A searchable listing of most recent publications using IRIS Kinetics technologies.
You can search for any words contained in the title or abstract.
61.
Sevenler, Derin; Trueb, Jacob; Ünlü, M. Selim
Beating the reaction limits of biosensor sensitivity with dynamic tracking of single binding events Journal Article
In: PNAS, vol. 116, iss. 10, pp. 4129-4134, 2019.
Abstract | Links | BibTeX | Tags:
@article{nokeyy,
title = {Beating the reaction limits of biosensor sensitivity with dynamic tracking of single binding events},
author = {Derin Sevenler and Jacob Trueb and M. Selim Ünlü},
url = {https://www.pnas.org/doi/abs/10.1073/pnas.1815329116},
doi = {https://doi.org/10.1073/pnas.1815329116},
year = {2019},
date = {2019-02-19},
journal = {PNAS},
volume = {116},
issue = {10},
pages = {4129-4134},
abstract = {The clinical need for ultrasensitive molecular analysis has motivated the development of several endpoint-assay technologies capable of single-molecule readout. These endpoint assays are now primarily limited by the affinity and specificity of the molecular-recognition agents for the analyte of interest. In contrast, a kinetic assay with single-molecule readout could distinguish between low-abundance, high-affinity (specific analyte) and high-abundance, low-affinity (nonspecific background) binding by measuring the duration of individual binding events at equilibrium. Here, we describe such a kinetic assay, in which individual binding events are detected and monitored during sample incubation. This method uses plasmonic gold nanorods and interferometric reflectance imaging to detect thousands of individual binding events across a multiplex solid-phase sensor with a large area approaching that of leading bead-based endpoint-assay technologies. A dynamic tracking procedure is used to measure the duration of each event. From this, the total rates of binding and debinding as well as the distribution of binding-event durations are determined. We observe a limit of detection of 19 fM for a proof-of-concept synthetic DNA analyte in a 12-plex assay format.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The clinical need for ultrasensitive molecular analysis has motivated the development of several endpoint-assay technologies capable of single-molecule readout. These endpoint assays are now primarily limited by the affinity and specificity of the molecular-recognition agents for the analyte of interest. In contrast, a kinetic assay with single-molecule readout could distinguish between low-abundance, high-affinity (specific analyte) and high-abundance, low-affinity (nonspecific background) binding by measuring the duration of individual binding events at equilibrium. Here, we describe such a kinetic assay, in which individual binding events are detected and monitored during sample incubation. This method uses plasmonic gold nanorods and interferometric reflectance imaging to detect thousands of individual binding events across a multiplex solid-phase sensor with a large area approaching that of leading bead-based endpoint-assay technologies. A dynamic tracking procedure is used to measure the duration of each event. From this, the total rates of binding and debinding as well as the distribution of binding-event durations are determined. We observe a limit of detection of 19 fM for a proof-of-concept synthetic DNA analyte in a 12-plex assay format.
62.
Sevenler, Derin; Trueb, Jacob; Ünlü, M. Selim
Beating the reaction limits of biosensor sensitivity with dynamic tracking of single binding events Journal Article
In: PNAS, vol. 116, iss. 10, pp. 4129-4134, 2019.
