Bioconjugation techniques for microfluidic biosensors

Fucoidan and topography modification improved in situ endothelialization on acellular synthetic vascular grafts

Thrombogenesis remains the primary failure of synthetic vascular grafts. Endothelial coverage is crucial to provide an antithrombogenic surface. However, most synthetic materials do not support cell adhesion, and transanastomotic endothelial migration is limited. Here, a surface modification strategy using fucoidan and topography was developed to enable fast in situ endothelialization of polyvinyl alcohol, which is not endothelial cell-adhesive. Among three different immobilization approaches compared, conjugation of aminated-fucoidan promoted endothelial monolayer formation while minimizing thrombogenicity in both in vitro platelet rich plasma testing and ex vivo non-human primate shunt assay. Screening of six topographical patterns showed that 2 μm gratings increased endothelial cell migration without inducing inflammation responses of endothelial cells. Mechanistic studies demonstrated that fucoidan could attract fibronectin, enabling integrin binding and focal adhesion formation and activating focal adhesion kinase (FAK) signaling, and 2 μm gratings further enhanced FAK-mediated cell migration. In a clinically relevant rabbit carotid artery end-to-side anastomosis model, 60% in situ endothelialization was observed throughout the entire lumen of 1.7 mm inner diameter modified grafts, compared to 0% of unmodified graft, and the four-week graft patency also increased. This work presents a promising strategy to stimulate in situ endothelialization on synthetic materials for improving long-term performance.

Efficient Chemical Surface Modification Protocol on SiO2 Transducers Applied to MMP9 Biosensing

The bioreceptor immobilization process (biofunctionalization) turns to be one of the bottlenecks when developing a competent and high sensitivity label-free biosensor. Classical approaches seem to be effective but not efficient. Although biosensing capacities are shown in many cases, the performance of the biosensor is truncated by the inefficacious biofunctionalization protocol and the lack of reproducibility. In this work, we describe a unique biofunctionalization protocol based on chemical surface modification through silane chemistry on SiO₂ optical sensing transducers. Even though silane chemistry is commonly used for sensing applications, here we present a different mode of operation, applying an unusual silane compound used for this purpose (3-Ethoxydimethylsilyl)propylamine, APDMS, able to create ordered monolayers, and minimizing fouling events. To endorse this protocol as a feasible method for biofunctionalization, we performed multiple surface characterization techniques after all the process steps: Contact angle (CA), X-ray photoelectron spectroscopy (XPS), ellipsometry, and fluorescence microscopy. Finally, to evidence the outputs from the SiO₂ surface characterization, we used those SiO₂ surfaces as optical transducers for the label-free biosensing of matrix metalloproteinase 9 (MMP9). We found and demonstrated that the originally designed protocol is reproducible, stable, and suitable for SiO2-based optical sensing transducers.

1,1'-Carbonyldiimidazole-copper nanoflower enhanced collapsible laser scribed graphene engraved microgap capacitive aptasensor for the detection of milk allergen

The bovine milk allergenic protein, 'β-lactoglobulin' is one of the leading causes of milk allergic reaction. In this research, a novel label-free non-faradaic capacitive aptasensor was designed to detect β-lactoglobulin using a Laser Scribed Graphene (LSG) electrode. The graphene was directly engraved into a microgapped (~ 95 µm) capacitor-electrode pattern on a flexible polyimide (PI) film via a simple one-step CO₂ laser irradiation. The novel hybrid nanoflower (NF) was synthesized using 1,1'-carbonyldiimidazole (CDI) as the organic molecule and copper (Cu) as the inorganic molecule via one-pot biomineralization by tuning the reaction time and concentration. NF was fixed on the pre-modified PI film at the triangular junction of the LSG microgap specifically for bio-capturing β-lactoglobulin. The fine-tuned CDI-Cu NF revealed the flower-like structures was viewed through field emission scanning electron microscopy. Fourier-transform infrared spectroscopy showed the interactions with PI film, CDI-Cu NF, oligoaptamer and β-lactoglobulin. The non-faradaic sensing of milk allergen β-lactoglobulin corresponds to a higher loading of oligoaptamer on 3D-structured CDI-Cu NF, with a linear range detection from 1 ag/ml to 100 fg/ml and attomolar (1 ag/ml) detection limit (S/N = 3:1). This novel CDI-Cu NF/LSG microgap aptasensor has a great potential for the detection of milk allergen with high-specificity and sensitivity.

