iRiS Kinetics Publications

@article{nokey,

title = {Multiplexed, High-Sensitivity Measurements of Antibody Affinity Using Interferometric Reflectance Imaging Sensor},

author = {Allison M Marn and James Needham and Elisa Chiodi and M Selim Ünlü},

url = {https://www.mdpi.com/2079-6374/11/12/483/htm},

doi = {https://doi.org/10.3390/bios11120483},

year  = {2021},

date = {2021-12-01},

urldate = {2021-12-01},

journal = {Biosensors and Bioelectronics },

volume = {11},

issue = {12},

pages = {483},

abstract = {Anthrax lethal factor (LF) is one of the enzymatic components of the anthrax toxin responsible for the pathogenic responses of the anthrax disease. The ability to screen multiplexed ligands against LF and subsequently estimate the effective kinetic rates (kon and koff) and complementary binding behavior provides critical information useful in diagnostic and therapeutic development for anthrax. Tools such as biolayer interferometry (BLI) and surface plasmon resonance imaging (SPRi) have been developed for this purpose; however, these tools suffer from limitations such as signal jumps when the solution in the chamber is switched or low sensitivity. Here, we present multiplexed antibody affinity measurements obtained by the interferometric reflectance imaging sensor (IRIS), a highly sensitive, label-free optical biosensor, whose stability, simplicity, and imaging modality overcomes many of the limitations of other multiplexed methods. We compare the multiplexed binding results obtained with the IRIS system using two ligands targeting the anthrax lethal factor (LF) against previously published results obtained with more traditional surface plasmon resonance (SPR), which showed consistent results, as well as kinetic information previously unattainable with SPR. Additional exemplary data demonstrating multiplexed binding and the corresponding complementary binding to sequentially injected ligands provides an additional layer of information immediately useful to the researcher.},

keywords = {Protein},

pubstate = {published},

tppubtype = {article}

}

@article{nokeye,

title = {Multiplexed, High-Sensitivity Measurements of Antibody Affinity Using Interferometric Reflectance Imaging Sensor},

author = {Allison M Marn and James Needham and Elisa Chiodi and M Selim Ünlü},

url = {https://www.mdpi.com/2079-6374/11/12/483/htm},

doi = {https://doi.org/10.3390/bios11120483},

year  = {2021},

date = {2021-12-01},

urldate = {2021-12-01},

journal = {Biosensors and Bioelectronics},

volume = {11},

issue = {12},

pages = {483},

abstract = {Anthrax lethal factor (LF) is one of the enzymatic components of the anthrax toxin responsible for the pathogenic responses of the anthrax disease. The ability to screen multiplexed ligands against LF and subsequently estimate the effective kinetic rates (kon and koff) and complementary binding behavior provides critical information useful in diagnostic and therapeutic development for anthrax. Tools such as biolayer interferometry (BLI) and surface plasmon resonance imaging (SPRi) have been developed for this purpose; however, these tools suffer from limitations such as signal jumps when the solution in the chamber is switched or low sensitivity. Here, we present multiplexed antibody affinity measurements obtained by the interferometric reflectance imaging sensor (IRIS), a highly sensitive, label-free optical biosensor, whose stability, simplicity, and imaging modality overcomes many of the limitations of other multiplexed methods. We compare the multiplexed binding results obtained with the IRIS system using two ligands targeting the anthrax lethal factor (LF) against previously published results obtained with more traditional surface plasmon resonance (SPR), which showed consistent results, as well as kinetic information previously unattainable with SPR. Additional exemplary data demonstrating multiplexed binding and the corresponding complementary binding to sequentially injected ligands provides an additional layer of information immediately useful to the researcher.},

keywords = {Protein},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Background-Suppressed High-Throughput Mid-Infrared Photothermal Microscopy via Pupil Engineering},

author = {Haonan Zong and Celalettin Yurdakul and Yeran Bai and Meng Zhang and M. Selim Ünlü and Ji-Xin Cheng},

