Brian Cunningham - Academia.edu (original) (raw)

Papers by Brian Cunningham

bioRxiv (Cold Spring Harbor Laboratory), Jun 24, 2024

The ability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to infect a wide-rang... more The ability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to infect a wide-range of species raises significant concerns regarding both human-to-animal and animal-tohuman transmission. There is an increasing demand for highly sensitive, rapid, and simple diagnostic assays that can detect viral infection across various species. In this study, we developed a biosensor assay that adapted a monoclonal-antibody (mAb)-based blocking ELISA format into an Activate Capture + Digital Counting (AC + DC)-based immunoassay. The assay employs a photonic crystal (PC) biosensor, gold-nanoparticle (AuNP) tags, SARS-CoV-2 nucleocapsid (N) protein, and specific anti-N mAb to detect antibody responses in animals exposed with SARS-CoV-2. We demonstrated a simple 2-step 15-min test that was capable of detecting as low as 12.5 ng of antibody in controlled standard serum samples. Based on an evaluation of 176 cat serum samples with known antibody status, an optimal percentage of inhibition (PI) cutoff value of 0.588 resulted in a diagnostic sensitivity of 98.3% and a diagnostic specificity of 96.5%. The test is highly repeatable with low variation coefficients of 2.04%, 2.73%, and 4.87% across different runs, within a single run, and on a single chip, respectively. The test was further employed to detect antibody responses in multiple animal species as well as investigate dynamics of antibody response in experimentally infected cats. This test platform provides an important tool for rapid field surveillance of SARS-CoV-2 infection across multiple species.

Chemical Society Reviews, 2017

Biosensors are extensively employed for diagnosing a broad array of diseases and disorders in cli... more Biosensors are extensively employed for diagnosing a broad array of diseases and disorders in clinical settings worldwide. The implementation of biosensors at the point-of-care (POC), such as at primary clinics or the bedside, faces impediments because they may require highly trained personnel, have long assay times, large sizes, and high instrumental cost. Thus, there exists a need to develop inexpensive, reliable, user-friendly, and compact biosensing systems at the POC. Biosensors incorporated with photonic crystal (PC) structures hold promise to address many of the aforementioned challenges facing the development of new POC diagnostics. Currently, PC-based biosensors have been employed for detecting a variety of biotargets, such as cells, pathogens, proteins, antibodies, and nucleic acids, with high efficiency and selectivity. In this review, we provide a broad overview of PCs by explaining their structures, fabrication techniques, and sensing principles. Furthermore, we discuss recent applications of PC-based biosensors incorporated with emerging technologies, including telemedicine, flexible and wearable sensing, smart materials and metamaterials. Finally, we discuss current challenges associated with existing biosensors, and provide an outlook for PC-based biosensors and their promise at the POC.

Analytical Chemistry, Jan 21, 2011

We report on the use of photonic crystal surfaces as a high-sensitivity platform for detection of... more We report on the use of photonic crystal surfaces as a high-sensitivity platform for detection of a panel of cancer biomarkers in a protein microarray format. The photonic crystal surface is designed to provide an optical resonance at the excitation wavelength of cyanine-5 (Cy5), thus providing an increase in fluorescent intensity for Cy5-labeled analytes measured with a confocal microarray scanner, compared to a glass surface. The sandwich enzyme-linked immunosorbent assay (ELISA) is undertaken on a microarray platform to undertake a simultaneous, multiplex analysis of 24 antigens on a single chip. Our results show that the resonant excitation effect increases the signal-to-noise ratio by 3.8-to 6.6-fold, resulting in a decrease in detection limits of 5-90%, with the exact enhancement dependent upon the antibody-antigen interaction. Doseresponse characterization of the photonic crystal antibody microarrays shows the capability to detect common cancer biomarkers in the < 2 pg/ml concentration range within a mixed sample.