A Three-Dimensional Micromixer Using Oblique Embedded Ridges

A micromixer is one of the most significant components in a microfluidic system. A three-dimensional micromixer was developed with advantages of high efficiency, simple fabrication, easy integration, and ease of mass production. The designed principle is based on the concepts of splitting-recombination and chaotic advection. A numerical model of this micromixer was established to characterize the mixing performance for different parameters. A critical Reynolds number (Re) was obtained from the simulation results. When the Re number is smaller than the critical value, the fluid mixing is mainly dependent on the mechanism of splitting-recombination, therefore, the length of the channel capable of complete mixing (complete mixing length) increases as the Re number increases. When the Re number is larger than the critical value, the fluid mixing is dominated by chaotic advection, and the complete mixing length decreases as the Re number increases. For normal fluids, a complete mixing length of 500 µm can be achieved at a very small Re number of 0.007 and increases to 2400 µm as the Re number increases to the critical value of 4.7. As the Re number keep increasing and passes the critical Re number, the complete mixing length continues to descend to 650 µm at the Re number of 66.7. For hard-to-mix fluids (generally referring to fluids with high viscosity and low diffusion coefficient, which are difficult to mix), even though no evidence of strong chaotic advection is presented in the simulation, the micromixer can still achieve a complete mixing length of 2550 µm. The mixing performance of the micromixer was also verified by experiments. The experimental results showed a consistent trend with the numerical simulation results, which both climb upward when the Re number is around 0.007 (flow rate of 0.03 μm/min) to around 10 (flow rate of 50 μm/min), then descend when the Re number is around 13.3 (flow rate of 60 µm/min).

Plasma-induced covalent immobilization and patterning of bioactive species in microfluidic devices

Here, we present a straightforward technique to create bio-functional microfluidic channels using CO2 plasma to induce both carboxylic and hydroxyl groups onto the channel surface. Consequently, not only does the surface allow for irreversible covalent bonding to an oxygen plasma treated PDMS for microfluidic device fabrication, but it also provides functionality for biomolecular immobilization. Furthermore, we demonstrate integration of this technique with microcontact printing to covalently micropattern functional biomolecules inside microfluidic channels. The bio-functionality and efficacy of the microcontact printed antibodies is demonstrated for both bioassays as well as patterning and culturing different cell lines. Results show that the introduced method can be an excellent candidate for cell culture studies in microfluidics. With the new printing method, full cell confluency (∼400 cells per mm2) was achieved after incubation for only 1 day, which is significantly greater than other conventional cell culture techniques inside microfluidic devices. As a proof of concept, we demonstrated the endothelial cells functionality by stimulating von Willebrand Factor secretion under shear stress. This is done via perfusion of histamine through the channel and performing immunofluorescence labeling to observe the inflammatory response of the cells. The developed method eliminates the need for wet chemistry and significantly simplifies producing bio-functional chips which can be used for biosensing, organs-on-chips and tissue engineering applications.

Aptamer surface functionalization of microfluidic devices using dendrimers as multi-handled templates and its application in sensitive detections of foodborne pathogenic bacteria

A microfluidic system that incorporates both dendrimers and aptamers to detect E. coli O157:H7 is developed. To achieve this, generation 7-polyamidoamine dendrimers were immobilized onto the detection surfaces of PDMS microfluidic channels; subsequently aptamers against E. coli O157:H7 were conjugated onto the microchannel surfaces via the immobilized dendrimers as templates. Surface modifications were characterized by FTIR, XPS, water contact angles, fluorescence microscopy and AFM to confirm the success of each surface modification steps. The efficacy of this simple microchannel in detection was investigated using E. coli O157:H7 spiked samples. Our results showed that this interesting approach significantly increased the amount of aptamers available on the microfluidic channel surfaces to capture E. coli O157:H7 cells to allow sensitive detection, which in turn resulted in detections of E. coli O157:H7 cells at a low limit of detection of 10² cells mL^-1. The results also demonstrated that in comparison with the generation 4-polyamidoamine dendrimers (G4) modified microchannels, those modified with G7 showed enhanced detection signals, improved target capturing efficiencies, and at higher throughput. This simple whole cell detection design has not been reported in the literature and it is an interesting and effective approach to developing a sensitive and rapid detection platform for foodborne pathogenic bacteria.