url = {https://arxiv.org/pdf/2104.06247},

doi = {https://doi.org/10.1021/acsphotonics.1c01197},

year  = {2021},

date = {2021-10-14},

urldate = {2021-10-14},

journal = {ACS Photonics Article ASAP},

volume = {8},

issue = {11},

pages = {3323},

abstract = {Mid-infrared photothermal (MIP) microscopy has been a promising label-free chemical imaging technique for functional characterization of specimens owing to its enhanced spatial resolution and high specificity. Recently developed wide-field MIP imaging modalities have drastically improved speed and enabled high-throughput imaging of micron-scale subjects. However, the weakly scattered signal from subwavelength particles becomes indistinguishable from the shot-noise as a consequence of the strong background light, leading to limited sensitivity. Here, we demonstrate background-suppressed chemical fingerprinting at a single nanoparticle level by selectively attenuating the reflected light through pupil engineering in the collection path. Our technique provides over 3 orders of magnitude background suppression by quasi-darkfield illumination in the epi-configuration without sacrificing lateral resolution. We demonstrate 6-fold signal-to-background noise ratio improvement, allowing for simultaneous detection and discrimination of hundreds of nanoparticles across a field of view of 70 μm × 70 μm. A comprehensive theoretical framework for photothermal image formation is provided and experimentally validated with 300 and 500 nm PMMA beads. The versatility and utility of our technique are demonstrated via hyperspectral dark-field MIP imaging of S. aureus and E. coli bacteria and MIP imaging of subcellular lipid droplets inside C. albicans and cancer cells.},

keywords = {Bacteria},

pubstate = {published},

tppubtype = {article}

}

@article{nokeyf,

title = {Background-Suppressed High-Throughput Mid-Infrared Photothermal Microscopy via Pupil Engineering},

author = {Haonan Zong and Celalettin Yurdakul and Yeran Bai and Meng Zhang and M. Selim Ünlü and Ji-Xin Cheng},

url = {https://arxiv.org/pdf/2104.06247},

doi = {https://doi.org/10.1021/acsphotonics.1c01197},

year  = {2021},

date = {2021-10-14},

urldate = {2021-10-14},

journal = {ACS Photonics Article ASAP},

volume = {8},

issue = {11},

pages = {3323},

abstract = {Mid-infrared photothermal (MIP) microscopy has been a promising label-free chemical imaging technique for functional characterization of specimens owing to its enhanced spatial resolution and high specificity. Recently developed wide-field MIP imaging modalities have drastically improved speed and enabled high-throughput imaging of micron-scale subjects. However, the weakly scattered signal from subwavelength particles becomes indistinguishable from the shot-noise as a consequence of the strong background light, leading to limited sensitivity. Here, we demonstrate background-suppressed chemical fingerprinting at a single nanoparticle level by selectively attenuating the reflected light through pupil engineering in the collection path. Our technique provides over 3 orders of magnitude background suppression by quasi-darkfield illumination in the epi-configuration without sacrificing lateral resolution. We demonstrate 6-fold signal-to-background noise ratio improvement, allowing for simultaneous detection and discrimination of hundreds of nanoparticles across a field of view of 70 μm × 70 μm. A comprehensive theoretical framework for photothermal image formation is provided and experimentally validated with 300 and 500 nm PMMA beads. The versatility and utility of our technique are demonstrated via hyperspectral dark-field MIP imaging of S. aureus and E. coli bacteria and MIP imaging of subcellular lipid droplets inside C. albicans and cancer cells.},

keywords = {Bacteria},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Scattering-based Light Microscopy: From Metal Nanoparticles to Single Proteins},

