by constructing mesoporous TiO(2) films with heterogeneously distributed nanopores on the film surfaces. In comparison, TiO(2) films with densely packed nanoparticles were also prepared. The crystal structure and morphology of the films were characterized with Raman spectroscopy, field emission scanning electron microscopy (FESEM), and atomic force microscopy (AFM). It was found that the TiO(2)(B) phase exists in the mesoporuos TiO(2) films but not in the densely packed films. The existence of TiO(2)(B) plays a significant role in creating and maintaining the nanopores in the mesoporous TiO(2) films. The frictional and adhesive forces were measured on both films using AFM. The mesoporous films exhibit two typical adhesion forces of around 3 and 12 nN in the force distribution profile whereas the densely packed films show only one around 12 nN. The frictional coefficients were 2.6 × 10(-3) and 6.7 × 10(-2) for the mesoporous and densely packed TiO(2) films, respectively. A model based on the atomic structures of a thin film of water molecules adsorbed on TiO(2) surfaces leading to hydrophobic effects was proposed to understand the lower frictional and adhesive forces observed on the mesoporous TiO(2) films. This simple physical approach to reducing the frictional and adhesive forces on TiO(2) films could have broad applications to a variety of surface coatings.

Dry film refractive index as an important parameter for ultra-low fouling surface coatings.

Here we demonstrate that the film refractive index (RI) can be an even more important parameter than film thickness for identifying nonfouling polymer films to undiluted human blood plasma and serum. The film thickness and RI are two parameters obtained from ellipsometry. Previously, film thickness has been correlated to ultra-low fouling properties. Practically, the film RI can be used to characterize polymer density but is often overlooked. By varying the water content in the surface-initiated atom transfer radical polymerization of zwitterionic carboxybetaine, a minimum of ∼1.5 RI units was necessary to achieve <5 ng/cm(2) of adsorption from undiluted human serum. A model of the film structure versus water content was also developed. These results point to an important parameter and simple approach for identifying surface coatings suitable for real-world applications involving complex media. Therefore, ultra-low fouling using a thin film is possible if it is densely packed.