Detection of cancer antigens (CA-125) using gold nano particles on interdigitated electrode-based microfluidic biosensor

Integrating microfluidics with biosensors is of great research interest with the increasing trend of lab-on-the chip and point-of-care devices. Though there have been numerous studies performed relating microfluidics to the biosensing mechanisms, the study of the sensitivity variation due to microfluidic flow is very much limited. In this paper, the sensitivity of interdigitated electrodes was evaluated at the static drop condition and the microfluidic flow condition. In addition, this study demonstrates the use of gold nanoparticles to enhance the sensor signal response and provides experimental results of the capacitance difference during cancer antigen-125 (CA-125) antigen-antibody conjugation at multiple concentrations of CA-125 antigens. The experimental results also provide evidence of disease-specific detection of CA-125 antigen at multiple concentrations with the increase in capacitive signal response proportional to the concentration of the CA-125 antigens. The capacitive signal response of antigen-antibody conjugation on interdigitate electrodes has been enhanced by approximately 2.8 times (from 260.80 to 736.33 pF at 20 kHz frequency) in static drop condition and approximately 2.5 times (from 205.85 to 518.48 pF at 20 kHz frequency) in microfluidic flow condition with gold nanoparticle-coating. The capacitive signal response is observed to decrease at microfluidic flow condition at both plain interdigitated electrodes (from 260.80 to 205.85 pF at 20 kHz frequency) and gold nano particle coated interdigitated electrodes (from 736.33 to 518.48 pF at 20 kHz frequency), due to the strong shear effect compared to static drop condition. However, the microfluidic channel in the biosensor has the potential to increase the signal to noise ratio due to plasma separation from the whole blood and lead to the increase concentration of the biomarkers in the blood volume for sensing.

Microfluidic Exponential Rolling Circle Amplification for Sensitive microRNA Detection Directly from Biological Samples

There is an urgent need of sensitive bioanalytical platforms for sensitive and precise quantification of low-abundance microRNA targets in complex biological samples, including liquid biopsies of tumors. Many of current miRNA biosensing methods require laborious sample pretreatment procedures, including extraction of total RNA, which largely limits their biomedical and clinical applications. Herein we developed an integrated Microfluidic Exponential Rolling Circle Amplification (MERCA) platform for sensitive and specific detection of microRNAs directly in minimally processed samples. The MERCA system integrates and streamlines solid-phase miRNA isolation, miRNA-adapter ligation, and a dualphase exponential rolling circle amplification (eRCA) assay in one analytical workflow. By marrying the advantages of microfluidics in leveraging bioassay performance with the high sensitivity of eRCA, our method affords a remarkably low limit of detection at <10 zeptomole levels, with the ability to discriminate single-nucleotide difference. Using the MERCA chip, we demonstrated quantitative detection of miRNAs in total RNA, raw cell lysate, and cellderived exosomes. Comparing with the parallel TaqMan RT-qPCR measurements verified the adaptability of the MERCA system for detection of miRNA biomarkers in complex biological materials. In particular, high sensitivity of our method enables direct detection of low-level exosomal miRNAs in as few as 2 × 10⁶ exosomes. Such analytical capability immediately addresses the unmet challenge in sample consumption, a key setback in clinical development of exosome-based liquid biopsies. Therefore, the MERCA would provide a useful platform to facilitate miRNA analysis in broad biological and clinical applications.