Biosensors

The ability to self-test for HIV is vital to preventing transmission, particularly when used in c... more The ability to self-test for HIV is vital to preventing transmission, particularly when used in concert with HIV biomedical prevention modalities, such as pre-exposure prophylaxis (PrEP). In this paper, we review recent developments in HIV self-testing and self-sampling methods, and the potential future impact of novel materials and methods that emerged through efforts to develop more effective point-of-care (POC) SARS-CoV-2 diagnostics. We address the gaps in existing HIV self-testing technologies, where improvements in test sensitivity, sample-to-answer time, simplicity, and cost are needed to enhance diagnostic accuracy and widespread accessibility. We discuss potential paths toward the next generation of HIV self-testing through sample collection materials, biosensing assay techniques, and miniaturized instrumentation. We discuss the implications for other applications, such as self-monitoring of HIV viral load and other infectious diseases.

Exosomal microRNAs (miRNAs) have considerable potential as pivotal biomarkers to monitor cancer d... more Exosomal microRNAs (miRNAs) have considerable potential as pivotal biomarkers to monitor cancer development, dis-ease progression, treatment effects and prognosis. Here, we report an efficient target recycling amplification process (TRAP) for the digital detection of exosomal miRNAs using photonic resonator absorption microscopy (PRAM). Through toehold-mediated DNA strand displacement reactions, we achieve multiplex digital detection with sub-attomolar sensitivity in 20 minutes, robust selectivity for single nucleotide variants, and a broad dynamic range from 1 aM to 1 pM. We then applied our TRAP system to quantify miRNA in exosomal total RNAs isolated from human cancer cell lines. Compared with traditional qRT-PCR methods, TRAP showed similar accuracy in profiling exosomal miRNAs derived from cancer cells, but also exhibited at least 31-fold and 61-fold enhancement in the limits of miRNA-375 and miRNA-21 detection, respectively. The TRAP approach is ideal for exosomal or circulati...

bioRxiv (Cold Spring Harbor Laboratory), Dec 13, 2022

Label-free detection and digital counting of nanometer-scaled objects such as nanoparticles, viru... more Label-free detection and digital counting of nanometer-scaled objects such as nanoparticles, viruses, extracellular vesicles, and protein molecules enable a wide range of applications in cancer diagnostics, pathogen detection, and life science research. The contrast of interferometric scattering microscopy is amplified through a photonic crystal surface, upon which scattered light from an object combines with illumination from a monochromatic plane wave source. The use of a photonic crystal substrate for interference scattering microscopy results in reduced requirements for high-intensity lasers or oil-immersion objectives, thus opening a pathway toward instruments that are more suitable for environments outside the optics laboratory. Here, we report the design, implementation, and characterization of a compact Photonic Resonator Interferometric Scattering Microscope (PRISM) designed for point-of-use environments and applications. The instrument incorporates two innovative elements that facilitate operation on a desktop in ordinary laboratory environments by users that do not have optics expertise. First, because scattering microscopes are extremely sensitive to vibration, we incorporated an inexpensive but effective solution of suspending the instrument's main components from a rigid metal framework using elastic bands, resulting in an average of 28.7 dBV reduction in vibration amplitude compared to an office desk. Second, an automated focusing module based on the principle of total internal reflection maintains the stability of image contrast over time and spatial position, facilitating automated data collection. In this work, we characterize the system's performance by measuring the contrast from gold nanoparticles with diameters in the 10-40 nm range and by observing various biological analytes, including HIV virus, SARS-CoV-2 virus, exosomes, and ferritin protein.

ABSTRACTAssays utilizing molecular fluorophores are common throughout life science research and d... more ABSTRACTAssays utilizing molecular fluorophores are common throughout life science research and diagnostic testing, although detection limits are generally limited by weak emission intensity, thus requiring many labeled target molecules to combine their output to achieve signal-to-noise greater than the background. Here, we describe how the synergistic coupling of plasmonic and photonic resonance modes can significantly boost the emission from fluorescent dye molecules without increasing the illumination intensity while utilizing a microscopy approach with a broad field of view. By optimally matching the resonant modes of a plasmonic fluor (PF) nanoparticle and a photonic crystal (PC) surface with the absorption and emission spectrum of the PF’s fluorescent dye, we observe a 52-fold improvement in signal intensity, enabling individual PFs to be observed and digitally counted, using an approach in which one PF tag represents detection of one target molecule. The photonic amplificatio...

