Parallel, quantitative measurement of protein binding to a 120-element double-stranded DNA array in real time using surface plasmon resonance microscopy

Finding Needles in the Haystack: Strategies for Uncovering Noncoding Regulatory Variants

Despite accumulating evidence implicating noncoding variants in human diseases, unraveling their functionality remains a significant challenge. Systematic annotations of the regulatory landscape and the growth of sequence variant data sets have fueled the development of tools and methods to identify causal noncoding variants and evaluate their regulatory effects. Here, we review the latest advances in the field and discuss potential future research avenues to gain a more in-depth understanding of noncoding regulatory variants.

Plasmonic Nanotweezers and Nanosensors for Point-of-Care Applications

The capabilities of manipulating and analyzing biological cells, bacteria, viruses, DNAs, and proteins at high resolution are significant in understanding biology and enabling early disease diagnosis. We discuss progress in developments and applications of plasmonic nanotweezers and nanosensors where the plasmon-enhanced light-matter interactions at the nanoscale improve the optical manipulation and analysis of biological objects. Selected examples are presented to illustrate their design and working principles. In the context of plasmofluidics, which merges plasmonics and fluidics, the integration of plasmonic nanotweezers and nanosensors with microfluidic systems for point-of-care (POC) applications is envisioned. We provide our perspectives on the challenges and opportunities in further developing and applying the plasmofluidic POC devices.

A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA

Transcription factors regulate gene activity by binding specific regions of genomic DNA thanks to a subtle interplay of specific and nonspecific interactions that is challenging to quantify. Here, we exploit Reflective Phantom Interface (RPI), a label-free biosensor based on optical reflectivity, to investigate the binding of the N-terminal domain of Gal4, a well-known gene regulator, to double-stranded DNA fragments containing or not its consensus sequence. The analysis of RPI-binding curves provides interaction strength and kinetics and their dependence on temperature and ionic strength. We found that the binding of Gal4 to its cognate site is stronger, as expected, but also markedly slower. We performed a combined analysis of specific and nonspecific binding—equilibrium and kinetics—by means of a simple model based on nested potential wells and found that the free energy gap between specific and nonspecific binding is of the order of one kcal/mol only. We investigated the origin of such a small value by performing all-atom molecular dynamics simulations of Gal4–DNA interactions. We found a strong enthalpy–entropy compensation, by which the binding of Gal4 to its cognate sequence entails a DNA bending and a striking conformational freezing, which could be instrumental in the biological function of Gal4.

Emergent Biosensing Technologies Based on Fluorescence Spectroscopy and Surface Plasmon Resonance

The purpose of this work is to provide an exhaustive overview of the emerging biosensor technologies for the detection of analytes of interest for food, environment, security, and health. Over the years, biosensors have acquired increasing importance in a wide range of applications due to synergistic studies of various scientific disciplines, determining their great commercial potential and revealing how nanotechnology and biotechnology can be strictly connected. In the present scenario, biosensors have increased their detection limit and sensitivity unthinkable until a few years ago. The most widely used biosensors are optical-based devices such as surface plasmon resonance (SPR)-based biosensors and fluorescence-based biosensors. Here, we will review them by highlighting how the progress in their design and development could impact our daily life.

Deep Learning Approach for Enhanced Detection of Surface Plasmon Scattering

A deep learning approach has been taken to improve detection characteristics of surface plasmon microscopy (SPM) of light scattering. Deep learning based on the convolutional neural network algorithm was used to estimate the effect of scattering parameters, mainly the number of scatterers. The improvement was assessed on a quantitative basis by applying the approach to SPM images formed by coherent interference of scatterers. It was found that deep learning significantly improves the accuracy over conventional detection: the enhancement in the accuracy was shown to be significantly higher by almost 6 times and useful for scattering by polydisperse mixtures. This suggests that deep learning can be used to find scattering objects effectively in the noisy environment. Furthermore, deep learning can be extended directly to label-free molecular detection assays and provide considerably improved detection in imaging and microscopy techniques.

Recent Advances in Surface Plasmon Resonance Imaging Sensors

The surface plasmon resonance (SPR) sensor is an important tool widely used for studying binding kinetics between biomolecular species. The SPR approach offers unique advantages in light of its real-time and label-free sensing capabilities. Until now, nearly all established SPR instrumentation schemes are based on single- or several-channel configurations. With the emergence of drug screening and investigation of biomolecular interactions on a massive scale these days for finding more effective treatments of diseases, there is a growing demand for the development of high-throughput 2-D SPR sensor arrays based on imaging. The so-called SPR imaging (SPRi) approach has been explored intensively in recent years. This review aims to provide an up-to-date and concise summary of recent advances in SPRi. The specific focuses are on practical instrumentation designs and their respective biosensing applications in relation to molecular sensing, healthcare testing, and environmental screening.