Focused Glycomic Profiling With an Integrated Microfluidic Lectin Barcode System

Protein glycosylation is one of the key processes that play essential roles in biological functions and dysfunctions. However, progress in glycomics has considerably lagged behind genomics and proteomics, due in part to the enormous challenges associated with the analysis of glycans. Here we present a new integrated and automated microfluidic lectin barcode platform to substantially improve the performance of lectin array for focused glycomic profiling. The chip design and flow control were optimized to promote the lectin-glycan binding kinetics and the speed of lectin microarrays. Moreover, we established an on-chip lectin assay which employs a very simple blocking method to effectively suppress the undesired background due to lectin binding of antibodies. Using this technology, we demonstrated focused differential profiling of tissue-specific glycosylation changes of a biomarker, the CA125 protein purified from ovarian cancer cell lines, and different tissues from ovarian cancer patients in a fast, reproducible, and high-throughput fashion. Highly sensitive CA125 detection was also demonstrated with a detection limit much lower than the clinical cutoff value for cancer diagnosis. This microfluidic platform holds the potential to integrate with sample preparation functions to construct a fully integrated "sample-to-answer" microsystem for focused differential glycomic analysis. Thus, our technology should present a powerful tool in support of rapid advance in glycobiology and glycobiomarker development.

Fast, Sensitive, and Quantitative Point-of-Care Platform for the Assessment of Drugs of Abuse in Urine, Serum, and Whole Blood

Drug abuse is a major public health problem in many countries in Europe and North America. Currently available platforms for drug abuse assessment are facing technical challenges of nonquantitation, inaccuracy, low throughput, incompatibility with diverse complex specimens, long assay times, and requirement of instrument and/or expertise for readout. Here, we report an integrated competitive volumetric-bar-chart chip (CV-Chip) to assay multiple drug targets at the point-of-care (POC). To the best of our knowledge, it is the first time that a POC platform has been demonstrated to fully address the above-mentioned limitations. We applied this integrated CV-chip platform to assay multiple drugs in 38 patient urine and serum samples and validated the on-chip results with an LC-MS/MS method, indicating a clinical sensitivity and specificity of 0.94 and 1.00, respectively. We further demonstrated that the combination of an on-chip blood separator with the CV-Chip enabled the platform to directly assay finger-prick whole blood samples, which have always been recognized as an ideal biospecimen for POC detections. In summary, this integrated CV-Chip is able to serve as a sensitive, accurate, fast, portable, readout visible, and minimally invasive platform for drug abuse assessment.

Group III nitride nanomaterials for biosensing

Biosensing has found wide applications in biological and medical research, and in clinical diagnosis, environmental monitoring and other analytical tasks. Recognized as novel and outstanding transducing materials because of their superior and unique physical/chemical properties, group III nitride (III-nitride) nanomaterials have been introduced into biosensor development with remarkable advancements achieved in the past few decades. This paper presents the first comprehensive review on biosensor development with III-nitride nanomaterials. The review starts with the introduction of the material properties and biocompatibility of III-nitrides that are useful for biosensing. The focus is then placed on surface treatments of III-nitrides, which lay the foundation for biosensing, and on biosensing mechanisms where the exceptional properties of III-nitride nanomaterials lead to superior biosensing performance. From a practical point of view, techniques for biosensor fabrication are then summarized. Finally, existing biosensing applications and future directions are discussed.

Versatile Bottom-Up Synthesis of Tethered Bilayer Lipid Membranes on Nanoelectronic Biosensor Devices

Interfacing nanoelectronic devices with cell membranes can enable multiplexed detection of fundamental biological processes (such as signal transduction, electrophysiology, and import/export control) even down to the single ion channel level, which can lead to a variety of applications in pharmacology and clinical diagnosis. Therefore, it is necessary to understand and control the chemical and electrical interface between the device and the lipid bilayer membrane. Here, we develop a simple bottom-up approach to assemble tethered bilayer lipid membranes (tBLMs) on silicon wafers and glass slides, using a covalent tether attachment chemistry based on silane functionalization, followed by step-by-step stacking of two other functional molecular building blocks (oligo-poly(ethylene glycol) (PEG) and lipid). A standard vesicle fusion process was used to complete the bilayer formation. The monolayer synthetic scheme includes three well-established chemical reactions: self-assembly, epoxy-amine reaction, and EDC/NHS cross-linking reaction. All three reactions are facile and simple and can be easily implemented in many research labs, on the basis of common, commercially available precursors using mild reaction conditions. The oligo-PEG acts as the hydrophilic spacer, a key role in the formation of a homogeneous bilayer membrane. To explore the broad applicability of this approach, we have further demonstrated the formation of tBLMs on three common classes of (nano)electronic biosensor devices: indium-tin oxide-coated glass, silicon nanoribbon devices, and high-density single-walled carbon nanotubes (SWNT) networks on glass. More importantly, we incorporated alemethicin into tBLMs and realized the real-time recording of single ion channel activity with high sensitivity and high temporal resolution using the tBLMs/SWNT network transistor hybrid platform. This approach can provide a covalently bonded lipid coating on the oxide layer of nanoelectronic devices, which will enable a variety of applications in the emerging field of nanoelectronic interfaces to electrophysiology.