Abstract | Links | BibTeX | Tags:
@article{nokey,
title = {Beating the reaction limits of biosensor sensitivity with dynamic tracking of single binding events},
author = {Derin Sevenler and Jacob Trueb and M. Selim Ünlü},
url = {https://www.pnas.org/doi/abs/10.1073/pnas.1815329116},
doi = {https://doi.org/10.1073/pnas.1815329116},
year = {2019},
date = {2019-02-19},
journal = {PNAS},
volume = {116},
issue = {10},
pages = {4129-4134},
abstract = {The clinical need for ultrasensitive molecular analysis has motivated the development of several endpoint-assay technologies capable of single-molecule readout. These endpoint assays are now primarily limited by the affinity and specificity of the molecular-recognition agents for the analyte of interest. In contrast, a kinetic assay with single-molecule readout could distinguish between low-abundance, high-affinity (specific analyte) and high-abundance, low-affinity (nonspecific background) binding by measuring the duration of individual binding events at equilibrium. Here, we describe such a kinetic assay, in which individual binding events are detected and monitored during sample incubation. This method uses plasmonic gold nanorods and interferometric reflectance imaging to detect thousands of individual binding events across a multiplex solid-phase sensor with a large area approaching that of leading bead-based endpoint-assay technologies. A dynamic tracking procedure is used to measure the duration of each event. From this, the total rates of binding and debinding as well as the distribution of binding-event durations are determined. We observe a limit of detection of 19 fM for a proof-of-concept synthetic DNA analyte in a 12-plex assay format.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The clinical need for ultrasensitive molecular analysis has motivated the development of several endpoint-assay technologies capable of single-molecule readout. These endpoint assays are now primarily limited by the affinity and specificity of the molecular-recognition agents for the analyte of interest. In contrast, a kinetic assay with single-molecule readout could distinguish between low-abundance, high-affinity (specific analyte) and high-abundance, low-affinity (nonspecific background) binding by measuring the duration of individual binding events at equilibrium. Here, we describe such a kinetic assay, in which individual binding events are detected and monitored during sample incubation. This method uses plasmonic gold nanorods and interferometric reflectance imaging to detect thousands of individual binding events across a multiplex solid-phase sensor with a large area approaching that of leading bead-based endpoint-assay technologies. A dynamic tracking procedure is used to measure the duration of each event. From this, the total rates of binding and debinding as well as the distribution of binding-event durations are determined. We observe a limit of detection of 19 fM for a proof-of-concept synthetic DNA analyte in a 12-plex assay format.
63.
Ozkumur, Ayca Yalcin; Kanik, Fulya Ekiz; Trueb, Jacob; Yurdakul, Celalettin; Ünlü, M. Selim
Interferometric Detection and Enumeration of Viral Particles using Si-Based Microfluidics Journal Article
In: IEEE Journal of Selected Topics in Quantum Electronics,, vol. 25, iss. 1, pp. 1-7, 2018.
Abstract | Links | BibTeX | Tags:
@article{nokey,
title = {Interferometric Detection and Enumeration of Viral Particles using Si-Based Microfluidics},
author = {Ayca Yalcin Ozkumur and Fulya Ekiz Kanik and Jacob Trueb and Celalettin Yurdakul and M. Selim Ünlü},
doi = {https://doi.org/10.1109/JSTQE.2018.2854548},
year = {2018},
date = {2018-07-18},
journal = {IEEE Journal of Selected Topics in Quantum Electronics,},
volume = {25},
issue = {1},
pages = {1-7},
abstract = {Single-particle interferometric reflectance imaging sensor enables optical visualization and characterization of individual nanoparticles without any labels. Using this technique, we have shown end-point and real-time detection of viral particles using laminate-based active and passive cartridge configurations. Here, we present a new concept for low-cost microfluidic integration of the sensor chips into compact cartridges through utilization of readily available silicon fabrication technologies. This new cartridge configuration will allow simultaneous detection of individual virus binding events on a 9-spot microarray, and provide the needed simplicity and robustness for routine real-time operation for discrete detection of viral particles in a multiplex format.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Single-particle interferometric reflectance imaging sensor enables optical visualization and characterization of individual nanoparticles without any labels. Using this technique, we have shown end-point and real-time detection of viral particles using laminate-based active and passive cartridge configurations. Here, we present a new concept for low-cost microfluidic integration of the sensor chips into compact cartridges through utilization of readily available silicon fabrication technologies. This new cartridge configuration will allow simultaneous detection of individual virus binding events on a 9-spot microarray, and provide the needed simplicity and robustness for routine real-time operation for discrete detection of viral particles in a multiplex format.
64.