Surface plasmon resonance imaging for ABH antigen detection on red blood cells and in saliva: secretor status-related ABO subgroup identification

Low antigenic expression of ABO subgroup system on red blood cell (RBC) is cause of discrepancy between forward and reverse blood typing in the standard agglutination technique. Neutralization agglutination is employed for verification of the detection of ABH substances in saliva. However, the neutralization technique is complicated, time-consuming and requires expertise. To overcome these drawbacks, surface plasmon resonance (SPR) imaging was developed for ABH antigen detection on RBCs and in saliva. An antibody array was designed to classify the ABO subgroups by anti-A, anti-B, and anti-H antibodies; the array was immobilized on a carboxymethyl-dextran sensor-surface. RBCs and saliva specimens from sixty-four donors were analysed by passing them over the antibody array, where the secretor status and blood group could be simultaneously identified. Consequently, the immobilized antibodies could specifically and quantitatively detect the ABH antigen on RBCs. Using the direct assay, the SPR signal of saliva detection was weaker than that of RBC detection. However, a sandwich assay with a mixture of anti-A, anti-B, and anti-H antibodies could efficiently enhance the signal. The sensor chip provided high specificity (cut-off at 100 to 175 micro refractive index units) and high precision at 0.06%-4.9% CV. The blood group results of the sixty-four donor specimens obtained by SPR agreed with the standard agglutination test with 100% accuracy. SPR could indicate different ABH antigen densities on the RBCs and nearly the same amounts of ABH substances in the saliva of strong and weak subgroups. Finally, we also demonstrated reduced assay time and fewer complications with the SPR imaging platform compared to the neutralization technique.

Label-Free Sensing on Microarrays

Microarrays of biological molecules such as DNAs, proteins, carbohydrates, and small molecules provide a high-throughput platform for screening tens of thousands of biomolecular interactions simultaneously, facilitating the functional characterization of these biomolecules in areas of genomics, proteomics, glycomics, and cytomics. Routinely, analysis of binding reactions between solution-phased probes and surface-immobilized targets involves some kinds of fluorescence-based detection methods. Even though these methods have advantages of high sensitivity and wide dynamic range, labeling probes and/or targets inevitably changes their innate properties and in turn affects probe-target interactions in often uncharacterized ways. Therefore, in recent years, various label-free sensing technologies have been developed for characterizing biomolecular interactions in microarray format. These biosensors, to a certain extent, take the place of fluorescent methods by providing a comparable sensitivity as well as retaining the conformational and functional integrality of biomolecules to be investigated. More importantly, some of these biosensors are capable of real-time monitoring probe-target interactions, providing the binding affinities of these reactions. Using label-free biosensors in microarrays has become a current trend in developing high-throughput screening platforms for drug discoveries and applications in all areas of "-omics." This article is aimed to provide principles and recent developments in label-free sensing technologies applicable to microarrays, with special attentions being paid to surface plasmon resonance microscopy and oblique-incidence reflectivity difference microscopy.

Optical Microscopy for Detecting Binding on Small Molecule Microarrays

Small molecule microarrays (SMMs) have revolutionized parallel screening of multiple biological interactions. SMMs are a high-throughput technique for simultaneous detection of up to thousands of biological interactions. Conventional detection technique employed in SMMs is fluorescence spectroscopy. However, the possibility of fluorescent labels affecting the binding properties of small molecules drives the development of label-free screening techniques. Here, we describe two label-free detection techniques using optical microscopy for the detection of binding on SMMs. The first optical detection technique-ellipsometry, and more specifically, oblique incidence reflectivity difference to study the kinetics of the association between small molecule targets and protein probes is discussed. Then, we describe another optical detection technique-surface plasmon resonance microscopy. The sample preparation steps and protocols of the two techniques to study the interactions between SMMs and their protein targets are elaborated in great detail.

Dry and wet approaches for genome-wide functional annotation of conventional and unconventional transcriptional activators

Transcription factors (TFs) are master gene products that regulate gene expression in response to a variety of stimuli. They interact with DNA in a sequence-specific manner using a variety of DNA-binding domain (DBD) modules. This allows to properly position their second domain, called "effector domain", to directly or indirectly recruit positively or negatively acting co-regulators including chromatin modifiers, thus modulating preinitiation complex formation as well as transcription elongation. At variance with the DBDs, which are comprised of well-defined and easily recognizable DNA binding motifs, effector domains are usually much less conserved and thus considerably more difficult to predict. Also not so easy to identify are the DNA-binding sites of TFs, especially on a genome-wide basis and in the case of overlapping binding regions. Another emerging issue, with many potential regulatory implications, is that of so-called "moonlighting" transcription factors, i.e., proteins with an annotated function unrelated to transcription and lacking any recognizable DBD or effector domain, that play a role in gene regulation as their second job. Starting from bioinformatic and experimental high-throughput tools for an unbiased, genome-wide identification and functional characterization of TFs (especially transcriptional activators), we describe both established (and usually well affordable) as well as newly developed platforms for DNA-binding site identification. Selected combinations of these search tools, some of which rely on next-generation sequencing approaches, allow delineating the entire repertoire of TFs and unconventional regulators encoded by the any sequenced genome.

