Direct electrical transduction of antibody binding to a covalent virus layer using electrochemical impedance

Strategies for Surface Immobilization of Whole Bacteriophages: A Review

Bacteriophage immobilization is a key unit operation in emerging biotechnologies, enabling new possibilities for biodetection of pathogenic microbes at low concentration, production of materials with novel antimicrobial properties, and fundamental research on bacteriophages themselves. Wild type bacteriophages exhibit extreme binding specificity for a single species, and often for a particular subspecies, of bacteria. Since their specificity originates in epitope recognition by capsid proteins, which can be altered by chemical or genetic modification, their binding specificity may also be redirected toward arbitrary substrates and/or a variety of analytes in addition to bacteria. The immobilization of bacteriophages on planar and particulate substrates is thus an area of active and increasing scientific interest. This review assembles the knowledge gained so far in the immobilization of whole phage particles, summarizing the main chemistries, and presenting the current state-of-the-art both for an audience well-versed in bioconjugation methods as well as for those who are new to the field.

Viruses Masquerading as Antibodies in Biosensors: The Development of the Virus BioResistor

The 2018 Nobel Prize in Chemistry recognized in vitro evolution, including the development by George Smith and Gregory Winter of phage display, a technology for engineering the functional capabilities of antibodies into viruses. Such bacteriophages solve inherent problems with antibodies, including their high cost, thermal lability, and propensity to aggregate. While phage display accelerated the discovery of peptide and protein motifs for recognition and binding to proteins in a variety of applications, the development of biosensors using intact phage particles was largely unexplored in the early 2000s. Virus particles, 16.5 MDa in size and assembled from thousands of proteins, could not simply be substituted for antibodies in any existing biosensor architectures.Incorporating viruses into biosensors required us to answer several questions: What process will allow the incorporation of viruses into a functional bioaffinity layer? How can the binding of a protein disease marker to a virus particle be electrically transduced to produce a signal? Will the variable salt concentration of a bodily fluid interfere with electrical transduction? A completely new biosensor architecture and a new scheme for electrical transduction of the binding of molecules to viruses were required.This Account describes the highlights of a research program launched in 2006 that answered these questions. These efforts culminated in 2018 in the invention of a biosensor specifically designed to interface with virus particles: the Virus BioResistor (VBR). The VBR is a resistor consisting of a conductive polymer matrix in which M13 virus particles are entrained. The electrical impedance of this resistor, measured across 4 orders of magnitude in frequency, simultaneously measures the concentration of a target protein and the ionic conductivity of the medium in which the resistor is immersed. Large signal amplitudes coupled with the inherent simplicity of the VBR sensor design result in high signal-to-noise ratio (S/N > 100) and excellent sensor-to-sensor reproducibility. Using this new device, we have measured the urinary bladder cancer biomarker nucleic acid deglycase (DJ-1) in urine samples. This optimized VBR is characterized by extremely low sensor-to-sensor coefficients of variation in the range of 3-7% across the DJ-1 binding curve down to a limit of quantitation of 30 pM, encompassing 4 orders of magnitude in concentration.

Molecular Sensing with Host Systems for Hyperpolarized 129Xe

Hyperpolarized noble gases have been used early on in applications for sensitivity enhanced NMR. 129Xe has been explored for various applications because it can be used beyond the gas-driven examination of void spaces. Its solubility in aqueous solutions and its affinity for hydrophobic binding pockets allows "functionalization" through combination with host structures that bind one or multiple gas atoms. Moreover, the transient nature of gas binding in such hosts allows the combination with another signal enhancement technique, namely chemical exchange saturation transfer (CEST). Different systems have been investigated for implementing various types of so-called Xe biosensors where the gas binds to a targeted host to address molecular markers or to sense biophysical parameters. This review summarizes developments in biosensor design and synthesis for achieving molecular sensing with NMR at unprecedented sensitivity. Aspects regarding Xe exchange kinetics and chemical engineering of various classes of hosts for an efficient build-up of the CEST effect will also be discussed as well as the cavity design of host molecules to identify a pool of bound Xe. The concept is presented in the broader context of reporter design with insights from other modalities that are helpful for advancing the field of Xe biosensors.