Ozkumur, Ayca Yalcin; Kanik, Fulya Ekiz; Trueb, Jacob; Yurdakul, Celalettin; Ünlü, M. Selim
Interferometric Detection and Enumeration of Viral Particles using Si-Based Microfluidics Journal Article
In: IEEE Journal of Selected Topics in Quantum Electronics,, vol. 25, iss. 1, pp. 1-7, 2018.
Abstract | Links | BibTeX | Tags:
@article{nokeyz,
title = {Interferometric Detection and Enumeration of Viral Particles using Si-Based Microfluidics},
author = {Ayca Yalcin Ozkumur and Fulya Ekiz Kanik and Jacob Trueb and Celalettin Yurdakul and M. Selim Ünlü},
doi = {https://doi.org/10.1109/JSTQE.2018.2854548},
year = {2018},
date = {2018-07-18},
journal = {IEEE Journal of Selected Topics in Quantum Electronics,},
volume = {25},
issue = {1},
pages = {1-7},
abstract = {Single-particle interferometric reflectance imaging sensor enables optical visualization and characterization of individual nanoparticles without any labels. Using this technique, we have shown end-point and real-time detection of viral particles using laminate-based active and passive cartridge configurations. Here, we present a new concept for low-cost microfluidic integration of the sensor chips into compact cartridges through utilization of readily available silicon fabrication technologies. This new cartridge configuration will allow simultaneous detection of individual virus binding events on a 9-spot microarray, and provide the needed simplicity and robustness for routine real-time operation for discrete detection of viral particles in a multiplex format.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Single-particle interferometric reflectance imaging sensor enables optical visualization and characterization of individual nanoparticles without any labels. Using this technique, we have shown end-point and real-time detection of viral particles using laminate-based active and passive cartridge configurations. Here, we present a new concept for low-cost microfluidic integration of the sensor chips into compact cartridges through utilization of readily available silicon fabrication technologies. This new cartridge configuration will allow simultaneous detection of individual virus binding events on a 9-spot microarray, and provide the needed simplicity and robustness for routine real-time operation for discrete detection of viral particles in a multiplex format.
65.
Ünlü, M. Selim; Trueb, Jacob; Needham, James; Yurdakul, Celalettin; Sevenler, Derin; Kanik, Fulya Ekiz; Ozkumur, Ayca Yalcin; Ünlü, Nese Lortlar; Geib, Matthew T
Interferometric Reflectance Imaging Sensor using Si-based Microfluidics Journal Article
In: Advanced Photonics, 2018, ISBN: 978-1-943580-43-9.
Abstract | Links | BibTeX | Tags:
@article{nokey,
title = {Interferometric Reflectance Imaging Sensor using Si-based Microfluidics},
author = {M. Selim Ünlü and Jacob Trueb and James Needham and Celalettin Yurdakul and Derin Sevenler and Fulya Ekiz Kanik and Ayca Yalcin Ozkumur and Nese Lortlar Ünlü and Matthew T Geib},
url = {https://opg.optica.org/viewmedia.cfm?uri=IPRSN-2018-ITh1I.4&seq=0
},
doi = {https://doi.org/10.1364/IPRSN.2018.ITh1I.4},
isbn = {978-1-943580-43-9},
year = {2018},
date = {2018-07-02},
journal = {Advanced Photonics},
abstract = {There is a need for biological sensing and diagnostics tools with sensitivity compared to existing state-of-the-art technologies without complicated assays, sample preparation, and bulky equipment. Our platform technology, IRIS offers kinetic analysis of biomolecular binding and detection of proteins, nucleic acids, and individual biological nanoparticles in a simple assay format and with high sensitivity. We have shown that low-cost and disposable sensor chips and microfluidic cartridges compatible with this optical sensing technology can be manufactured using standard Si processing techniques.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
There is a need for biological sensing and diagnostics tools with sensitivity compared to existing state-of-the-art technologies without complicated assays, sample preparation, and bulky equipment. Our platform technology, IRIS offers kinetic analysis of biomolecular binding and detection of proteins, nucleic acids, and individual biological nanoparticles in a simple assay format and with high sensitivity. We have shown that low-cost and disposable sensor chips and microfluidic cartridges compatible with this optical sensing technology can be manufactured using standard Si processing techniques.