author = {lee Priest and Jack S. Peters and Philipp Kukura},

url = {https://pubs.acs.org/doi/full/10.1021/acs.chemrev.1c00271},

doi = {https://doi.org/10.1021/acs.chemrev.1c00271},

year  = {2021},

date = {2021-09-29},

journal = {Chem. Rev.},

volume = {121},

issue = {19},

pages = {11937-11970},

abstract = {Our ability to detect, image, and quantify nanoscopic objects and molecules with visible light has undergone dramatic improvements over the past few decades. While fluorescence has historically been the go-to contrast mechanism for ultrasensitive light microscopy due to its superior background suppression and specificity, recent developments based on light scattering have reached single-molecule sensitivity. They also have the advantages of universal applicability and the ability to obtain information about the species of interest beyond its presence and location. Many of the recent advances are driven by novel approaches to illumination, detection, and background suppression, all aimed at isolating and maximizing the signal of interest. Here, we review these developments grouped according to the basic principles used, namely darkfield imaging, interferometric detection, and surface plasmon resonance microscopy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokeyg,

title = {Scattering-based Light Microscopy: From Metal Nanoparticles to Single Proteins},

author = {Priest and Jack S. Peters and Philipp Kukura},

url = {https://pubs.acs.org/doi/full/10.1021/acs.chemrev.1c00271},

doi = {https://doi.org/10.1021/acs.chemrev.1c00271},

year  = {2021},

date = {2021-09-29},

journal = {Chem. Rev.},

volume = {121},

issue = {19},

pages = {11937-11970},

abstract = {Our ability to detect, image, and quantify nanoscopic objects and molecules with visible light has undergone dramatic improvements over the past few decades. While fluorescence has historically been the go-to contrast mechanism for ultrasensitive light microscopy due to its superior background suppression and specificity, recent developments based on light scattering have reached single-molecule sensitivity. They also have the advantages of universal applicability and the ability to obtain information about the species of interest beyond its presence and location. Many of the recent advances are driven by novel approaches to illumination, detection, and background suppression, all aimed at isolating and maximizing the signal of interest. Here, we review these developments grouped according to the basic principles used, namely darkfield imaging, interferometric detection, and surface plasmon resonance microscopy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokeyi,

title = {Bond-selective interferometric scattering microscopy},

author = {Celalettin Yurdakul and Haonan Zong and Yeran Bai and Ji-Xin Cheng and M Selim Ünlü},

url = {https://arxiv.org/pdf/2106.02931},

doi = {https://doi.org/10.1088/1361-6463/ac0b0d},

year  = {2021},

date = {2021-06-25},

urldate = {2021-06-25},

journal = {Journal of Physics D: Applied Physics},

volume = {54},

issue = {36},

pages = {364002},

abstract = {Interferometric scattering (iSCAT) microscopy has been a very promising technology for highly sensitive label-free imaging of a broad spectrum of biological nanoparticles from proteins to viruses in a high-throughput manner. Although it can reveal the specimen's size and shape information, the chemical composition is inaccessible in interferometric measurements. Infrared (IR) spectroscopic imaging provides chemical specificity based on inherent chemical bond vibrations of specimens but lacks the ability to image and resolve individual nanoparticles due to long IR wavelengths. Here, we describe a bond-selective iSCAT microscope where the mid-IR induced photothermal signal is detected by a visible beam in a wide-field common-path interferometry configuration. A thin film layered substrate is utilized to reduce the reflected light and provide a reference field for the interferometric detection of the weakly scattered field. A pulsed mid-IR laser is employed to modulate the interferometric signal. Subsequent demodulation via a virtual lock-in camera offers simultaneous chemical information about tens of micro- or nano-particles. The chemical contrast arises from a minute change in the particle's scattered field in consequence of the vibrational absorption at the target molecule. We characterize the system with sub-wavelength polymer beads and highlight biological applications by chemically imaging several microorganisms including Staphylococcus aureus, Escherichia coli, and Candida albicans. A theoretical framework is established to extend bond-selective iSCAT microscopy to a broad range of biological micro- and nano-particles.},

keywords = {Bacteria},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Bond-selective interferometric scattering microscopy},

author = {Celalettin Yurdakul and Haonan Zong and Yeran Bai and Ji-Xin Cheng and M Selim Ünlü},