Surface modification of SOI-FET sensors for label-free and specific detection of short RNA analyte

AIM

A new type of surface modification of SOI-FET sensors with ultrathin sensor-probe transition layer and uncharged probes for highly specific detection of short RNA (saRNA) was suggested.

MATERIALS & METHODS

Carbonyldiimidazole (CDI) or glycidoxypropyltrimethoxysilane were used as precursors of sensor-probe interface layers, together with peptide nucleic acids and new NA analogues - phosphoryl guanidine oligo(2'-OMe)ribonucleotides (PGO) as probes for RNA hybridization. RNA sequences corresponding to mRNA NELFA (NM_005663) and microRNA-29a (cancer markers) were used as saRNA targets. Real-time saRNA detection by SOI-FET sensors and fluorescence analysis were applied.

RESULTS

Highly specific response with femtomolar sensitivity to saRNA was demonstrated for CDI-PGO-modified sensors fabricated by optical lithography.

CONCLUSION

The proposed CDI-PGO protocol of modification of Si sensor surface is a promising procedure for biomedical applications.

Integrated Microfluidic Lectin Barcode Platform for High-Performance Focused Glycomic Profiling

Protein glycosylation is one of the key processes that play essential roles in biological functions and dysfunctions. However, progress in glycomics has considerably lagged behind genomics and proteomics, due in part to the enormous challenges in analysis of glycans. Here we present a new integrated and automated microfluidic lectin barcode platform to substantially improve the performance of lectin array for focused glycomic profiling. The chip design and flow control were optimized to promote the lectin-glycan binding kinetics and speed of lectin microarray. Moreover, we established an on-chip lectin assay which employs a very simple blocking method to effectively suppress the undesired background due to lectin binding of antibodies. Using this technology, we demonstrated focused differential profiling of tissue-specific glycosylation changes of a biomarker, CA125 protein purified from ovarian cancer cell line and different tissues from ovarian cancer patients in a fast, reproducible, and high-throughput fashion. Highly sensitive CA125 detection was also demonstrated with a detection limit much lower than the clinical cutoff value for cancer diagnosis. This microfluidic platform holds the potential to integrate with sample preparation functions to construct a fully integrated "sample-to-answer" microsystem for focused differential glycomic analysis. Thus, our technology should present a powerful tool in support of rapid advance in glycobiology and glyco-biomarker development.

Imaging and spectroscopic comparison of multi-step methods to form DNA arrays based on the biotin-streptavidin system

Three multi-step multi-molecular approaches using the biotin-streptavidin system to contact-print DNA arrays on SiO2 surfaces modified with (3-glycidoxypropyl)trimethoxysilane are examined after each deposition/reaction step by atomic force microscopy, X-ray photoelectron spectroscopy and time of flight secondary ion mass spectrometry. Surface modification involves the spotting of preformed conjugates of biotinylated oligonucleotides with streptavidin onto surfaces coated with biotinylated bovine serum albumin b-BSA (approach I) or the spotting of biotinylated oligonucleotides onto a streptavidin coating, the latter prepared through a reaction with immobilized b-BSA (approach II) or direct adsorption (approach III). AFM micrographs, quantified by autocorrelation and height histogram parameters (e.g. roughness), reveal uniform coverage after each modification step with distinct nanostructures after the reaction of biotinylated BSA with streptavidin or of a streptavidin conjugate with biotinylated oligonucleotides. XPS relates the immobilization of biomolecules with covalent binding to the epoxy-silanized surface. Protein coverage, estimated from photoelectron attenuation, shows that regarding streptavidin the highest and the lowest immobilization efficiency is achieved by following approaches I and III, respectively, as confirmed by TOF-SIMS microanalysis. The size of the DNA spot reflects the contact radius of the printed droplet and increases with protein coverage (and roughness) prior to the spotting, as epoxy-silanized surfaces are hardly hydrophilic. Representative TOF-SIMS images show sub-millimeter spots: uniform for approach I, doughnut-like (with a small non-zero minimum) for approach II, both with coffee-rings or peak-shaped for approach III. Spot features, originating from pinned contact lines and DNA surface binding and revealed by complementary molecular distributions (all material, DNA, streptavidin, BSA, epoxy, SiO2), indicate two modes of droplet evaporation depending on the details of each applied approach.