Experimental and numerical evaluation of a genetically engineered M13 bacteriophage with high sensitivity and selectivity for 2,4,6-trinitrotoluene

Selective and sensitive detection of desired targets is very critical in sensor design. Here, we report a genetically engineered M13 bacteriophage-based sensor system evaluated by quantum mechanics (QM) calculations. Phage display is a facile way to develop the desired peptide sequences, but the resulting sequences can be imperfect peptides for binding of target molecules. A TNT binding peptide (WHW) carrying phage was self-assembled to fabricate thin films and tested for the sensitive and selective surface plasmon resonance-based detection of TNT molecules at the 500 femtomole level. SPR studies performed with the WHW peptide and control peptides (WAW, WHA, AHW) were well-matched with those of the QM calculations. Our combined method between phage engineering and QM calculation will significantly enhance our ability to design selective and sensitive sensors.

Phage-based Electrochemical Sensors: A Review

Phages based electrochemical sensors have received much attention due to their high specificity, sensitivity and simplicity. Phages or bacteriophages provide natural affinity to their host bacteria cells and can serve as the recognition element for electrochemical sensors. It can also act as a tool for bacteria infection and lysis followed by detection of the released cell contents, such as enzymes and ions. In addition, possible detection of the other desired targets, such as antibodies have been demonstrated with phage display techniques. In this paper, the recent development of phage-based electrochemical sensors has been reviewed in terms of the different immobilization protocols and electrochemical detection techniques.

Electrochemical Quantification of Glycated and Non-glycated Human Serum Albumin in Synthetic Urine

A polymer-based electrode capable of specific detection of human serum albumin, and its glycated derivatives, is described. The sensor is constructed from a glass microscope slide coated with a synthesized, polythiophene film bearing a protected, iminodiacetic acid motif. The electrode surface is then further elaborated to a functional biosensor through deprotection of the iminodiacetic acid, followed by metal-affinity immobilization of a specific and high-affinity, albumin ligand. Albumin was then quantified in buffer and synthetic urine via electrochemical impedance spectroscopy. Glycated albumin was next bound to a boronic acid-modified, single-cysteine dihydrofolate reductase variant to quantify glycation ratios by square-wave voltammetry. The platform offers high sensitivity, specificity, and reproducibility in an inexpensive arrangement. The detection limits exceed the requirements for intermediate-term glycemic control monitoring in diabetes patients at 5 and 1 nM for albumin and its glycated forms, respectively.

Chemically Modifying Viruses for Diverse Applications

Long fascinating to biologists, viruses offer nanometer-scale benchtops for building molecular-scale devices and materials. Viruses tolerate a wide range of chemical modifications including reaction conditions, pH values, and temperatures. Recent examples of nongenetic manipulation of viral surfaces have extended viruses into applications ranging from biomedical imaging, drug delivery, tissue regeneration, and biosensors to materials for catalysis and energy generation. Chemical reactions on the phage surface include both covalent and noncovalent modifications, including some applied in conjunction with genetic modifications. Here, we survey viruses chemically augmented with capabilities limited only by imagination.

A Label-Free Electrochemical Impedance Cytosensor Based on Specific Peptide-Fused Phage Selected from Landscape Phage Library

One of the major challenges in the design of biosensors for cancer diagnosis is to introduce a low-cost and selective probe that can recognize cancer cells. In this paper, we combined the phage display technology and electrochemical impedance spectroscopy (EIS) to develop a label-free cytosensor for the detection of cancer cells, without complicated purification of recognition elements. Fabrication steps of the cytosensing interface were monitored by EIS. Due to the high specificity of the displayed octapeptides and avidity effect of their multicopy display on the phage scaffold, good biocompatibility of recombinant phage, the fibrous nanostructure of phage, and the inherent merits of EIS technology, the proposed cytosensor demonstrated a wide linear range (2.0 × 10(2) - 2.0 × 10(8) cells mL(-1)), a low limit of detection (79 cells mL(-1), S/N = 3), high specificity, good inter-and intra-assay reproducibility and satisfactory storage stability. This novel cytosensor designing strategy will open a new prospect for rapid and label-free electrochemical platform for tumor diagnosis.