66.
Ünlü, M. Selim; Trueb, Jacob; Needham, James; Yurdakul, Celalettin; Sevenler, Derin; Kanik, Fulya Ekiz; Ozkumur, Ayca Yalcin; Ünlü, Nese Lortlar; Geib, Matthew T
Interferometric Reflectance Imaging Sensor using Si-based Microfluidics Journal Article
In: Advanced Photonics, 2018, ISBN: 978-1-943580-43-9.
Abstract | Links | BibTeX | Tags:
@article{nokey_27,
title = {Interferometric Reflectance Imaging Sensor using Si-based Microfluidics},
author = {M. Selim Ünlü and Jacob Trueb and James Needham and Celalettin Yurdakul and Derin Sevenler and Fulya Ekiz Kanik and Ayca Yalcin Ozkumur and Nese Lortlar Ünlü and Matthew T Geib},
url = {https://opg.optica.org/viewmedia.cfm?uri=IPRSN-2018-ITh1I.4&seq=0},
doi = {https://doi.org/10.1364/IPRSN.2018.ITh1I.4},
isbn = {978-1-943580-43-9},
year = {2018},
date = {2018-07-02},
journal = {Advanced Photonics},
abstract = {There is a need for biological sensing and diagnostics tools with sensitivity compared to existing state-of-the-art technologies without complicated assays, sample preparation, and bulky equipment. Our platform technology, IRIS offers kinetic analysis of biomolecular binding and detection of proteins, nucleic acids, and individual biological nanoparticles in a simple assay format and with high sensitivity. We have shown that low-cost and disposable sensor chips and microfluidic cartridges compatible with this optical sensing technology can be manufactured using standard Si processing techniques.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
There is a need for biological sensing and diagnostics tools with sensitivity compared to existing state-of-the-art technologies without complicated assays, sample preparation, and bulky equipment. Our platform technology, IRIS offers kinetic analysis of biomolecular binding and detection of proteins, nucleic acids, and individual biological nanoparticles in a simple assay format and with high sensitivity. We have shown that low-cost and disposable sensor chips and microfluidic cartridges compatible with this optical sensing technology can be manufactured using standard Si processing techniques.
67.
Sevenler, Derin; Daaboul, George G.; Kanik, Fulya Ekiz; Ünlü, Nese Lortlar; Ünlü, M. Selim
Digital Microarrays: Single-Molecule Readout with Interferometric Detection of Plasmonic Nanorod Labels Journal Article
In: ACS Nano, vol. 12, iss. 6, pp. 5880-5887, 2018.
Abstract | Links | BibTeX | Tags:
@article{nokey_28,
title = {Digital Microarrays: Single-Molecule Readout with Interferometric Detection of Plasmonic Nanorod Labels},
author = {Derin Sevenler and George G. Daaboul and Fulya Ekiz Kanik and Nese Lortlar Ünlü and M. Selim Ünlü},
url = {https://pubs.acs.org/doi/abs/10.1021/acsnano.8b02036},
doi = {https://doi.org/10.1021/acsnano.8b02036},
year = {2018},
date = {2018-05-14},
journal = {ACS Nano},
volume = {12},
issue = {6},
pages = {5880-5887},
abstract = {DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and limited dynamic range of traditional fluorescence microarrays compared to other detection techniques have been the technology’s Achilles’ heel and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule (“digital”) regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform’s primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about 3 orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10× objective lens. This approach does not require any chemical signal enhancement such as silver deposition and scans arrays with a throughput similar to commercial fluorescence scanners. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about 6 orders of magnitude directly from a single scan. As a proof-of-concept digital protein microarray assay, we demonstrated detection of hepatitis B virus surface antigen in buffer with a limit of detection of 3.2 pg/mL. More broadly, the technique’s simplicity and high-throughput nature make digital microarrays a flexible platform technology with a wide range of potential applications in biomedical research and clinical diagnostics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and limited dynamic range of traditional fluorescence microarrays compared to other detection techniques have been the technology’s Achilles’ heel and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule (“digital”) regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform’s primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about 3 orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10× objective lens. This approach does not require any chemical signal enhancement such as silver deposition and scans arrays with a throughput similar to commercial fluorescence scanners. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about 6 orders of magnitude directly from a single scan. As a proof-of-concept digital protein microarray assay, we demonstrated detection of hepatitis B virus surface antigen in buffer with a limit of detection of 3.2 pg/mL. More broadly, the technique’s simplicity and high-throughput nature make digital microarrays a flexible platform technology with a wide range of potential applications in biomedical research and clinical diagnostics.