url = {https://arxiv.org/pdf/2106.02931},

doi = {https://doi.org/10.1088/1361-6463/ac0b0d},

year  = {2021},

date = {2021-06-25},

urldate = {2021-06-25},

journal = {Journal of Physics D: Applied Physics},

volume = {54},

issue = {36},

pages = {364002},

abstract = {Interferometric scattering (iSCAT) microscopy has been a very promising technology for highly sensitive label-free imaging of a broad spectrum of biological nanoparticles from proteins to viruses in a high-throughput manner. Although it can reveal the specimen's size and shape information, the chemical composition is inaccessible in interferometric measurements. Infrared (IR) spectroscopic imaging provides chemical specificity based on inherent chemical bond vibrations of specimens but lacks the ability to image and resolve individual nanoparticles due to long IR wavelengths. Here, we describe a bond-selective iSCAT microscope where the mid-IR induced photothermal signal is detected by a visible beam in a wide-field common-path interferometry configuration. A thin film layered substrate is utilized to reduce the reflected light and provide a reference field for the interferometric detection of the weakly scattered field. A pulsed mid-IR laser is employed to modulate the interferometric signal. Subsequent demodulation via a virtual lock-in camera offers simultaneous chemical information about tens of micro- or nano-particles. The chemical contrast arises from a minute change in the particle's scattered field in consequence of the vibrational absorption at the target molecule. We characterize the system with sub-wavelength polymer beads and highlight biological applications by chemically imaging several microorganisms including Staphylococcus aureus, Escherichia coli, and Candida albicans. A theoretical framework is established to extend bond-selective iSCAT microscopy to a broad range of biological micro- and nano-particles.},

keywords = {Bacteria},

pubstate = {published},

tppubtype = {article}

}

@article{nokeyj,

title = {Multiplexed Affinity Measurements of Extracellular Vesicles Binding Kinetics},

author = {Elisa Chiodi and George G. Daaboul and Allison M Marn and M. Selim Ünlü},

url = {https://www.mdpi.com/1424-8220/21/8/2634},

doi = {https://doi.org/10.3390/s21082634},

year  = {2021},

date = {2021-04-09},

journal = {Sensors},

volume = {21},

issue = {8},

pages = {2634},

abstract = {Extracellular vesicles (EVs) have attracted significant attention as impactful diagnostic biomarkers, since their properties are closely related to specific clinical conditions. However, designing experiments that involve EVs phenotyping is usually highly challenging and time-consuming, due to laborious optimization steps that require very long or even overnight incubation durations. In this work, we demonstrate label-free, real-time detection, and phenotyping of extracellular vesicles binding to a multiplexed surface. With the ability for label-free kinetic binding measurements using the Interferometric Reflectance Imaging Sensor (IRIS) in a microfluidic chamber, we successfully optimize the capture reaction by tuning various assay conditions (incubation time, flow conditions, surface probe density, and specificity). A single (less than 1 h) experiment allows for characterization of binding affinities of the EVs to multiplexed probes. We demonstrate kinetic characterization of 18 different probe conditions, namely three different antibodies, each spotted at six different concentrations, simultaneously. The affinity characterization is then analyzed through a model that considers the complexity of multivalent binding of large structures to a carpet of probes and therefore introduces a combination of fast and slow association and dissociation parameters. Additionally, our results confirm higher affinity of EVs to aCD81 with respect to aCD9 and aCD63. Single-vesicle imaging measurements corroborate our findings, as well as confirming the EVs nature of the captured particles through fluorescence staining of the EVs membrane and cargo.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Multiplexed Affinity Measurements of Extracellular Vesicles Binding Kinetics},

author = {Elisa Chiodi and George G. Daaboul and Allison M Marn and M. Selim Ünlü},