Solid-phase covalent immobilization of upconverting nanoparticles for biosensing by luminescence resonance energy transfer

Monodisperse water-soluble upconverting nanoparticles (UCNPs) were immobilized onto modified glass substrates for development of biosensing surfaces that operated using luminescence resonance energy transfer (LRET). Amine modified UCNPs were prepared from oleic acid capped UCNPs by ligand exchange using o-phosphorylethanolamine (PEA). PEA-UCNPs were covalently immobilized on aldehyde functionalized coverslips. Environmental scanning electron microscopy (ESEM) images indicated a homogeneous distribution of UCNPs on surfaces with a high immobilization density of approximately 1.3 × 10(11) UCNP cm(-2). This is the first account of covalent immobilization of UCNPs for bioassay and biosensor development where the density is on par with the high immobilization densities reported for other types of nanoparticles. The functionality and stability of the immobilized NPs were demonstrated by examining an LRET-based bioassay. The well-known sandwich assay for the detection of thrombin was selected as a model in which UCNPs were used as donors and quantum dots (QDs) as acceptors. The closely packed UCNPs on the glass surface showed a 2.5-fold enhancement in assay sensitivity compared to less-densely packed surfaces. In addition, a 1.5-fold enhancement in energy transfer efficiency was shown for solid-phase compared to solution-phase LRET.

Lanthanide upconversion nanoparticles and applications in bioassays and bioimaging: a review

Through the process of photon upconversion, trivalent lanthanide doped nanocrystals convert long-wavelength excitation radiation in the infrared or near infrared region to higher energy emission radiation from ultraviolet to infrared. Such materials offer potential for numerous advantages in analytical applications in comparison to molecular fluorophores and quantum dots. The use of IR radiation as an excitation source reduces autofluorescence and scattering of excitation radiation, which leads to a reduction of background in optical experiments. The upconverting nanocrystals offer excellent photostability and are composed of materials that are not particularly toxic to biological organisms. Excitation at long wavelengths also minimizes damage to biological materials. In this review, the different mechanisms responsible for the upconversion process, and methods that are used to synthesize and decorate upconverting nanoparticles are presented to indicate how absorption and emission can be tuned. Examples of recent applications of upconverting nanoparticles in bioassays for the detection of proteins, nucleic acids, metabolites and metal ions offer indications of analytical advantages in the development of methods of analysis. Examples include multi-color and multi-modal imaging, and the use of upconverting nanoparticles in theranostics.

Nanosensor dosimetry of mouse blood proteins after exposure to ionizing radiation

Giant magnetoresistive (GMR) nanosensors provide a novel approach for measuring protein concentrations in blood for medical diagnosis. Using an in vivo mouse radiation model, we developed protocols for measuring Flt3 ligand (Flt3lg) and serum amyloid A1 (Saa1) in small amounts of blood collected during the first week after X-ray exposures of sham, 0.1, 1, 2, 3, or 6 Gy. Flt3lg concentrations showed excellent dose discrimination at ≥ 1 Gy in the time window of 1 to 7 days after exposure except 1 Gy at day 7. Saa1 dose response was limited to the first two days after exposure. A multiplex assay with both proteins showed improved dose classification accuracy. Our magneto-nanosensor assay demonstrates the dose and time responses, low-dose sensitivity, small volume requirements, and rapid speed that have important advantages in radiation triage biodosimetry.