Photonic crystal (PC) surfaces have been demonstrated as a compelling platform for improving the ... more Photonic crystal (PC) surfaces have been demonstrated as a compelling platform for improving the sensitivity of surface-based fluorescent assays used in disease diagnostics and life science research. PCs can be engineered to support optical resonances at specific wavelengths at which strong electromagnetic fields are utilized to enhance the intensity of surface-bound fluorophore excitation. Meanwhile, the leaky resonant modes of PCs can be used to direct emitted photons within a narrow range of angles for more efficient collection by a fluorescence detection system. The multiplicative effects of enhanced excitation combined with enhanced photon extraction combine to provide improved signal-to-noise ratios for detection of fluorescent emitters, which in turn can be used to reduce the limits of detection of low concentration analytes, such as disease biomarker proteins. Fabrication of PCs using inexpensive manufacturing methods and materials that include replica molding on plastic, nano-imprint lithography on quartz substrates result in devices that are practical for single-use disposable applications. In this review, we will describe the motivation for implementing high-sensitivity fluorescence detection in the context of molecular diagnosis and gene expression analysis though the use of PC surfaces. Recent efforts to improve the design and fabrication of PCs and their

Registered Charity Number 207890 Showcasing Photonic Crystal Enhanced Microscopy: A new label-fre... more Registered Charity Number 207890 Showcasing Photonic Crystal Enhanced Microscopy: A new label-free imaging method for quantitative imaging of live cell adhesion, representing one of the optics-based biosensor technologies developed by the Nano Sensors Group at the University of Illinois at Urbana-Champaign, directed by Professor Brian T. Cunningham. More information can be found at: nano.ece.illinois.edu.

Proceedings of the National Academy of Sciences, 2019

Significance Highly selective and sensitive detection of microRNA is a key challenge in the devel... more Significance Highly selective and sensitive detection of microRNA is a key challenge in the development of liquid-biopsy approaches. Technologies that can achieve high diagnostic performance without the requirement of complicated processing steps or expensive equipment are necessary for broad use. With these features in mind, we demonstrate a digital-readout microRNA diagnostic that fundamentally relies on microRNA-activated nanoparticle-photonic crystal hybrid coupling. The hybrid formation allows for clear detection of single-particle binding events due to enhanced nanoparticle absorption at the binding location. Whereas the applied photonics lend the assay concentration sensitivity, we additionally demonstrate broad placement single-base mismatch selectivity and complex media detection by applying free-energy tuned toehold probes.

Biomedical Microdevices, 2017

Infectious diseases remain the world's top contributors to death and disability, and, with recent... more Infectious diseases remain the world's top contributors to death and disability, and, with recent outbreaks of Zika virus infections there has been an urgency for simple, sensitive and easily translatable point-of-care tests. Here we demonstrate a novel point-of-care platform to diagnose infectious diseases from whole blood samples. A microfluidic platform performs minimal sample processing in a user-friendly diagnostics card followed by real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) on the same card with pre-dried primers specific to viral targets. Our point-of-care platform uses a commercial smartphone to acquire real-time images of the amplification reaction and displays a visual read-out of the assay. We apply this system to detect closely related Zika, Dengue (types 1 and 3) and Chikungunya virus infections from whole blood on the same pre-printed chip with high specificity and clinically relevant sensitivity. Limit of detection of 1.56e5 PFU/mL of Zika virus from whole blood was achieved through our platform. With the ability to quantitate the target nucleic acid, this platform can also perform point-of-care patient surveillance for pathogen load or select biomarkers in whole blood.

Lab on a chip, Sep 28, 2017

We demonstrate a smartphone-integrated handheld detection instrument capable of utilizing the int... more We demonstrate a smartphone-integrated handheld detection instrument capable of utilizing the internal rear-facing camera as a high-resolution spectrometer for measuring the colorimetric absorption spectrum, fluorescence emission spectrum, and resonant reflection spectrum from a microfluidic cartridge inserted into the measurement light path. Under user selection, the instrument gathers light from either the white "flash" LED of the smartphone or an integrated green laser diode to direct illumination into a liquid test sample or onto a photonic crystal biosensor. Light emerging from each type of assay is gathered via optical fiber and passed through a diffraction grating placed directly over the smartphone camera to generate spectra from the assay when an image is collected. Each sensing modality is associated with a unique configuration of a microfluidic "stick" containing a linear array of liquid chambers that are swiped through the instrument while the smartph...