The effects of magnetic fields exposure on relative permittivity of saline solutions measured by a high resolution SPR system

A measurement system for the relative permittivity of a physiological solution under 50 Hz magnetic fields (MF) is presented. It is based on a phase-sensitive surface plasmon resonance (SPR) system. Relative permittivity was analyzed for different solute concentrations of sodium chloride under various MF exposure parameters. We found that MF exposure at 0.2-4.0 mT step-wise decreased significantly the SPR phase signal of a 0.9% sodium chloride solution while 0.1 mT of MF exposure did not. The decreases in the SPR phase signal depended on the duration of MF exposure, and the signal reached a plateau after 15 min of exposure. Interestingly, the decreased SPR phase signal showed a gradual increase and approached the background level when the exposure was drawn off. In addition, we found that the response of the sodium chloride solution to MF also depended on its concentration. In brief, the relative permittivity of sodium chloride in solutions appears to be practically affected by 50 Hz MF exposure. Our data indicates that the relative permittivity of the saline solution influenced by MF exposure should be considered when investigating the biological effects of MF exposure on organisms in experimental study.

Integrated microfluidic approach for quantitative high-throughput measurements of transcription factor binding affinities

Protein binding to DNA is a fundamental process in gene regulation. Methodologies such as ChIP-Seq and mapping of DNase I hypersensitive sites provide global information on this regulation in vivo In vitro methodologies provide valuable complementary information on protein-DNA specificities. However, current methods still do not measure absolute binding affinities. There is a real need for large-scale quantitative protein-DNA affinity measurements. We developed QPID, a microfluidic application for measuring protein-DNA affinities. A single run is equivalent to 4096 gel-shift experiments. Using QPID, we characterized the different affinities of ATF1, c-Jun, c-Fos and AP-1 to the CRE consensus motif and CRE half-site in two different genomic sequences on a single device. We discovered that binding of ATF1, but not of AP-1, to the CRE half-site is highly affected by its genomic context. This effect was highly correlated with ATF1 ChIP-seq and PBM experiments. Next, we characterized the affinities of ATF1 and ATF3 to 128 genomic CRE and CRE half-site sequences. Our affinity measurements explained that in vivo binding differences between ATF1 and ATF3 to CRE and CRE half-sites are partially mediated by differences in the minor groove width. We believe that QPID would become a central tool for quantitative characterization of biophysical aspects affecting protein-DNA binding.

Functionalized Polymer Microgel Particles Enable Customizable Production of Label-Free Sensor Arrays

Probe molecule immobilization onto surfaces is a critical step in the production of many analytical devices, including labeled and label-free microarrays. New methods to increase the density and uniformity of probe deposition have the potential to significantly enhance the ultimate limits of detection and reproducibility. Hydrogel-based materials have been employed in the past to provide a 3D protein-friendly surface for deposition of antibodies and nucleic acids. However, these methods are susceptible to variation during polymerization of the hydrogel scaffold and provide limited opportunities for tuning deposition parameters on an antibody-by-antibody basis. In this work, a versatile hydrogel nanoparticle deposition method was developed for the production of label-free microarrays and tested in the context of antibody-antigen binding. Poly(N-isopropylacrylamide) nanoparticles (PNIPAM) were conjugated to antibodies using an avidin/biotin system and deposited onto surfaces using a noncontact printing system. After drying, these gel spots formed uniform and thin layers <10 nm in height. The conjugates were characterized with dynamic light scattering, scanning electron microscopy, and atomic force microscopy. We tested this format in the context of tumor necrosis factor-alpha (TNF-α) detection via arrayed imaging reflectometry (AIR), a label-free protein microarray method. This method of probe molecule deposition should be generally useful in the production of microarrays for label-free detection.

Using protein-binding microarrays to study transcription factor specificity: homologs, isoforms and complexes

Protein-DNA binding is central to specificity in gene regulation, and methods for characterizing transcription factor (TF)-DNA binding remain crucial to studies of regulatory specificity. High-throughput (HT) technologies have revolutionized our ability to characterize protein-DNA binding by significantly increasing the number of binding measurements that can be performed. Protein-binding microarrays (PBMs) are a robust and powerful HT platform for studying DNA-binding specificity of TFs. Analysis of PBM-determined DNA-binding profiles has provided new insight into the scope and mechanisms of TF binding diversity. In this review, we focus specifically on the PBM technique and discuss its application to the study of TF specificity, in particular, the binding diversity of TF homologs and multi-protein complexes.

Multimodal electrochemical sensing of transcription factor–operator complexes

Changes in diffusive movements, surface potential, and interfacial impedance of DNA monolayers are combined to analyze binding of unlabeled transcription factors.