68.
Sevenler, Derin; Daaboul, George G.; Kanik, Fulya Ekiz; Ünlü, Nese Lortlar; Ünlü, M. Selim
Digital Microarrays: Single-Molecule Readout with Interferometric Detection of Plasmonic Nanorod Labels Journal Article
In: ACS Nano, vol. 12, iss. 6, pp. 5880-5887, 2018.
Abstract | Links | BibTeX | Tags:
@article{nokey,
title = {Digital Microarrays: Single-Molecule Readout with Interferometric Detection of Plasmonic Nanorod Labels},
author = {Derin Sevenler and George G. Daaboul and Fulya Ekiz Kanik and Nese Lortlar Ünlü and M. Selim Ünlü},
url = {https://pubs.acs.org/doi/abs/10.1021/acsnano.8b02036},
doi = {https://doi.org/10.1021/acsnano.8b02036},
year = {2018},
date = {2018-05-14},
journal = {ACS Nano},
volume = {12},
issue = {6},
pages = {5880-5887},
abstract = {DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and limited dynamic range of traditional fluorescence microarrays compared to other detection techniques have been the technology’s Achilles’ heel and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule (“digital”) regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform’s primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about 3 orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10× objective lens. This approach does not require any chemical signal enhancement such as silver deposition and scans arrays with a throughput similar to commercial fluorescence scanners. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about 6 orders of magnitude directly from a single scan. As a proof-of-concept digital protein microarray assay, we demonstrated detection of hepatitis B virus surface antigen in buffer with a limit of detection of 3.2 pg/mL. More broadly, the technique’s simplicity and high-throughput nature make digital microarrays a flexible platform technology with a wide range of potential applications in biomedical research and clinical diagnostics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
DNA and protein microarrays are a high-throughput technology that allow the simultaneous quantification of tens of thousands of different biomolecular species. The mediocre sensitivity and limited dynamic range of traditional fluorescence microarrays compared to other detection techniques have been the technology’s Achilles’ heel and prevented their adoption for many biomedical and clinical diagnostic applications. Previous work to enhance the sensitivity of microarray readout to the single-molecule (“digital”) regime have either required signal amplifying chemistry or sacrificed throughput, nixing the platform’s primary advantages. Here, we report the development of a digital microarray which extends both the sensitivity and dynamic range of microarrays by about 3 orders of magnitude. This technique uses functionalized gold nanorods as single-molecule labels and an interferometric scanner which can rapidly enumerate individual nanorods by imaging them with a 10× objective lens. This approach does not require any chemical signal enhancement such as silver deposition and scans arrays with a throughput similar to commercial fluorescence scanners. By combining single-nanoparticle enumeration and ensemble measurements of spots when the particles are very dense, this system achieves a dynamic range of about 6 orders of magnitude directly from a single scan. As a proof-of-concept digital protein microarray assay, we demonstrated detection of hepatitis B virus surface antigen in buffer with a limit of detection of 3.2 pg/mL. More broadly, the technique’s simplicity and high-throughput nature make digital microarrays a flexible platform technology with a wide range of potential applications in biomedical research and clinical diagnostics.