Scientific reports, Jan 12, 2017

Human Papillomavirus (HPV) infection has been recognized as the main etiologic factor in the deve... more Human Papillomavirus (HPV) infection has been recognized as the main etiologic factor in the development of various cancers including penile, vulva, oropharyngeal and cervical cancers. In the development of cancer, persistent HPV infections induce E6 and E7 oncoproteins, which promote cell proliferation and carcinogenesis resulting elevated levels of host antibodies (e.g., anti-HPV16 E7 antibody). Currently, these cancers are clinically diagnosed using invasive biopsy-based tests, which are performed only in centralized labs by experienced clinical staff using time-consuming and expensive tools and technologies. Therefore, these obstacles constrain their utilization at primary care clinics and in remote settings, where resources are limited. Here, we present a rapid, inexpensive, reliable, easy-to-use, customized immunoassay platform following a microfluidic filter device to detect and quantify anti-HPV16 E7 antibodies from whole blood as a non-invasive assisting technology for diag...

Chemical Society Reviews, 2017

This review describes photonic crystal-based biosensors and discusses their potential application... more This review describes photonic crystal-based biosensors and discusses their potential applications and promise at the point-of-care settings.

2012 IEEE Sensors, 2012

We report for the first time the combination of a quartz-based photonic crystal (PC) with a detec... more We report for the first time the combination of a quartz-based photonic crystal (PC) with a detection instrument designed to perform label-free (LF) and enhanced fluorescence (EF) imaging for antibody microarray applications. Label-free detection is used to quantify binding density of immobilized capture antibodies. Angle-scanning approach is implemented to achieve more uniform fluorescence enhancement by reducing the coefficient of variation of replicate assays by 20-99% compared to ordinary fluorescence microscopy. I.

CLEO: 2014, 2014

We demonstrate a label-free biosensor imaging approach that utilizes a photonic-crystal surface t... more We demonstrate a label-free biosensor imaging approach that utilizes a photonic-crystal surface to detect attachment of individual nanoparticles down to ~65×30×30nm 3. Matching nanoparticle plasmon resonant-frequency to the photonic-crystal resonance substantially increases sensitivity of the approach.

Journal of Fluorescence, 2010

The effect of resonant fluorescent enhancement from a photonic crystal surface upon the fluoresce... more The effect of resonant fluorescent enhancement from a photonic crystal surface upon the fluorescent photobleaching rate of Cyanine-5 labeled protein has been investigated. We show that the enhanced excitation mechanism for photonic crystal enhanced fluorescence, in which the device surface resonantly couples light from an excitation laser, accelerates photobleaching in proportion to the coupling efficiency of the laser to the photonic crystal. We also show that the enhanced extraction mechanism, in which the photonic crystal directs emitted photons approximately normal to the surface, does not play a role in the rate of photobleaching. We show that the photobleaching rate of dye molecules on the photonic crystal surface is accelerated by 30x compared to an ordinary glass surface, but substantial signal gain is still evident, even after extended periods of continuous illumination at the resonant condition.

Sensors, 2022

In recent years, the biosensor research community has made rapid progress in the development of n... more In recent years, the biosensor research community has made rapid progress in the development of nanostructured materials capable of amplifying the interaction between light and biological matter. A common objective is to concentrate the electromagnetic energy associated with light into nanometer-scale volumes that, in many cases, can extend below the conventional Abbé diffraction limit. Dating back to the first application of surface plasmon resonance (SPR) for label-free detection of biomolecular interactions, resonant optical structures, including waveguides, ring resonators, and photonic crystals, have proven to be effective conduits for a wide range of optical enhancement effects that include enhanced excitation of photon emitters (such as quantum dots, organic dyes, and fluorescent proteins), enhanced extraction from photon emitters, enhanced optical absorption, and enhanced optical scattering (such as from Raman-scatterers and nanoparticles). The application of photonic metama...