ABO blood-typing using an antibody array technique based on surface plasmon resonance imaging

In this study, readily available antibodies that are used in standard agglutination tests were evaluated for their use in ABO blood typing by a surface plasmon resonance imaging (SPR imaging) technique. Five groups of antibodies, including mixed clones of anti-A, anti-B, and anti-AB, and single clones of anti-A and anti-B, were used to construct the five-line detection arrays using a multichannel flow cell in the SPR imager. The red blood cell (RBC) samples were applied to a multichannel flow cell that was orthogonal to the detection line arrays for blood group typing. We found that the blood samples were correctly grouped in less than 12 min by the SPR imaging technique, and the results were consistent with those of the standard agglutination technique for all 60 samples. We found that mixed clones of antibodies provided 33%-68% greater change in the SPR signal than the single-clone antibodies. Applying the SPR imaging technique using readily available antibodies may reduce the costs of the antibodies, shorten the measurement time, and increase the throughput.

Multiplexed surface plasmon resonance imaging for protein biomarker analysis

The reliable detection of ligand and analyte binding is of significant importance for the field of medical diagnostics. Recent advances in proteomics and the rapid expansion in the number of identified protein biomarkers enhance the need for reliable techniques for their identification in complex samples. Surface plasmon resonance imaging (SPRi) provides label-free detection of this binding process in real-time. This chapter details the fabrication of an SPR imaging instrument and its use in analyzing molecular binding interactions with the use of a high-density microfluidic SPRi chip, capable of multiplexed analysis as well as various immobilization chemistries. Controlled recovery of bound biomarkers is demonstrated to enable their identification using mass spectrometry. Finally, activated leukocyte cell adhesion molecule (ALCAM), a protein biomarker associated with a variety of cancers, is identified from human crude cell lysates using the microfluidic surface plasmon resonance imaging (SPRi) instrument.

Ultrasmooth metallic films with buried nanostructures for backside reflection-mode plasmonic biosensing

We present a new plasmonic device architecture based on ultrasmooth metallic surfaces with buried plasmonic nanostructures. Using template-stripping techniques, ultrathin gold films with less than 5 Å surface roughness are optically coupled to an arbitrary arrangement of buried metallic gratings, rings, and nanodots. As a prototypical example, we present linear plasmonic gratings buried under an ultrasmooth 20 nm thick gold surface for biosensing. The optical illumination and collection are completely decoupled from the microfluidic delivery of liquid samples due to the backside, reflection-mode geometry. This allows for sensing with opaque or highly scattering liquids. With the buried nanostructure design, we maintain high sensitivity and decoupled backside (reflective) optical access as with traditional prism-based surface plasmon resonance (SPR) sensors. In addition, we also gain the benefits offered by nanoplasmonic sensors such as spectral tunability and high-resolution, wide-field SPR imaging with normal-incidence epi-illumination that is simple to construct and align. Beyond sensing, our buried plasmonic nanostructures with ultrasmooth metallic surfaces can benefit nanophotonic waveguides, surface-enhanced spectroscopy, nanolithography, and optical trapping.

Real-time full-spectral imaging and affinity measurements from 50 microfluidic channels using nanohole surface plasmon resonance

With recent advances in high-throughput proteomics and systems biology, there is a growing demand for new instruments that can precisely quantify a wide range of receptor-ligand binding kinetics in a high-throughput fashion. Here we demonstrate a surface plasmon resonance (SPR) imaging spectroscopy instrument capable of simultaneously extracting binding kinetics and affinities from 50 parallel microfluidic channels. The instrument utilizes large-area (~ cm(2)) metallic nanohole arrays as SPR sensing substrates and combines a broadband light source, a high-resolution imaging spectrometer and a low-noise CCD camera to extract spectral information from every channel in real time with a refractive index resolution of 7.7 × 10(-6) refractive index units. To demonstrate the utility of our instrument for quantifying a wide range of biomolecular interactions, each parallel microfluidic channel is coated with a biomimetic supported lipid membrane containing ganglioside (GM1) receptors. The binding kinetics of cholera toxin b (CTX-b) to GM1 are then measured in a single experiment from 50 channels. By combining the highly parallel microfluidic device with large-area periodic nanohole array chips, our SPR imaging spectrometer system enables high-throughput, label-free, real-time SPR biosensing, and its full-spectral imaging capability combined with nanohole arrays could enable integration of SPR imaging with concurrent surface-enhanced Raman spectroscopy.

Surface plasmon resonance based biosensor technique: a review

Optical Surface plasmon resonance (SPR) biosensors represent the most advanced and developed optical label-free biosensor technology. Optical SPR biosensors are a powerful detection and analysis tool that has vast applications in environmental protection, biotechnology, medical diagnostics, drug screening, food safety and security. This article reviews the recent development of SPR biosensor techniques, including bulk SPR and localized SPR (LSPR) biosensors, for detecting interactions between an analyte of interest in solution and a biomolecular recognition. The concepts of bulk and localized SPs and the working principles of both sensing techniques are introduced. Major sensing advances on biorecognition elements, measurement formats, and sensing platforms are presented. Finally, the discussions on both biosensor techniques as well as comparison of both SPR sensing techniques are made.