69.
Sevenler, Derin; Briars, Emma A.; Daaboul, George G.; Kanik, Fulya Ekiz; Greene, Joseph; Khalil, Ahmad; Ünlü, M. Selim
14.03.2018.
Abstract | Links | BibTeX | Tags:
@misc{nokey_29,
title = {A digital microarray for transcriptional biomarkers of antibiotic resistance utilizing plasmonic nanorods and interferometric imaging},
author = {Derin Sevenler and Emma A. Briars and George G. Daaboul and Fulya Ekiz Kanik and Joseph Greene and Ahmad Khalil and M. Selim Ünlü},
url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/10479/1047908/Adigital-microarray-for-transcriptional-biomarkers-of-antibiotic-resistance-utilizing-plasmonic/10.1117/12.2290068.short?SSO=1},
doi = {https://doi.org/10.1117/12.2290068},
year = {2018},
date = {2018-03-14},
issuetitle = {SPIE Proceedings},
volume = {10479},
publisher = {SPIE},
abstract = {The standard laboratory procedure for determining the antibiotic susceptibility of a pathogen (an antimicrobial susceptibility test, AST) measures the inhibition of growth, and requires several days. This can delay effective therapy and lead to antibiotic overuse and misuse. Recent work (Wei Hou et al, Lab on a Chip 2015) has shown that resistant and susceptible pathogens will have very different gene expression profiles shortly following antibiotic exposure, and that these expression biomarkers may be used to accurately identify the pathogen species, strain and antibiotic susceptibility without growth. We therefore developed an ultrasensitive ‘digital microarray’ for performing rapid & quantitative gene expression analysis as part of a rapid AST. The digital microarray uses plasmonic gold nanorods (GNRs) functionalized with DNA to specifically label each target RNA that binds to the microarray. Each GNR on the array is then individually detected based on its light scattering, with an interferometric microscopy technique called SP- IRIS. Our optimized high-throughput version of SP-IRIS is able to scan a typical array of 500 spots in less than 10 minutes. Due to its single molecule readout, the assay has a limit of detection of less than 1 femtomolar following just 2 hours of incubation. Altogether, digital microarrays are about 10,000-fold more sensitive than fluorescence microarrays, yet maintain all of the strengths of the platform including low cost and high multiplexing. The reproducibility and robustness of the multiplexed assay will next be evaluated with clinically relevant pathogenic strains of E. coli as part of a functional rapid AST.},
keywords = {},
pubstate = {published},
tppubtype = {presentation}
}
The standard laboratory procedure for determining the antibiotic susceptibility of a pathogen (an antimicrobial susceptibility test, AST) measures the inhibition of growth, and requires several days. This can delay effective therapy and lead to antibiotic overuse and misuse. Recent work (Wei Hou et al, Lab on a Chip 2015) has shown that resistant and susceptible pathogens will have very different gene expression profiles shortly following antibiotic exposure, and that these expression biomarkers may be used to accurately identify the pathogen species, strain and antibiotic susceptibility without growth. We therefore developed an ultrasensitive ‘digital microarray’ for performing rapid & quantitative gene expression analysis as part of a rapid AST. The digital microarray uses plasmonic gold nanorods (GNRs) functionalized with DNA to specifically label each target RNA that binds to the microarray. Each GNR on the array is then individually detected based on its light scattering, with an interferometric microscopy technique called SP- IRIS. Our optimized high-throughput version of SP-IRIS is able to scan a typical array of 500 spots in less than 10 minutes. Due to its single molecule readout, the assay has a limit of detection of less than 1 femtomolar following just 2 hours of incubation. Altogether, digital microarrays are about 10,000-fold more sensitive than fluorescence microarrays, yet maintain all of the strengths of the platform including low cost and high multiplexing. The reproducibility and robustness of the multiplexed assay will next be evaluated with clinically relevant pathogenic strains of E. coli as part of a functional rapid AST.