Biosensing with Virus Electrode Hybrids

Virus electrodes address two major challenges associated with biosensing. First, the surface of the viruses can be readily tailored for specific, high affinity binding to targeted biomarkers. Second, the viruses are entrapped in a conducting polymer for electrical resistance-based, quantitative measurement of biomarker concentration. To further enhance device sensitivity, two different ligands can be attached to the virus surface, and increase the apparent affinity for the biomarker. In the example presented here, the two ligands bind to the analyte in a bidentate binding mode with a chelate-based avidity effect, and result in a 100 pM experimentally observed limit of detection for the cancer biomarker prostate-specific membrane antigen. The approach does not require enzymatic amplification, and allows reagent-free, real-time measurements. This article presents general protocols for the development of such biosensors with modified viruses for the enhanced detection of arbitrary target proteins.

Sub-nanomolar detection of prostate-specific membrane antigen in synthetic urine by synergistic, dual-ligand phage

The sensitive detection of cancer biomarkers in urine could revolutionize cancer diagnosis and treatment. Such detectors must be inexpensive, easy to interpret, and sensitive. This report describes a bioaffinity matrix of viruses integrated into PEDOT films for electrochemical sensing of prostate-specific membrane antigen (PSMA), a prostate cancer biomarker. High sensitivity to PSMA resulted from synergistic action by two different ligands to PSMA on the same phage particle. One ligand was genetically encoded, and the secondary recognition ligand was chemically synthesized to wrap around the phage. The dual ligands result in a bidentate binder with high-copy, dense ligand display for enhanced PSMA detection through a chelate-based avidity effect. Biosensing with virus-PEDOT films provides a 100 pM limit of detection for PSMA in synthetic urine without requiring enzymatic or other amplification.

Virus-poly(3,4-ethylenedioxythiophene) biocomposite films

Virus-poly(3,4-ethylenedioxythiophene) (virus-PEDOT) biocomposite films are prepared by electropolymerizing 3,4-ethylenedioxythiophene (EDOT) in aqueous electrolytes containing 12 mM LiClO(4) and the bacteriophage M13. The concentration of virus in these solutions, [virus](soln), is varied from 3 to 15 nM. A quartz crystal microbalance is used to directly measure the total mass of the biocomposite film during its electrodeposition. In combination with a measurement of the electrodeposition charge, the mass of the virus incorporated into the film is calculated. These data show that the concentration of the M13 within the electropolymerized film, [virus](film), increases linearly with [virus](soln). The incorporation of virus particles into the PEDOT film from solution is efficient, resulting in a concentration ratio of [virus](film):[virus](soln) ≈ 450. Virus incorporation into the PEDOT causes roughening of the film topography that is observed using scanning electron microscopy and atomic force microscopy (AFM). The electrical conductivity of the virus-PEDOT film, measured perpendicular to the plane of the film using conductive tip AFM, decreases linearly with virus loading, from 270 μS/cm for pure PEDOT films to 50 μS/cm for films containing 100 μM virus. The presence on the virus surface of displayed affinity peptides did not significantly influence the efficiency of incorporation into virus-PEDOT biocomposite films.