Engineering metallic nanostructures for plasmonics and nanophotonics

Metallic nanostructures now play an important role in many applications. In particular, for the emerging fields of plasmonics and nanophotonics, the ability to engineer metals on nanometric scales allows the development of new devices and the study of exciting physics. This review focuses on top-down nanofabrication techniques for engineering metallic nanostructures, along with computational and experimental characterization techniques. A variety of current and emerging applications are also covered.

Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance

Several proteins, like transcription factors, bind to certain DNA sequences, thereby regulating biochemical pathways that determine the fate of the corresponding cell. Due to these key positions, it is indispensable to analyze protein-DNA interactions and to identify their mode of action. Surface plasmon resonance is a label-free method that facilitates the elucidation of real-time kinetics of biomolecular interactions. In this article, we focus on this biosensor-based method and provide a detailed guide how SPR can be utilized to study binding of proteins to oligonucleotides. After a description of the physical phenomenon and the instrumental realization including fiber-optic-based SPR and SPR imaging, we will continue with a survey of immobilization methods. Subsequently, we will focus on the optimization of the experiment, expose pitfalls, and introduce how data should be analyzed and published. Finally, we summarize several interesting publications of the last decades dealing with protein-DNA and RNA interaction analysis by SPR.

Nanohole-based surface plasmon resonance instruments with improved spectral resolution quantify a broad range of antibody-ligand binding kinetics

We demonstrate an affordable low-noise surface plasmon resonance (SPR) instrument based on extraordinary optical transmission (EOT) in metallic nanohole arrays and quantify a broad range of antibody-ligand binding kinetics with equilibrium dissociation constants ranging from 200 pM to 40 nM. This nanohole-based SPR instrument is straightforward to construct, align, and operate, since it is built around a standard microscope and a portable fiber-optic spectrometer. The measured refractive index resolution of this platform is 3.1 × 10(-6) without on-chip cooling, which is among the lowest reported for SPR sensors based on EOT. This is accomplished via rapid full-spectrum acquisition in 10 ms followed by frame averaging of the EOT spectra, which is made possible by the production of template-stripped gold nanohole arrays with homogeneous optical properties over centimeter-sized areas. Sequential SPR measurements are performed using a 12-channel microfluidic flow cell after optimizing surface modification protocols and antibody injection conditions to minimize mass-transport artifacts. The immobilization of a model ligand, the protective antigen of anthrax on the gold surface, is monitored in real-time with a signal-to-noise ratio of ~860. Subsequently, real-time binding kinetic curves were measured quantitatively between the antigen and a panel of small, 25 kDa single-chain antibodies at concentrations down to 1 nM. These results indicate that nanohole-based SPR instruments have potential for quantitative antibody screening and as a general-purpose platform for integrating SPR sensors with other bioanalytical tools.

A microarray biosensor for multiplexed detection of microbes using grating-coupled surface plasmon resonance imaging

Grating-coupled surface plasmon resonance imaging (GCSPRI) utilizes an optical diffraction grating embossed on a gold-coated sensor chip to couple collimated incident light into surface plasmons. The angle at which this coupling occurs is sensitive to the capture of analyte at the chip surface. This approach permits the use of disposable biosensor chips that can be mass-produced at low cost and spotted in microarray format to greatly increase multiplexing capabilities. The current GCSPRI instrument has the capacity to simultaneously measure binding at over 1000 unique, discrete regions of interest (ROIs) by utilizing a compact microarray of antibodies or other specific capture molecules immobilized on the sensor chip. In this report, we describe the use of GCSPRI to directly detect multiple analytes over a large dynamic range, including soluble protein toxins, bacterial cells, and viruses, in near real-time. GCSPRI was used to detect a variety of agents that would be useful for diagnostic and environmental sensing purposes, including macromolecular antigens, a nontoxic form of Pseudomonas aeruginosa exotoxin A (ntPE), Bacillus globigii, Mycoplasma hyopneumoniae, Listeria monocytogenes, Escherichia coli, and M13 bacteriophage. These studies indicate that GCSPRI can be used to simultaneously assess the presence of toxins and pathogens, as well as quantify specific antibodies to environmental agents, in a rapid, label-free, and highly multiplexed assay requiring nanoliter amounts of capture reagents.

Assembly of the transcription machinery: ordered and stable, random and dynamic, or both?

The assembly of the transcription machinery is a key step in gene activation, but even basic details of this process remain unclear. Here we discuss the apparent discrepancy between the classic sequential assembly model based mostly on biochemistry and an emerging dynamic assembly model based mostly on fluorescence microscopy. The former model favors a stable transcription complex with subunits that cooperatively assemble in order, whereas the latter model favors an unstable complex with subunits that may assemble more randomly. To confront this apparent discrepancy, we review the merits and drawbacks of the different experimental approaches and list potential biasing factors that could be responsible for the different interpretations of assembly. We then discuss how these biases might be overcome in the future with improved experiments or new techniques. Finally, we discuss how kinetic models for assembly may help resolve the ordered and stable vs. random and dynamic assembly debate.