Scalable photonic crystal chips for high sensitivity protein detection

Scalable microfabrication technology has enabled semiconductor and microelectronics industries, among other fields. Meanwhile, rapid and sensitive bio-molecule detection is increasingly important for drug discovery and biomedical diagnostics. In this work, we designed and demonstrated that photonic crystal sensor chips have high sensitivity for protein detection and can be mass-produced with scalable deep-UV lithography. We demonstrated label-free detection of carcinoembryonic antigen from pg/mL to μg/mL, with high quality factor photonic crystal nanobeam cavities.

Label-free detection with high-Q microcavities: a review of biosensing mechanisms for integrated devices

Optical microcavities that confine light in high-Q resonance promise all of the capabilities required for a successful next-generation microsystem biodetection technology. Label-free detection down to single molecules as well as operation in aqueous environments can be integrated cost-effectively on microchips, together with other photonic components, as well as electronic ones. We provide a comprehensive review of the sensing mechanisms utilized in this emerging field, their physics, engineering and material science aspects, and their application to nanoparticle analysis and biomolecular detection. We survey the most recent developments such as the use of mode splitting for self-referenced measurements, plasmonic nanoantennas for signal enhancements, the use of optical force for nanoparticle manipulation as well as the design of active devices for ultra-sensitive detection. Furthermore, we provide an outlook on the exciting capabilities of functionalized high-Q microcavities in the life sciences.

Surface functionalization chemistries on highly sensitive silica-based sensor chips

The surfaces of silica-based sensor chips, designed for evanescent-field-coupled waveguide-mode sensors, were functionalized using various surface chemistries. The immobilization of molecular entities on the functionalized silica surfaces was monitored using various microscopic techniques (scanning electron, fluorescence, and atomic force microscopies). Further, gold nanoparticle-based signal enhancement analyses were performed with protein conjugation on different functionalized surfaces using a waveguide-mode sensor. Based on these analyses, the sensor surfaces modified with glutaraldehyde (Glu) and carbonyldiimidazole were found to be good for molecules of different sizes. In addition, it can be inferred that the Glu-modified surface may be suitable for small molecules with diameters around 5 nm owing to its surface roughness. The modified surface with carbonyldiimidazole is suitable for the direct immobilization of larger molecules especially for biomolecular assemblies without intermediate chemical modifications.

Selective patterning of Si-based biosensor surfaces using isotropic silicon etchants

Ultra-sensitive, label-free biosensors have the potential to have a tremendous impact on fields like medical diagnostics. For the majority of these Si-based integrated devices, it is necessary to functionalize the surface with a targeting ligand in order to perform specific biodetection. To do this, silane coupling agents are commonly used to immobilize the targeting ligand. However, this method typically results in the bioconjugation of the entire device surface, which is undesirable. To compensate for this effect, researchers have developed complex blocking strategies that result in selective patterning of the sensor surface. Recently, silane coupling agents were used to attach biomolecules to the surface of silica toroidal biosensors integrated on a silicon wafer. Interestingly, only the silica biosensor surface was conjugated. Here, we hypothesize why this selective patterning occurred. Specifically, the silicon etchant (xenon difluoride), which is used in the fabrication of the biosensor, appears to reduce the efficiency of the silane coupling attachment to the underlying silicon wafer. These results will enable future researchers to more easily control the bioconjugation of their sensor surfaces, thus improving biosensor device performance.

Fiber surface modification technology for fiber-optic localized surface plasmon resonance biosensors

Considerable studies have been performed on the development of optical fiber sensors modified by gold nanoparticles based on the localized surface plasmon resonance (LSPR) technique. The current paper presents a new approach in fiber surface modification technology for biosensors. Star-shaped gold nanoparticles obtained through the seed-mediated solution growth method were found to self-assemble on the surface of tapered optical fibers via amino- and mercapto-silane coupling agents. Transmitted power spectra of 3-aminopropyltrimethoxy silane (APTMS)-modified fiber were obtained, which can verify that the silane coupling agent surface modification method is successful. Transmission spectra are characterized in different concentrations of ethanol and gentian violet solutions to validate the sensitivity of the modified fiber. Assembly using star-shaped gold nanoparticles and amino/mercapto silane coupling agent are analyzed and compared. The transmission spectra of the gold nanoparticles show that the nanoparticles are sensitive to the dielectric properties of the surrounding medium. After the fibers are treated in t-dodecylmercaptan to obtain their transmission spectra, APTMS-modified fiber becomes less sensitive to different media, except that modified by 3-mercaptopropyltrimethoxy silane (MPTMS). Experimental results of the transmission spectra show that the surface modified by the gold nanoparticles using MPTMS is firmer compared to that obtained using APTMS.