Portable and quantitative detection of protein biomarkers and small molecular toxins using antibodies and ubiquitous personal glucose meters

Developing portable and low-cost methods for quantitative detection of large protein biomarkers and small molecular toxins can play a significant role in controlling and preventing diseases or toxins outbreaks. Despite years of research, most current methods still require laboratory-based or customized devices that are not widely available to the general public for quantitative analysis. We have previously demonstrated the use of personal glucose meters (PGMs) and functional DNAs for the detection of many nonglucose targets. However, the range of targets detectable by functional DNAs is limited at the current stage. To expand the range of targets that can be detected by PGMs, we report here the use of antibodies in combination with sandwich and competitive assays for quantitative detection of protein biomarkers (PSA, with a detection limit of 0.4 ng/mL) and small molecular toxins (Ochratoxin A, with a detection limit of 6.8 ng/mL), respectively. In both assay methods, with invertase conjugates as the link, quantitative detection is achieved via the dependence between the concentrations of the targets in the sample and the glucose measured by PGMs. Given the wide availability of antibodies for numerous targets, the methods demonstrated here can expand the range of target detection by PGMs significantly.

Chemical sensing with nanowires

Transformational advances in the performance of nanowire-based chemical sensors and biosensors have been achieved over the past two to three years. These advances have arisen from a better understanding of the mechanisms of transduction operating in these devices, innovations in nanowire fabrication, and improved methods for incorporating receptors into or onto nanowires. Nanowire-based biosensors have detected DNA in undiluted physiological saline. For silicon nanowire nucleic acid sensors, higher sensitivities have been obtained by eliminating the passivating oxide layer on the nanowire surface and by substituting uncharged protein nucleic acids for DNA as the capture strands. Biosensors for peptide and protein cancer markers, based on both semiconductor nanowires and nanowires of conductive polymers, have detected these targets at physiologically relevant concentrations in both blood plasma and whole blood. Nanowire chemical sensors have also detected several gases at the parts-per-million level. This review discusses these and other recent advances, concentrating on work published in the past three years.

Virus-polymer hybrid nanowires tailored to detect prostate-specific membrane antigen

We demonstrate the de novo fabrication of a biosensor, based upon virus-containing poly(3,4-ethylene-dioxythiophene) (PEDOT) nanowires, that detects prostate-specific membrane antigen (PSMA). This development process occurs in three phases: (1) isolation of a M13 virus with a displayed polypeptide receptor, from a library of ≈10(11) phage-displayed peptides, which binds PSMA with high affinity and selectivity, (2) microfabrication of PEDOT nanowires that entrain these virus particles using the lithographically patterned nanowire electrodeposition (LPNE) method, and (3) electrical detection of the PSMA in high ionic strength (150 mM salt) media, including synthetic urine, using an array of virus-PEDOT nanowires with the electrical resistance of these nanowires for transduction. The electrical resistance of an array of these nanowires increases linearly with the PSMA concentration from 20 to 120 nM in high ionic strength phosphate-buffered fluoride (PBF) buffer, yielding a limit of detection (LOD) for PSMA of 56 nM.

Virus-poly(3,4-ethylenedioxythiophene) composite films for impedance-based biosensing

Composite films composed of poly(3,4-ethylenedioxythiophene), PEDOT, and the filamentous virus M13-K07 were prepared by electrooxidation of 3,4-ethylenedioxythiophene (EDOT) in aqueous solutions containing 8 nM of the virus at planar gold electrodes. These films were characterized using atomic force microscopy and scanning electron microscopy. The electrochemical impedance of virus-PEDOT films increases upon exposure to an antibody (p-Ab) that selectively binds to the M13 coat peptide. Exposure to p-Ab causes a shift in both real (Z(RE)) and imaginary (Z(IM)) impedance components across a broad range of frequencies from 50 Hz to 10 kHz. Within a narrower frequency range from 250 Hz to 5 kHz, the increase of the total impedance (Z(total)) with p-Ab concentration conforms to a Langmuir adsorption isotherm over the concentration range from from 6 to 66 nM, yielding a value for K(d) = 16.9 nM at 1000 Hz.