Luminescent detection of DNA-binding proteins

Transcription factors play a central role in cell development, differentiation and growth in biological systems due to their ability to regulate gene expression by binding to specific DNA sequences within the nucleus. The dysregulation of transcription factor signaling has been implicated in the pathogenesis of a number of cancers, developmental disorders, inflammation and autoimmunity. There is thus a high demand for convenient high-throughput methodologies able to detect sequence-specific DNA-binding proteins and monitor their DNA-binding activities. Traditional approaches for protein detection include gel mobility shift assays, DNA footprinting and enzyme-linked immunosorbent assays (ELISAs) which tend to be tedious, time-consuming, and may necessitate the use of radiographic labeling. By contrast, luminescence technologies offer the potential for rapid, sensitive and low-cost detection that are amenable to high-throughput and real-time analysis. The discoveries of molecular beacons and aptamers have spear-headed the development of new luminescent methodologies for the detection of proteins over the last decade. We survey here recent advances in the development of luminescent detection methods for DNA-binding proteins, including those based on molecular beacons, aptamer beacons, label-free techniques and exonuclease protection.

Combined optical and acoustical method for determination of thickness and porosity of transparent organic layers below the ultra-thin film limit

Analysis techniques are needed to determine the quantity and structure of materials composing an organic layer that is below an ultra-thin film limit and in a liquid environment. Neither optical nor acoustical techniques can independently distinguish between thickness and porosity of ultra-thin films due to parameter correlation. A combined optical and acoustical approach yields sufficient information to determine both thickness and porosity. We describe application of the combinatorial approach to measure single or multiple organic layers when the total layer thickness is small compared to the wavelength of the probing light. The instrumental setup allows for simultaneous in situ spectroscopic ellipsometry and quartz crystal microbalance dynamic measurements, and it is combined with a multiple-inlet fluid control system for different liquid solutions to be introduced during experiments. A virtual separation approach is implemented into our analysis scheme, differentiated by whether or not the organic adsorbate and liquid ambient densities are equal. The analysis scheme requires that the film be assumed transparent and rigid (non-viscoelastic). We present and discuss applications of our approach to studies of organic surfactant adsorption, self-assembled monolayer chemisorption, and multiple-layer target DNA sensor preparation and performance testing.

Facile assembly of micro- and nanoarrays for sensing with natural cell membranes

Microarray technology has facilitated many powerful high-throughput studies in the fields of genetics and proteomics, among others. However, preparation of microarrays composed of cell-derived membranes with embedded receptors has proven difficult. Here we describe a new method for forming microarrays composed of synthetic lipid vesicles and natural cell membranes. The method is based upon assembly of vesicles and natural membranes into recessed micro- and nanowells and using a polydimethylsiloxane (PDMS) block as a "squeegee." This method is used to assemble phospholipid vesicles into arrays with micrometer and nanoscale dimensions. Native myelin and neuronal lipid raft arrays are also formed in 30 min or less. We show the natural membrane arrays can be used for sensing lipid-protein interactions by detecting cholera toxin binding to ganglioside GM1 in neuronal lipid rafts. In multicomponent arrays myelin can be distinguished from neuronal rafts by antibody binding to cell-specific surface antigens. Finally, myelin arrays formed in gold nanowells are used for surface plasmon resonance sensing. This assembly approach is simple, broadly applicable, and opens up new avenues of research not easily accomplished with standard microarray technology.

Effect of the N-terminal sequence on the binding affinity of transthyretin for human retinol-binding protein

During vertebrate evolution, the N-terminal region of transthyretin (TTR) subunit has undergone a change in both length and hydropathy. This was previously shown to change the binding affinity for thyroid hormones (THs). However, it was not known whether this change affects other functions of TTR. In the present study, the effect of these changes on the binding of TTR to retinol-binding protein (RBP) was determined. Two wild-type TTRs from human and Crocodylus porosus, and three chimeric TTRs, including a human chimeric TTR in which its N-terminal sequence was changed to that of C. porosus TTR (croc/huTTR) and two C. porosus chimeric TTRs (hu/crocTTR in which its N-terminal sequence was changed to that of human TTR and xeno/crocTTR in which its N-terminal sequence was changed to that of Xenopus laevis TTR), were analyzed for their binding to human RBP by native-PAGE followed by immunoblotting and a chemilluminescence assay. The K(d) of human TTR was 30.41 ± 2.03 μm, and was similar to that reported for the second binding site, whereas that of crocodile TTR was 2.19 ± 0.24 μm. The binding affinities increased in croc/huTTR (K(d) = 23.57 ± 3.54 μm) and xeno/crocTTR (K(d) = 0.61 ± 0.16 μm) in which their N-termini were longer and more hydrophobic, but decreased in hu/crocTTR (K(d) = 5.03 ± 0.68 μm) in which its N-terminal region was shorter and less hydrophobic. These results suggest an influence of the N-terminal primary structure of TTR on its function as a co-carrier for retinol with RBP.