url = {https://www.mdpi.com/1424-8220/21/8/2634},

doi = {https://doi.org/10.3390/s21082634},

year  = {2021},

date = {2021-04-09},

journal = {Sensors},

volume = {21},

issue = {8},

pages = {2634},

abstract = {Extracellular vesicles (EVs) have attracted significant attention as impactful diagnostic biomarkers, since their properties are closely related to specific clinical conditions. However, designing experiments that involve EVs phenotyping is usually highly challenging and time-consuming, due to laborious optimization steps that require very long or even overnight incubation durations. In this work, we demonstrate label-free, real-time detection, and phenotyping of extracellular vesicles binding to a multiplexed surface. With the ability for label-free kinetic binding measurements using the Interferometric Reflectance Imaging Sensor (IRIS) in a microfluidic chamber, we successfully optimize the capture reaction by tuning various assay conditions (incubation time, flow conditions, surface probe density, and specificity). A single (less than 1 h) experiment allows for characterization of binding affinities of the EVs to multiplexed probes. We demonstrate kinetic characterization of 18 different probe conditions, namely three different antibodies, each spotted at six different concentrations, simultaneously. The affinity characterization is then analyzed through a model that considers the complexity of multivalent binding of large structures to a carpet of probes and therefore introduces a combination of fast and slow association and dissociation parameters. Additionally, our results confirm higher affinity of EVs to aCD81 with respect to aCD9 and aCD63. Single-vesicle imaging measurements corroborate our findings, as well as confirming the EVs nature of the captured particles through fluorescence staining of the EVs membrane and cargo.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Bulk-Effect-Free Method for Binding Kinetic Measurements Enabling Small-Molecule Affinity Characterization},

author = {AM Marn and E Chiodi and MS Ünlü},

url = {https://pubs.acs.org/doi/pdf/10.1021/acsomega.0c05994},

doi = {https://dx.doi.org/10.1021/acsomega.0c05994},

year  = {2021},

date = {2021-03-03},

urldate = {2021-03-03},

journal = {ACS Omega },

volume = {6},

issue = {10},

pages = {6836},

abstract = {Optical technologies for label-free detection are an attractive solution for

monitoring molecular binding kinetics; however, these techniques measure the changes in

the refractive index, making it difficult to distinguish surface binding from a change in the

refractive index of the analyte solution in the proximity of the sensor surface. The solution

refractive index changes, due to solvents, temperature changes, or pH variations, can create

an unwanted background signal known as the bulk effect. Technologies such as biolayer

interferometry and surface plasmon resonance offer no bulk-effect compensation, or they

alternatively offer a reference channel to correct in postprocessing. Here, we present a

virtually bulk-effect-free method, without a reference channel or any computational

correction, for measuring kinetic binding using the interferometric reflectance imaging

sensor (IRIS), an optical label-free biomolecular interaction analysis tool. Dynamic

spectral illumination engineering, through tailored LED contributions, is combined with

the IRIS technology to minimize the bulk effect, with the potential to enable kinetic

measurements of a broader range of analytes. We demonstrate that the deviation in the

reflectivity signal is reduced to ∼8 × 10−6 for a solution change from phosphate-buffered saline (PBS) (n = 1.335) to 1% dimethyl sulfoxide (DMSO) in PBS (n = 1.336). As a proof of concept, we applied the method to a biotin−streptavidin interaction, where biotin (MW = 244.3 Da) was dissolved at a final concentration of 1 μM in a 1% solution of DMSO in PBS and flowed over immobilized streptavidin. Clear binding results were obtained without a reference channel or any computational correction.},

keywords = {Small Molecule},

pubstate = {published},

tppubtype = {article}

}

@article{nokeyk,

title = {Bulk-Effect-Free Method for Binding Kinetic Measurements Enabling Small-Molecule Affinity Characterization},

author = {AM Marn and E Chiodi and MS Ünlü},

url = {https://pubs.acs.org/doi/pdf/10.1021/acsomega.0c05994},

doi = {https://dx.doi.org/10.1021/acsomega.0c05994},

year  = {2021},

date = {2021-03-03},

urldate = {2021-03-03},

journal = {ACS Omega},

volume = {6},

issue = {10},

pages = {6836},

abstract = {Optical technologies for label-free detection are an attractive solution for 

monitoring molecular binding kinetics; however, these techniques measure the changes in 