ABSTRACTWe present a net-shaped DNA nanostructure (called “DNA Net” herein) design strategy for s... more ABSTRACTWe present a net-shaped DNA nanostructure (called “DNA Net” herein) design strategy for selective recognition and high-affinity capture of the intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers releases fluorescent signal upon virus binding that is easily read by a hand-held fluorimeter for a rapid (in 10 mins), simple (mix- and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive (∼ $1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1×103-fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like...

bioRxiv (Cold Spring Harbor Laboratory), Jun 24, 2024

The ability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to infect a wide-rang... more The ability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) to infect a wide-range of species raises significant concerns regarding both human-to-animal and animal-tohuman transmission. There is an increasing demand for highly sensitive, rapid, and simple diagnostic assays that can detect viral infection across various species. In this study, we developed a biosensor assay that adapted a monoclonal-antibody (mAb)-based blocking ELISA format into an Activate Capture + Digital Counting (AC + DC)-based immunoassay. The assay employs a photonic crystal (PC) biosensor, gold-nanoparticle (AuNP) tags, SARS-CoV-2 nucleocapsid (N) protein, and specific anti-N mAb to detect antibody responses in animals exposed with SARS-CoV-2. We demonstrated a simple 2-step 15-min test that was capable of detecting as low as 12.5 ng of antibody in controlled standard serum samples. Based on an evaluation of 176 cat serum samples with known antibody status, an optimal percentage of inhibition (PI) cutoff value of 0.588 resulted in a diagnostic sensitivity of 98.3% and a diagnostic specificity of 96.5%. The test is highly repeatable with low variation coefficients of 2.04%, 2.73%, and 4.87% across different runs, within a single run, and on a single chip, respectively. The test was further employed to detect antibody responses in multiple animal species as well as investigate dynamics of antibody response in experimentally infected cats. This test platform provides an important tool for rapid field surveillance of SARS-CoV-2 infection across multiple species.

Chemical Society Reviews, 2017

Biosensors are extensively employed for diagnosing a broad array of diseases and disorders in cli... more Biosensors are extensively employed for diagnosing a broad array of diseases and disorders in clinical settings worldwide. The implementation of biosensors at the point-of-care (POC), such as at primary clinics or the bedside, faces impediments because they may require highly trained personnel, have long assay times, large sizes, and high instrumental cost. Thus, there exists a need to develop inexpensive, reliable, user-friendly, and compact biosensing systems at the POC. Biosensors incorporated with photonic crystal (PC) structures hold promise to address many of the aforementioned challenges facing the development of new POC diagnostics. Currently, PC-based biosensors have been employed for detecting a variety of biotargets, such as cells, pathogens, proteins, antibodies, and nucleic acids, with high efficiency and selectivity. In this review, we provide a broad overview of PCs by explaining their structures, fabrication techniques, and sensing principles. Furthermore, we discuss recent applications of PC-based biosensors incorporated with emerging technologies, including telemedicine, flexible and wearable sensing, smart materials and metamaterials. Finally, we discuss current challenges associated with existing biosensors, and provide an outlook for PC-based biosensors and their promise at the POC.

Analytical Chemistry, Jan 21, 2011

We report on the use of photonic crystal surfaces as a high-sensitivity platform for detection of... more We report on the use of photonic crystal surfaces as a high-sensitivity platform for detection of a panel of cancer biomarkers in a protein microarray format. The photonic crystal surface is designed to provide an optical resonance at the excitation wavelength of cyanine-5 (Cy5), thus providing an increase in fluorescent intensity for Cy5-labeled analytes measured with a confocal microarray scanner, compared to a glass surface. The sandwich enzyme-linked immunosorbent assay (ELISA) is undertaken on a microarray platform to undertake a simultaneous, multiplex analysis of 24 antigens on a single chip. Our results show that the resonant excitation effect increases the signal-to-noise ratio by 3.8-to 6.6-fold, resulting in a decrease in detection limits of 5-90%, with the exact enhancement dependent upon the antibody-antigen interaction. Doseresponse characterization of the photonic crystal antibody microarrays shows the capability to detect common cancer biomarkers in the < 2 pg/ml concentration range within a mixed sample.

Biosensors

The ability to self-test for HIV is vital to preventing transmission, particularly when used in c... more The ability to self-test for HIV is vital to preventing transmission, particularly when used in concert with HIV biomedical prevention modalities, such as pre-exposure prophylaxis (PrEP). In this paper, we review recent developments in HIV self-testing and self-sampling methods, and the potential future impact of novel materials and methods that emerged through efforts to develop more effective point-of-care (POC) SARS-CoV-2 diagnostics. We address the gaps in existing HIV self-testing technologies, where improvements in test sensitivity, sample-to-answer time, simplicity, and cost are needed to enhance diagnostic accuracy and widespread accessibility. We discuss potential paths toward the next generation of HIV self-testing through sample collection materials, biosensing assay techniques, and miniaturized instrumentation. We discuss the implications for other applications, such as self-monitoring of HIV viral load and other infectious diseases.