Chemical modification of M13 bacteriophage and its application in cancer cell imaging

The M13 bacteriophage has been demonstrated to be a robust scaffold for bionanomaterial development. In this paper, we report on the chemical modifications of three kinds of reactive groups, i.e., the amino groups of lysine residues or N-terminal, the carboxylic acid groups of aspartic acid or glutamic acid residues, and the phenol group of tyrosine residues, on M13 surface. The reactivity of each group was identified through conjugation with small fluorescent molecules. Furthermore, the regioselectivity of each reaction was investigated by HPLC-MS-MS. By optimizing the reaction condition, hundreds of fluorescent moieties could be attached to create a highly fluorescent M13 bacteriophage. In addition, cancer cell targeting motifs such as folic acid could also be conjugated onto the M13 surface. Therefore, dual-modified M13 particles with folic acid and fluorescent molecules were synthesized via the selective modification of two kinds of reactive groups. Such dual-modified M13 particles showed very good binding affinity to human KB cancer cells, which demonstrated the potential applications of M13 bacteriophage in bioimaging and drug delivery.

Electrochemical impedance spectroscopy

This review describes recent advances in electrochemical impedance spectroscopy (EIS) with an emphasis on its novel applications to various electrochemistry-related problems. Section 1 discusses the development of new EIS techniques to reduce measurement time. For this purpose, various forms of multisine EIS techniques were first developed via a noise signal synthesized by mixing ac waves of various frequencies, followed by fast Fourier transform of the signal and the resulting current. Subsequently, an entirely new concept was introduced in which true white noise was used as an excitation source, followed by Fourier transform of both excitation and response signals. Section 2 describes novel applications of the newly developed techniques to time-resolved impedance measurements as well as to impedance imaging. Section 3 is devoted to recent applications of EIS techniques, specifically traditional measurements in various fields with a special emphasis on biosensor detections.

Viruses and their potential in bioimaging and biosensing applications

Successful development of ultrasensitive constructs for bioimaging and biosensing is a challenging task. Recently, viruses have drawn increasing attention due to their exquisite three-dimensional structures and unique properties, including multivalency, orthogonal reactivities, and responsiveness to genetic modifications. With such well-characterized structures, functional units, such as imaging and binding motifs, can be engineered on the surface of viruses in a programmable, polyvalent manner, which leads to novel nanosized sensing/imaging systems with enhanced signaling and targeting performance. This review highlights some recent progress in the applications of viruses in bioimaging and biosensing.

Chemical and genetic wrappers for improved phage and RNA display

An Achilles heel inherent to all molecular display formats, background binding between target and display system introduces false positives into screens and selections. For example, the negatively charged surfaces of phage, mRNA, and ribosome display systems bind with unacceptably high nonspecificity to positively charged target molecules, which represent an estimated 35% of proteins in the human proteome. Here we report the first systematic attempt to understand why a broad class of molecular display selections fail, and then solve the underlying problem for both phage and RNA display. Firstly, a genetic strategy was used to introduce a short, charge-neutralizing peptide into the solvent-exposed, negatively charged phage coat. The modified phage (KO7(+)) reduced or eliminated nonspecific binding to the problematic high-pI proteins. In the second, chemical approach, nonspecific interactions were blocked by oligolysine wrappers in the cases of phage and total RNA. For phage display applications, the peptides Lys(n) (where n=16 to 24) emerged as optimal for wrapping the phage. Lys(8), however, provided effective wrappers for RNA binding in assays against the RNA binding protein HIV-1 Vif. The oligolysine peptides blocked nonspecific binding to allow successful selections, screens, and assays with five previously unworkable protein targets.

Virus-based chemical and biological sensing

Viruses have recently proven useful for the detection of target analytes such as explosives, proteins, bacteria, viruses, spores, and toxins with high selectivity and sensitivity. Bacteriophages (often shortened to phages), viruses that specifically infect bacteria, are currently the most studied viruses, mainly because target-specific nonlytic phages (and the peptides and proteins carried by them) can be identified by using the well-established phage display technique, and lytic phages can specifically break bacteria to release cell-specific marker molecules such as enzymes that can be assayed. In addition, phages have good chemical and thermal stability, and can be conjugated with nanomaterials and immobilized on a transducer surface in an analytical device. This Review focuses on progress made in the use of phages in chemical and biological sensors in combination with traditional analytical techniques. Recent progress in the use of virus-nanomaterial composites and other viruses in sensing applications is also highlighted.