the refractive index, making it difficult to distinguish surface binding from a change in the 

refractive index of the analyte solution in the proximity of the sensor surface. The solution 

refractive index changes, due to solvents, temperature changes, or pH variations, can create 

an unwanted background signal known as the bulk effect. Technologies such as biolayer 

interferometry and surface plasmon resonance offer no bulk-effect compensation, or they 

alternatively offer a reference channel to correct in postprocessing. Here, we present a 

virtually bulk-effect-free method, without a reference channel or any computational 

correction, for measuring kinetic binding using the interferometric reflectance imaging 

sensor (IRIS), an optical label-free biomolecular interaction analysis tool. Dynamic 

spectral illumination engineering, through tailored LED contributions, is combined with 

the IRIS technology to minimize the bulk effect, with the potential to enable kinetic measurements of a broader range of analytes. We demonstrate that the deviation in the reflectivity signal is reduced to ∼8 × 10−6 for a solution change from phosphate-buffered saline (PBS) (n = 1.335) to 1% dimethyl sulfoxide (DMSO) in PBS (n = 1.336). As a proof of concept, we applied the method to a biotin−streptavidin interaction, where biotin (MW = 244.3 Da) was dissolved at a final concentration of 1 μM in a 1% solution of DMSO in PBS and flowed over immobilized streptavidin. Clear binding results were obtained without a reference channel or any computational correction.},

keywords = {Small Molecule},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Vibrational spectroscopic detection of a single virus by mid-infrared photothermal microscopy},

author = {Yi Zhang and Celalettin Yurdakul and Alexander J Devaux and Le Wang and Xiaoji G Xu and John H Connor and M Selim Ünlü and Ji-Xin Cheng},

url = {https://sites.bu.edu/cheng-group/files/2021/02/277-analytical-chemistry-single-virus-detection-by-MIP.pdf},

doi = {https://dx.doi.org/10.1021/acs.analchem.0c05333},

year  = {2021},

date = {2021-02-17},

urldate = {2021-02-17},

journal = {Analytical Chemistry},

volume = {92},

issue = {8},

pages = {4100},

abstract = {We report a confocal interferometric mid-infrared photothermal (MIP) microscope for ultra-sensitive and spatially resolved chemical imaging of individual viruses. The interferometric scattering principle is applied to detect the very weak photothermal signal induced by infrared absorption of chemical bonds. Spectroscopic MIP detection of single vesicular stomatitis viruses (VSVs) and poxviruses is demonstrated. The single virus spectra show high consistency within the same virus type. The dominant spectral peaks are contributed by the amide I and amide II vibrations attributed to the viral proteins. The ratio of these two peaks is significantly different between VSVs and poxviruses, highlighting the potential of using interferometric MIP microscopy for label-free differentiation of viral particles. This all-optical chemical imaging method opens a new way for spectroscopic detection of biological nanoparticles in a label-free manner and may facilitate in predicting and controlling the outbreaks of emerging virus strains.},

keywords = {Virus},

pubstate = {published},

tppubtype = {article}

}

@article{nokeyl,

title = {Vibrational spectroscopic detection of a single virus by mid-infrared photothermal microscopy},

author = {Yi Zhang and Celalettin Yurdakul and Alexander J Devaux and Le Wang and Xiaoji G Xu and John H Connor and M Selim Ünlü and Ji-Xin Cheng},

url = {https://sites.bu.edu/cheng-group/files/2021/02/277-analytical-chemistry-single-virus-detection-by-MIP.pdf},