Exosomal microRNAs (miRNAs) have considerable potential as pivotal biomarkers to monitor cancer d... more Exosomal microRNAs (miRNAs) have considerable potential as pivotal biomarkers to monitor cancer development, dis-ease progression, treatment effects and prognosis. Here, we report an efficient target recycling amplification process (TRAP) for the digital detection of exosomal miRNAs using photonic resonator absorption microscopy (PRAM). Through toehold-mediated DNA strand displacement reactions, we achieve multiplex digital detection with sub-attomolar sensitivity in 20 minutes, robust selectivity for single nucleotide variants, and a broad dynamic range from 1 aM to 1 pM. We then applied our TRAP system to quantify miRNA in exosomal total RNAs isolated from human cancer cell lines. Compared with traditional qRT-PCR methods, TRAP showed similar accuracy in profiling exosomal miRNAs derived from cancer cells, but also exhibited at least 31-fold and 61-fold enhancement in the limits of miRNA-375 and miRNA-21 detection, respectively. The TRAP approach is ideal for exosomal or circulati...

bioRxiv (Cold Spring Harbor Laboratory), Dec 13, 2022

Label-free detection and digital counting of nanometer-scaled objects such as nanoparticles, viru... more Label-free detection and digital counting of nanometer-scaled objects such as nanoparticles, viruses, extracellular vesicles, and protein molecules enable a wide range of applications in cancer diagnostics, pathogen detection, and life science research. The contrast of interferometric scattering microscopy is amplified through a photonic crystal surface, upon which scattered light from an object combines with illumination from a monochromatic plane wave source. The use of a photonic crystal substrate for interference scattering microscopy results in reduced requirements for high-intensity lasers or oil-immersion objectives, thus opening a pathway toward instruments that are more suitable for environments outside the optics laboratory. Here, we report the design, implementation, and characterization of a compact Photonic Resonator Interferometric Scattering Microscope (PRISM) designed for point-of-use environments and applications. The instrument incorporates two innovative elements that facilitate operation on a desktop in ordinary laboratory environments by users that do not have optics expertise. First, because scattering microscopes are extremely sensitive to vibration, we incorporated an inexpensive but effective solution of suspending the instrument's main components from a rigid metal framework using elastic bands, resulting in an average of 28.7 dBV reduction in vibration amplitude compared to an office desk. Second, an automated focusing module based on the principle of total internal reflection maintains the stability of image contrast over time and spatial position, facilitating automated data collection. In this work, we characterize the system's performance by measuring the contrast from gold nanoparticles with diameters in the 10-40 nm range and by observing various biological analytes, including HIV virus, SARS-CoV-2 virus, exosomes, and ferritin protein.

ABSTRACTAssays utilizing molecular fluorophores are common throughout life science research and d... more ABSTRACTAssays utilizing molecular fluorophores are common throughout life science research and diagnostic testing, although detection limits are generally limited by weak emission intensity, thus requiring many labeled target molecules to combine their output to achieve signal-to-noise greater than the background. Here, we describe how the synergistic coupling of plasmonic and photonic resonance modes can significantly boost the emission from fluorescent dye molecules without increasing the illumination intensity while utilizing a microscopy approach with a broad field of view. By optimally matching the resonant modes of a plasmonic fluor (PF) nanoparticle and a photonic crystal (PC) surface with the absorption and emission spectrum of the PF’s fluorescent dye, we observe a 52-fold improvement in signal intensity, enabling individual PFs to be observed and digitally counted, using an approach in which one PF tag represents detection of one target molecule. The photonic amplificatio...