70.
Sevenler, Derin; Briars, Emma A.; Daaboul, George G.; Kanik, Fulya Ekiz; Greene, Joseph; Khalil, Ahmad; Ünlü, M. Selim
14.03.2018.
Abstract | Links | BibTeX | Tags:
@misc{nokey,
title = {A digital microarray for transcriptional biomarkers of antibiotic resistance utilizing plasmonic nanorods and interferometric imaging},
author = {Derin Sevenler and Emma A. Briars and George G. Daaboul and Fulya Ekiz Kanik and Joseph Greene and Ahmad Khalil and M. Selim Ünlü},
url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/10479/1047908/Adigital-microarray-for-transcriptional-biomarkers-of-antibiotic-resistance-utilizing-plasmonic/10.1117/12.2290068.short?SSO=1},
doi = {https://doi.org/10.1117/12.2290068},
year = {2018},
date = {2018-03-14},
issuetitle = {SPIE Proceedings},
volume = {10479},
publisher = {SPIE},
abstract = {The standard laboratory procedure for determining the antibiotic susceptibility of a pathogen (an antimicrobial susceptibility test, AST) measures the inhibition of growth, and requires several days. This can delay effective therapy and lead to antibiotic overuse and misuse. Recent work (Wei Hou et al, Lab on a Chip 2015) has shown that resistant and susceptible pathogens will have very different gene expression profiles shortly following antibiotic exposure, and that these expression biomarkers may be used to accurately identify the pathogen species, strain and antibiotic susceptibility without growth. We therefore developed an ultrasensitive ‘digital microarray’ for performing rapid & quantitative gene expression analysis as part of a rapid AST. The digital microarray uses plasmonic gold nanorods (GNRs) functionalized with DNA to specifically label each target RNA that binds to the microarray. Each GNR on the array is then individually detected based on its light scattering, with an interferometric microscopy technique called SP- IRIS. Our optimized high-throughput version of SP-IRIS is able to scan a typical array of 500 spots in less than 10 minutes. Due to its single molecule readout, the assay has a limit of detection of less than 1 femtomolar following just 2 hours of incubation. Altogether, digital microarrays are about 10,000-fold more sensitive than fluorescence microarrays, yet maintain all of the strengths of the platform including low cost and high multiplexing. The reproducibility and robustness of the multiplexed assay will next be evaluated with clinically relevant pathogenic strains of E. coli as part of a functional rapid AST.},
keywords = {},
pubstate = {published},
tppubtype = {presentation}
}
The standard laboratory procedure for determining the antibiotic susceptibility of a pathogen (an antimicrobial susceptibility test, AST) measures the inhibition of growth, and requires several days. This can delay effective therapy and lead to antibiotic overuse and misuse. Recent work (Wei Hou et al, Lab on a Chip 2015) has shown that resistant and susceptible pathogens will have very different gene expression profiles shortly following antibiotic exposure, and that these expression biomarkers may be used to accurately identify the pathogen species, strain and antibiotic susceptibility without growth. We therefore developed an ultrasensitive ‘digital microarray’ for performing rapid & quantitative gene expression analysis as part of a rapid AST. The digital microarray uses plasmonic gold nanorods (GNRs) functionalized with DNA to specifically label each target RNA that binds to the microarray. Each GNR on the array is then individually detected based on its light scattering, with an interferometric microscopy technique called SP- IRIS. Our optimized high-throughput version of SP-IRIS is able to scan a typical array of 500 spots in less than 10 minutes. Due to its single molecule readout, the assay has a limit of detection of less than 1 femtomolar following just 2 hours of incubation. Altogether, digital microarrays are about 10,000-fold more sensitive than fluorescence microarrays, yet maintain all of the strengths of the platform including low cost and high multiplexing. The reproducibility and robustness of the multiplexed assay will next be evaluated with clinically relevant pathogenic strains of E. coli as part of a functional rapid AST.