doi = {https://dx.doi.org/10.1021/acs.analchem.0c05333},

year  = {2021},

date = {2021-02-17},

urldate = {2021-02-17},

journal = {Analytical Chemistry},

volume = {92},

issue = {8},

pages = {4100},

abstract = {We report a confocal interferometric mid-infrared photothermal (MIP) microscope for ultra-sensitive and spatially resolved chemical imaging of individual viruses. The interferometric scattering principle is applied to detect the very weak photothermal signal induced by infrared absorption of chemical bonds. Spectroscopic MIP detection of single vesicular stomatitis viruses (VSVs) and poxviruses is demonstrated. The single virus spectra show high consistency within the same virus type. The dominant spectral peaks are contributed by the amide I and amide II vibrations attributed to the viral proteins. The ratio of these two peaks is significantly different between VSVs and poxviruses, highlighting the potential of using interferometric MIP microscopy for label-free differentiation of viral particles. This all-optical chemical imaging method opens a new way for spectroscopic detection of biological nanoparticles in a label-free manner and may facilitate in predicting and controlling the outbreaks of emerging virus strains.},

keywords = {Virus},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Configurable Digital Virus Counter on Robust Universal DNA Chips},

author = {Elif Seymour and Nese Lortlar Ünlü and Erik P Carter and John H Connor and M Selim Ünlü},

url = {https://www.biorxiv.org/content/biorxiv/early/2020/10/22/2020.10.22.350579.full.pdf},

doi = {https://doi.org/10.1101/2020.10.22.350579},

year  = {2021},

date = {2021-01-11},

urldate = {2021-01-11},

journal = {ACS sensors},

volume = {6},

issue = {10},

pages = {229},

abstract = {Here, we demonstrate real-time multiplexed virus detection by applying DNA-directed antibody immobilization technique to a single-particle interferometric reflectance imaging sensor (SP-IRIS). In this technique, the biosensor chip surface spotted with different DNA sequences is converted to a multiplexed antibody array by flowing antibody-DNA conjugates and allowing specific DNA-DNA hybridization. The resulting antibody array is shown to detect three different recombinant Vesicular Stomatitis Viruses (rVSVs) genetically engineered to express surface glycoproteins of Ebola, Marburg, and Lassa viruses in real-time in a disposable microfluidic cartridge. We also show that this method can be modified to produce a single-step, homogeneous assay format by mixing the antibody-DNA conjugates with the virus sample in solution phase prior to flowing in the microfluidic cartridge, eliminating the antibody immobilization step. This homogenous approach achieved detection of the model Ebola virus, rVSV-EBOV, at a concentration of 100 PFU/ml in 1 hour. Finally, we demonstrate the feasibility of this homogeneous technique as a rapid test using a passive microfluidic cartridge. A concentration of 104 PFU/ml was detectable under 10 minutes for the rVSV-Ebola virus. Utilizing DNA microarrays for antibody-based diagnostics is an alternative approach to antibody microarrays and offers advantages such as configurable sensor surface, long-term storage ability, and decreased antibody use. We believe these properties will make SP-IRIS a versatile and robust platform for point-of-care diagnostics applications.

  },

keywords = {Virus},

pubstate = {published},

tppubtype = {article}

}

@article{nokeym,

title = {Configurable Digital Virus Counter on Robust Universal DNA Chips},

author = {Elif Seymour and Nese Lortlar Ünlü and Erik P Carter and John H Connor and M Selim Ünlü},

url = {https://www.biorxiv.org/content/biorxiv/early/2020/10/22/2020.10.22.350579.full.pdf},