Photonic crystal (PC) surfaces have been demonstrated as a compelling platform for improving the ... more Photonic crystal (PC) surfaces have been demonstrated as a compelling platform for improving the sensitivity of surface-based fluorescent assays used in disease diagnostics and life science research. PCs can be engineered to support optical resonances at specific wavelengths at which strong electromagnetic fields are utilized to enhance the intensity of surface-bound fluorophore excitation. Meanwhile, the leaky resonant modes of PCs can be used to direct emitted photons within a narrow range of angles for more efficient collection by a fluorescence detection system. The multiplicative effects of enhanced excitation combined with enhanced photon extraction combine to provide improved signal-to-noise ratios for detection of fluorescent emitters, which in turn can be used to reduce the limits of detection of low concentration analytes, such as disease biomarker proteins. Fabrication of PCs using inexpensive manufacturing methods and materials that include replica molding on plastic, nano-imprint lithography on quartz substrates result in devices that are practical for single-use disposable applications. In this review, we will describe the motivation for implementing high-sensitivity fluorescence detection in the context of molecular diagnosis and gene expression analysis though the use of PC surfaces. Recent efforts to improve the design and fabrication of PCs and their

Registered Charity Number 207890 Showcasing Photonic Crystal Enhanced Microscopy: A new label-fre... more Registered Charity Number 207890 Showcasing Photonic Crystal Enhanced Microscopy: A new label-free imaging method for quantitative imaging of live cell adhesion, representing one of the optics-based biosensor technologies developed by the Nano Sensors Group at the University of Illinois at Urbana-Champaign, directed by Professor Brian T. Cunningham. More information can be found at: nano.ece.illinois.edu.

Proceedings of the National Academy of Sciences, 2019

Significance Highly selective and sensitive detection of microRNA is a key challenge in the devel... more Significance Highly selective and sensitive detection of microRNA is a key challenge in the development of liquid-biopsy approaches. Technologies that can achieve high diagnostic performance without the requirement of complicated processing steps or expensive equipment are necessary for broad use. With these features in mind, we demonstrate a digital-readout microRNA diagnostic that fundamentally relies on microRNA-activated nanoparticle-photonic crystal hybrid coupling. The hybrid formation allows for clear detection of single-particle binding events due to enhanced nanoparticle absorption at the binding location. Whereas the applied photonics lend the assay concentration sensitivity, we additionally demonstrate broad placement single-base mismatch selectivity and complex media detection by applying free-energy tuned toehold probes.

Biomedical Microdevices, 2017

Infectious diseases remain the world's top contributors to death and disability, and, with recent... more Infectious diseases remain the world's top contributors to death and disability, and, with recent outbreaks of Zika virus infections there has been an urgency for simple, sensitive and easily translatable point-of-care tests. Here we demonstrate a novel point-of-care platform to diagnose infectious diseases from whole blood samples. A microfluidic platform performs minimal sample processing in a user-friendly diagnostics card followed by real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) on the same card with pre-dried primers specific to viral targets. Our point-of-care platform uses a commercial smartphone to acquire real-time images of the amplification reaction and displays a visual read-out of the assay. We apply this system to detect closely related Zika, Dengue (types 1 and 3) and Chikungunya virus infections from whole blood on the same pre-printed chip with high specificity and clinically relevant sensitivity. Limit of detection of 1.56e5 PFU/mL of Zika virus from whole blood was achieved through our platform. With the ability to quantitate the target nucleic acid, this platform can also perform point-of-care patient surveillance for pathogen load or select biomarkers in whole blood.

Lab on a chip, Sep 28, 2017

We demonstrate a smartphone-integrated handheld detection instrument capable of utilizing the int... more We demonstrate a smartphone-integrated handheld detection instrument capable of utilizing the internal rear-facing camera as a high-resolution spectrometer for measuring the colorimetric absorption spectrum, fluorescence emission spectrum, and resonant reflection spectrum from a microfluidic cartridge inserted into the measurement light path. Under user selection, the instrument gathers light from either the white "flash" LED of the smartphone or an integrated green laser diode to direct illumination into a liquid test sample or onto a photonic crystal biosensor. Light emerging from each type of assay is gathered via optical fiber and passed through a diffraction grating placed directly over the smartphone camera to generate spectra from the assay when an image is collected. Each sensing modality is associated with a unique configuration of a microfluidic "stick" containing a linear array of liquid chambers that are swiped through the instrument while the smartph...