Hybridization in ssDNA films--a multi-technique spectroscopy study

A combination of X-ray photoelectron spectroscopy (XPS), high-resolution XPS, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and sum-frequency-generation (SFG) spectroscopy was used to monitor two types of ssDNA films on Au(111) before and after hybridization. As probe systems, films of thiolated and block-oligonucleotides were used, taking thiolated thymine d(T) homo-oligonucleotides and thymine-adenine d(A-T) diblock-oligonucleotides as representative examples. In accordance with previous work, hybridization of the shorter and more densely packed thiolated ssDNA films produced fewer (if any) hybrids, whereas the longer and less densely packed layers exhibited a larger hybridization yield. The above effects were less pronounced in the case of the d(A-T) films where the hybridization yield of the less densely packed monolayers was significantly lower. This was presumably due to the formation of internal dimeric hybrids in the immobilization step of the probe molecules, resulting in the generation of fewer probe-target hybrids upon exposure to the target molecules. In all ssDNA films displaying a reasonable number of hybrids present, significant orientational changes were observed and could be monitored in detail. These results suggest that the given combination of spectroscopic techniques can be a valuable tool to gain molecular-level information about hybrids at interfaces.

Sensitivity improved surface plasmon resonance biosensor for cancer biomarker detection based on plasmonic enhancement

In this study, we report the development of a nanoparticle-enhanced biosensor by integrating both the nanoparticles and immunoassay sensing technologies into a phase interrogation surface plasmon resonance (SPR) system for detecting antigen at a concentration as low as the femtomolar range. Our work has demonstrated that the plasmonic field extension generated from the gold film to gold nanorod (GNR) has led to a drastic sensitivity enhancement. Antibody-functionalized sensing film, together with antibody-conjugated GNRs, was readily served as a plasmonic coupling partner that can be used as a powerful ultrasensitive sandwich immunoassay for cancer-related disease detection. Experimentally, it was found that the bioconjugated GNR labels enhance the tumor necrosis factor alpha (TNF-α) antigen signal with more than 40-fold increase compared to the traditional SPR biosensing technique. The underlying principle was analyzed by simulating the near-field coupling between the sensing film and the GNR. The results have shown that GNRs were readily served as promising amplification labels in SPR sensing technology.

Label-free detection with surface plasmon resonance imaging

Sensors based on surface plasmon resonance have demonstrated, over the last 2 decades, to be an effective method of studying biomolecular interactions without the need for labeling. Recently, it has been adapted to high-throughput use for imaging microarray binding in real time. This provides a promising platform - a label-free protein microarray system - for the study of disease. In this example, antibody microarrays are used to efficiently profile the secretion of proteins from a cell line exposed to varying concentrations of a toxic compound.

Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro

Transcription of genes during development and in response to environmental stimuli is determined by genomic DNA sequence. The DNA sequences regulating transcription are read by sequence-specific transcription factors (TFs) that recognize relatively short sequences, generally between four and twenty base pairs in length. Transcriptional regulation generally requires binding of multiple TFs in close proximity to each other. Mechanistic understanding of transcription in an organism thus requires detailed knowledge of binding affinities of all its TFs to all possible DNA sequences, and the co-operative interactions between the TFs. However, very little is known about such co-operative binding interactions, and even the simple TF-DNA binding information exists only for a very small proportion of all TFs - for example, mammals have approximately 1,300-2,000 TFs [1, 2], yet the largest public databases for TF binding specificity, Jaspar and Uniprobe [3, 4] currently list only approximately 500 moderate to high resolution profiles for human or mouse. This lack of knowledge is in part due to the fact that analysis of TF DNA binding has been laborious and expensive. In this chapter, we review methods that can be used to determine binding specificity of TFs to DNA, mainly focusing on recently developed assays that allow high-resolution analysis of TF binding specificity in relatively high throughput.

Theory and applications of surface plasmon resonance, resonant mirror, resonant waveguide grating, and dual polarization interferometry biosensors

Biosensors have been used extensively in the scientific community for several purposes, most notably to determine association and dissociation kinetics, protein-ligand, protein-protein, or nucleic acid hybridization interactions. A number of different types of biosensors are available in the field, each with real or perceived benefits over the others. This review discusses the basic theory and operational arrangements of four commercially available types of optical biosensors: surface plasmon resonance, resonant mirror, resonance waveguide grating, and dual polarization interferometry. The different applications these techniques offer are discussed from experiments and results reported in recently published literature. Additionally, recent advancements or modifications to the current techniques are also discussed.