doi = {https://doi.org/10.1101/2020.10.22.350579},

year  = {2021},

date = {2021-01-11},

urldate = {2021-01-11},

journal = {ACS sensors},

volume = {6},

issue = {10},

pages = {229},

abstract = {Here, we demonstrate real-time multiplexed virus detection by applying DNA-directed antibody immobilization technique to a single-particle interferometric reflectance imaging sensor (SP-IRIS). In this technique, the biosensor chip surface spotted with different DNA sequences is converted to a multiplexed antibody array by flowing antibody-DNA conjugates and allowing specific DNA-DNA hybridization. The resulting antibody array is shown to detect three different recombinant Vesicular Stomatitis Viruses (rVSVs) genetically engineered to express surface glycoproteins of Ebola, Marburg, and Lassa viruses in real-time in a disposable microfluidic cartridge. We also show that this method can be modified to produce a single-step, homogeneous assay format by mixing the antibody-DNA conjugates with the virus sample in solution phase prior to flowing in the microfluidic cartridge, eliminating the antibody immobilization step. This homogenous approach achieved detection of the model Ebola virus, rVSV-EBOV, at a concentration of 100 PFU/ml in 1 hour. Finally, we demonstrate the feasibility of this homogeneous technique as a rapid test using a passive microfluidic cartridge. A concentration of 104 PFU/ml was detectable under 10 minutes for the rVSV-Ebola virus. Utilizing DNA microarrays for antibody-based diagnostics is an alternative approach to antibody microarrays and offers advantages such as configurable sensor surface, long-term storage ability, and decreased antibody use. We believe these properties will make SP-IRIS a versatile and robust platform for point-of-care diagnostics applications.},

keywords = {Virus},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {A reliable, label free quality control method for the production of DNA microarrays with clinical applications},

author = {Elisa Chiodi, Francesco Damin, Laura Sola, Lucia Ferraro, Dario Brambilla, M Selim Ünlü, Marcella Chiari},

url = {https://www.mdpi.com/2073-4360/13/3/340/pdf},

doi = {https://doi.org/10.3390/polym13030340},

year  = {2021},

date = {2021-01-03},

urldate = {2021-01-03},

journal = {Polymers},

volume = {13},

issue = {36},

pages = {340},

abstract = {The manufacture of a very high-quality microarray support is essential for the adoption of this assay format in clinical routine. In fact, poorly surface-bound probes can affect the diagnostic sensitivity or, in worst cases, lead to false negative results. Here we report on a reliable and easy quality control method for the evaluation of spotted probe properties in a microarray test, based on the Interferometric Reflectance Imaging Sensor (IRIS) system, a high-resolution label free technique able to evaluate the variation of the mass bound to a surface. In particular, we demonstrated that the IRIS analysis of microarray chips immediately after probe immobilization can detect the absence of probes, which recognizably causes a lack of signal when performing a test, with clinical relevance, using fluorescence detection. Moreover, the use of the IRIS technique allowed also to determine the optimal concentration of the probe, that has to be immobilized on the surface, to maximize the target recognition, thus the signal, but to avoid crowding effects. Finally, through this preliminary quality inspection it is possible to highlight differences in the immobilization chemistries. In particular, we have compared NHS ester versus click chemistry reactions using two different surface coatings, demonstrating that, in the diagnostic case used as an example (colorectal cancer) a higher probe density does not reflect a higher binding signal, probably because of a crowding effect.},

keywords = {Oligo},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {The Role of Surface Chemistry in the Efficacy of Protein and DNA Microarrays for Label-Free Detection: An Overview},

author = {Elisa Chiodi and Allison M Marn and Matthew T Geib and M Selim Ünlü},

url = {https://www.mdpi.com/2073-4360/13/7/1026/pdf},

doi = {https://doi.org/10.3390/polym13071026},

year  = {2021},

date = {2021-01-03},

urldate = {2021-01-03},

journal = {Polymers},

volume = {13},

issue = {7},

pages = {1026},

abstract = {The importance of microarrays in diagnostics and medicine has drastically increased in the last few years. Nevertheless, the efficiency of a microarray-based assay intrinsically depends on the density and functionality of the biorecognition elements immobilized onto each sensor spot. Recently, researchers have put effort into developing new functionalization strategies and technologies which provide efficient immobilization and stability of any sort of molecule. Here, we present an overview of the most widely used methods of surface functionalization of microarray substrates, as well as the most recent advances in the field, and compare their performance in terms of optimal immobilization of the bioreceptor molecules. We focus on label-free microarrays and, in particular, we aim to describe the impact of surface chemistry on two types of microarray-based sensors: microarrays for single particle imaging and for label-free measurements of binding kinetics. Both protein and DNA microarrays are taken into consideration, and the effect of different polymeric coatings on the molecules’ functionalities is critically analyzed.},

keywords = {Oligo, Protein},

pubstate = {published},

tppubtype = {article}

}