Scientific reports, Jan 12, 2017

Human Papillomavirus (HPV) infection has been recognized as the main etiologic factor in the deve... more Human Papillomavirus (HPV) infection has been recognized as the main etiologic factor in the development of various cancers including penile, vulva, oropharyngeal and cervical cancers. In the development of cancer, persistent HPV infections induce E6 and E7 oncoproteins, which promote cell proliferation and carcinogenesis resulting elevated levels of host antibodies (e.g., anti-HPV16 E7 antibody). Currently, these cancers are clinically diagnosed using invasive biopsy-based tests, which are performed only in centralized labs by experienced clinical staff using time-consuming and expensive tools and technologies. Therefore, these obstacles constrain their utilization at primary care clinics and in remote settings, where resources are limited. Here, we present a rapid, inexpensive, reliable, easy-to-use, customized immunoassay platform following a microfluidic filter device to detect and quantify anti-HPV16 E7 antibodies from whole blood as a non-invasive assisting technology for diag...

Chemical Society Reviews, 2017

This review describes photonic crystal-based biosensors and discusses their potential application... more This review describes photonic crystal-based biosensors and discusses their potential applications and promise at the point-of-care settings.

2012 IEEE Sensors, 2012

We report for the first time the combination of a quartz-based photonic crystal (PC) with a detec... more We report for the first time the combination of a quartz-based photonic crystal (PC) with a detection instrument designed to perform label-free (LF) and enhanced fluorescence (EF) imaging for antibody microarray applications. Label-free detection is used to quantify binding density of immobilized capture antibodies. Angle-scanning approach is implemented to achieve more uniform fluorescence enhancement by reducing the coefficient of variation of replicate assays by 20-99% compared to ordinary fluorescence microscopy. I.

CLEO: 2014, 2014

We demonstrate a label-free biosensor imaging approach that utilizes a photonic-crystal surface t... more We demonstrate a label-free biosensor imaging approach that utilizes a photonic-crystal surface to detect attachment of individual nanoparticles down to ~65×30×30nm 3. Matching nanoparticle plasmon resonant-frequency to the photonic-crystal resonance substantially increases sensitivity of the approach.

Journal of Fluorescence, 2010

The effect of resonant fluorescent enhancement from a photonic crystal surface upon the fluoresce... more The effect of resonant fluorescent enhancement from a photonic crystal surface upon the fluorescent photobleaching rate of Cyanine-5 labeled protein has been investigated. We show that the enhanced excitation mechanism for photonic crystal enhanced fluorescence, in which the device surface resonantly couples light from an excitation laser, accelerates photobleaching in proportion to the coupling efficiency of the laser to the photonic crystal. We also show that the enhanced extraction mechanism, in which the photonic crystal directs emitted photons approximately normal to the surface, does not play a role in the rate of photobleaching. We show that the photobleaching rate of dye molecules on the photonic crystal surface is accelerated by 30x compared to an ordinary glass surface, but substantial signal gain is still evident, even after extended periods of continuous illumination at the resonant condition.

Sensors, 2022

In recent years, the biosensor research community has made rapid progress in the development of n... more In recent years, the biosensor research community has made rapid progress in the development of nanostructured materials capable of amplifying the interaction between light and biological matter. A common objective is to concentrate the electromagnetic energy associated with light into nanometer-scale volumes that, in many cases, can extend below the conventional Abbé diffraction limit. Dating back to the first application of surface plasmon resonance (SPR) for label-free detection of biomolecular interactions, resonant optical structures, including waveguides, ring resonators, and photonic crystals, have proven to be effective conduits for a wide range of optical enhancement effects that include enhanced excitation of photon emitters (such as quantum dots, organic dyes, and fluorescent proteins), enhanced extraction from photon emitters, enhanced optical absorption, and enhanced optical scattering (such as from Raman-scatterers and nanoparticles). The application of photonic metama...

ABSTRACTWe present a net-shaped DNA nanostructure (called “DNA Net” herein) design strategy for s... more ABSTRACTWe present a net-shaped DNA nanostructure (called “DNA Net” herein) design strategy for selective recognition and high-affinity capture of the intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers releases fluorescent signal upon virus binding that is easily read by a hand-held fluorimeter for a rapid (in 10 mins), simple (mix- and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive (∼ $1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1×103-fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like...