Development of surface plasmon resonance imaging for detection of Acidovorax avenae subsp. citrulli (Aac) using specific monoclonal antibody

An immunosensor based on surface plasmon resonance imaging (SPR imaging) using a specific monoclonal antibody 11E5 (MAb 11E5) was developed for the detection of the seed-borne bacterium Acidovorax avenae subsp. citrulli (Aac), which causes fruit blotch in watermelons and cantaloupes, and compared to the conventional ELISA technique. The 1:40 mixed self-assembled monolayer (mixed SAM) surface was used for the immobilized MAb 11E5 on sensor surface for the detection of Aac. Both whole cells and broken cells of Aac were tested by using direct and sandwich detection assay. The limit of detection (LOD) of Aac using the SPR imaging technique and a direct detection assay was 10(6)cfu/ml and a subsequent amplification of the SPR signal using a polyclonal antibody (PAb) lowered the LOD to 5×10(5) cfu/ml. The LOD for the ELISA technique was 5×10(4) cfu/ml for the detection of Aac, which was slightly better than that for the SPR technique. However, the sensor surface based on SPR imaging offered a major advantage in terms of surface regeneration, allowing at least five cycles with a shorter time assay, multi-channel analysis with an application on multiplex detection, and an ease of the surface usage for the detection of Aac in the naturally infected plant. The surface was tested against the naturally infected sample and showed good selectivity toward the Aac bacteria.

Determining the specificity of protein-DNA interactions

Proteins, such as many transcription factors, that bind to specific DNA sequences are essential for the proper regulation of gene expression. Identifying the specific sequences that each factor binds can help to elucidate regulatory networks within cells and how genetic variation can cause disruption of normal gene expression, which is often associated with disease. Traditional methods for determining the specificity of DNA-binding proteins are slow and laborious, but several new high-throughput methods can provide comprehensive binding information much more rapidly. Combined with in vivo determinations of transcription factor binding locations, this information provides more detailed views of the regulatory circuitry of cells and the effects of variation on gene expression.

Digital holographic microscopy by use of surface plasmon resonance for imaging of cell membranes

A technique called surface plasmon resonance digital holographic microscopy (SPRDHM) for optical imaging of cell membranes is proposed. The intensity and phase distributions of the reflected light that is modulated by the cell membrane in surface plasmon resonance can be simultaneously obtained. The imaging principle and capability are theoretically analyzed and demonstrated by experiments. In addition, the technique is compared with total internal reflection digital holographic microscopy (TIRDHM) in theory and experiment, respectively. The results show that the SPRDHM technique is better in spatial resolution and phase sensitivity than the TIRDHM technique for imaging of cell membranes.

Measurement of biomarker proteins for point-of-care early detection and monitoring of cancer

This critical review evaluates progress toward viable point-of-care protein biomarker measurements for cancer detection and diagnostics. The ability to measure panels of specific, selective cancer biomarker proteins in physicians' surgeries and clinics has the potential to revolutionize cancer detection, monitoring, and therapy. The dream envisions reliable, cheap, automated, technically undemanding devices that can analyze a patient's serum or saliva in a clinical setting, allowing on-the-spot diagnosis. Existing commercial products for protein assays are reliable in laboratory settings, but have limitations for point-of-care applications. A number of ultrasensitive immunosensors and some arrays have been developed, many based on nanotechnology. Multilabel detection coupled with high capture molecule density in immunosensors and arrays seems to be capable of detecting a wide range of protein concentrations with sensitivity ranging into the sub pg mL(-1) level. Multilabel arrays can be designed to detect both high and ultralow abundance proteins in the same sample. However, only a few of the newer ultrasensitive methods have been evaluated with real patient samples, which is key to establishing clinical sensitivity and selectivity.

High-sensitivity detection of carbohydrate antigen 15-3 using a gold/zinc oxide thin film surface plasmon resonance-based biosensor

We report that gold/zinc oxide (Au/ZnO) nanocomposite films were effectively employed to enhance the performance of surface plasmon resonance (SPR) for the detection of tumor markers. Carbohydrate antigen 15.3 (CA15-3), a tumor marker for breast cancer, was chosen as a model analyte. We analyzed intensity response to the samples at various concentrations (0.0125 U/mL to 160 U/mL) in pleural fluid to evaluate the detection capability of the SPR biosensor based on Au/ZnO thin films. The linear range extended from 1 to 40 U/mL with a correlation coefficient of R(2) = 0.991 and a limit of detection reaching 0.025 U/mL at a signal-to-noise ratio of 3:1. Compared with the degree of the shift in SPR intensity induced by the specific binding event between antibody and antigen, the change of intensity on the Au/ZnO layers was increased by at least 2 fold over that on the gold/chromium (Au/Cr) layers. In addition, we determined that the Au/ZnO layers allowed for a detection limit 4 times lower than the Au/Cr layers, which are in widespread use as the sensing interfaces in current SPR-based detectors. In conclusion, the use of Au/ZnO films greatly enhanced the SPR signal yield for this bimolecular interaction and showed high sensitivity.

Plasmonic nanohole arrays for label-free kinetic biosensing in a lipid membrane environment

We integrate periodic nanohole arrays in a thin gold film with lipid membranes in a microfluidic channel. Surface plasmon-enhanced light transmission through the periodic nanohole arrays enables real-time label-free sensing of molecular binding on the lipid membrane surface. This membrane biosensor can potentially act as a natural platform for studying binding kinetics of proteins with their binding partners anchored in the lipid membrane. We also present the concept of using nanopore arrays for kinetic assays of transmembrane proteins in a free-standing lipid membrane.