Toward a solid-phase nucleic acid hybridization assay within microfluidic channels using immobilized quantum dots as donors in fluorescence resonance energy transfer

The optical properties and surface area of quantum dots (QDs) have made them an attractive platform for the development of nucleic acid biosensors based on fluorescence resonance energy transfer (FRET). Solid-phase assays based on FRET using mixtures of immobilized QD-oligonucleotide conjugates (QD biosensors) have been developed. The typical challenges associated with solid-phase detection strategies include non-specific adsorption, slow kinetics of hybridization, and sample manipulation. The new work herein has considered the immobilization of QD biosensors onto the surfaces of microfluidic channels in order to address these challenges. Microfluidic flow can be used to dynamically control stringency by adjustment of the potential in an electrokinetic-based microfluidics environment. The shearing force, Joule heating, and the competition between electroosmotic and electrophoretic mobilities allow the optimization of hybridization conditions, convective delivery of target to the channel surface to speed hybridization, amelioration of adsorption, and regeneration of the sensing surface. Microfluidic flow can also be used to deliver (for immobilization) and remove QD biosensors. QDs that were conjugated with two different oligonucleotide sequences were used to demonstrate feasibility. One oligonucleotide sequence on the QD was available as a linker for immobilization via hybridization with complementary oligonucleotides located on a glass surface within a microfluidic channel. A second oligonucleotide sequence on the QD served as a probe to transduce hybridization with target nucleic acid in a sample solution. A Cy3 label on the target was excited by FRET using green-emitting CdSe/ZnS QD donors and provided an analytical signal to explore this detection strategy. The immobilized QDs could be removed under denaturing conditions by disrupting the duplex that was used as the surface linker and thus allowed a new layer of QD biosensors to be re-coated within the channel for re-use of the microfluidic chip.

Heterobifunctional modification of DNA for conjugation to solid surfaces

Many biosensors, DNA arrays, and next-generation DNA sequencing technologies need common methods for end modification of random DNA sequences generated from a sample of DNA. Surface immobilization of chemically modified DNA is often the first step in creating appropriate sensing platforms. We describe a simple technique for efficient heterobifunctional modification of arbitrary double-stranded DNA fragments with chosen chemical groups. The modification requires the use of short (10-20 base pairs) synthetic adaptors having desired terminal functional groups and installs known sequences, which can be used for hybridization of primers in the sequencing-by-synthesis approaches. The method, based on ligation under optimized conditions, is selective and provides high yields of the target heterobifunctional DNA product. An additional two-step procedure can be applied to select further for the desired bifunctionalized product using PCR amplification with a chemically modified primer. Both functional groups in the modified DNA are chemically active and can be used in surface immobilization of the DNA strands to create the surface of a biosensor or sequencing chip.

Biopatterning for label-free detection

We present a biopatterning technique suitable for applications which demand a high degree of surface cleanliness, such as immobilization of biological recognition elements onto label-free biosensors. In the case of label-free biosensing, the mechanism of signal transduction is based on surface bound matter, making them highly sensitive to surface contamination including residues left during the biopatterning process. In this communication we introduce a simple, rapid processing step that removes 98% of the residues that often remain after standard parylene lift-off patterning. Residue-free parylene biopatterning is combined with microfluidics to localize biomolecule immobilization onto the sensing region and to enable multiplexed biopatterning. We demonstrate the applicability of this method to multiplexed label-free detection platforms by patterning nucleic acid capture probes corresponding to the four different serotypes of Dengue virus onto parallel 1D photonic crystal resonator sensors. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) are used to quantify surface cleanliness and uniformity. In addition to label-free biosensors, this technique is well suited to other nanobiotechnology patterning applications which demand a pristine, residue-free surface, such as immobilization of enzymes, antibodies, growth factors, or cell cultures.