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Mun J, Navarro N, Jeong S, Ouassil N, Leem E, Beyene AG, Landry MP. Near-infrared nanosensors enable optical imaging of oxytocin with selectivity over vasopressin in acute mouse brain slices. Proc Natl Acad Sci U S A 2024; 121:e2314795121. [PMID: 38905241 PMCID: PMC11214003 DOI: 10.1073/pnas.2314795121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 04/19/2024] [Indexed: 06/23/2024] Open
Abstract
Oxytocin plays a critical role in regulating social behaviors, yet our understanding of its function in both neurological health and disease remains incomplete. Real-time oxytocin imaging probes with spatiotemporal resolution relevant to its endogenous signaling are required to fully elucidate oxytocin's role in the brain. Herein, we describe a near-infrared oxytocin nanosensor (nIROXT), a synthetic probe capable of imaging oxytocin in the brain without interference from its structural analogue, vasopressin. nIROXT leverages the inherent tissue-transparent fluorescence of single-walled carbon nanotubes (SWCNT) and the molecular recognition capacity of an oxytocin receptor peptide fragment to selectively and reversibly image oxytocin. We employ these nanosensors to monitor electrically stimulated oxytocin release in brain tissue, revealing oxytocin release sites with a median size of 3 µm in the paraventricular nucleus of C57BL/6 mice, which putatively represents the spatial diffusion of oxytocin from its point of release. These data demonstrate that covalent SWCNT constructs, such as nIROXT, are powerful optical tools that can be leveraged to measure neuropeptide release in brain tissue.
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Affiliation(s)
- Jaewan Mun
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Nicole Navarro
- Department of Chemistry, University of California, Berkeley, CA94720
| | - Sanghwa Jeong
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan50612, South Korea
| | - Nicholas Ouassil
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
| | - Esther Leem
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
| | | | - Markita P. Landry
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA94720
- Chan Zuckerberg Biohub, San Francisco, CA94158
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2
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Adams JAM, Komatsu N, Navarro N, Leem E, Sun X, Zhao J, Arias-Soto OI, Landry MP. Near infrared fluorescent nanosensors for high spatiotemporal oxytocin imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593556. [PMID: 38766215 PMCID: PMC11100785 DOI: 10.1101/2024.05.10.593556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Oxytocin is a neuropeptide thought to play a central role in regulating social and emotional behavior. Current techniques for neuropeptide imaging are generally limited in spatial and temporal resolution, real-time imaging capacity, selectivity for oxytocin over vasopressin, and application in young and non-model organisms. To avoid the use of endogenous oxytocin receptors for oxytocin probe development, we employed a protocol to evolve purely synthetic molecular recognition on the surface of near-infrared fluorescent single-walled carbon nanotubes (SWCNT) using single-stranded DNA (ssDNA). This probe reversibly undergoes up to a 172% fluorescence increase in response to oxytocin with a K d of 4.93 μM. Furthermore, this probe responds selectively to oxytocin over oxytocin analogs, receptor agonists and antagonists, and most other neurochemicals. Lastly, we show our probe can image synaptic evoked oxytocin release in live mouse brain slices. Optical probes with the specificity and resolution requisite to image endogenous oxytocin signaling can advance the study of oxytocin neurotransmission for its role in both health and disease.
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3
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Song Y, Tian C, Lee Y, Yoon M, Yoon SE, Cho SY. Nanosensor Chemical Cytometry: Advances and Opportunities in Cellular Therapy and Precision Medicine. ACS MEASUREMENT SCIENCE AU 2023; 3:393-403. [PMID: 38145025 PMCID: PMC10740128 DOI: 10.1021/acsmeasuresciau.3c00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 12/26/2023]
Abstract
With the definition of therapeutics now encompassing transplanted or engineered cells and their molecular products, there is a growing scientific necessity for analytics to understand this new category of drugs. This Perspective highlights the recent development of new measurement science on label-free single cell analysis, nanosensor chemical cytometry (NCC), and their potential for cellular therapeutics and precision medicine. NCC is based on microfluidics integrated with fluorescent nanosensor arrays utilizing the optical lensing effect of a single cell to real-time extract molecular properties and correlate them with physical attributes of single cells. This new class of cytometry can quantify the heterogeneity of the multivariate physicochemical attributes of the cell populations in a completely label-free and nondestructive way and, thus, suggest the vein-to-vein conditions for the safe therapeutic applications. After the introduction of the NCC technology, we suggest the technological development roadmap for the maturation of the new field: from the sensor/chip design perspective to the system/software development level based on hardware automation and deep learning data analytics. The advancement of this new single cell sensing technology is anticipated to aid rich and multivariate single cell data setting and support safe and reliable cellular therapeutics. This new measurement science can lead to data-driven personalized precision medicine.
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Affiliation(s)
- Youngho Song
- School
of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Changyu Tian
- School
of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Yullim Lee
- School
of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Minyeong Yoon
- School
of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sang Eun Yoon
- Division
of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Soo-Yeon Cho
- School
of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
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4
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Demirer GS, Landry MP. Efficient Transient Gene Knock-down in Tobacco Plants Using Carbon Nanocarriers. Bio Protoc 2021; 11:e3897. [PMID: 33732771 DOI: 10.21769/bioprotoc.3897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/27/2022] Open
Abstract
Gene knock-down in plants is a useful approach to study genotype-phenotype relationships, render disease resistance to crops, and enable efficient biosynthesis of molecules in plants. Small interfering RNA (siRNA)-mediated gene silencing is one of the most common ways to achieve gene knock-down in plants. Traditionally, siRNA is delivered into intact plant cells by coding the siRNA sequences into DNA vectors, which are then delivered through viral and/or bacterial methods. In this protocol, we provide an alternative direct delivery method of siRNA molecules into intact plant cells for efficient transient gene knock-down in model tobacco plant, Nicotiana benthamiana, leaves. Our approach uses one dimensional carbon-based nanomaterials, single-walled carbon nanotubes (SWNTs), to deliver siRNA, and does not rely on viral/bacterial delivery. The distinct advantages of our method are i) there is no need for DNA coding of siRNA sequences, ii) this abiotic method could work in a broader range of plant species than biotic methods, and iii) there are fewer regulatory complications when using abiotic delivery methods, whereby gene silencing is transient without permanent modification of the plant genome. Graphic abstract.
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Affiliation(s)
- Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA 94720, USA.,Innovative Genomics Institute, Berkeley, CA 94702, USA.,Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
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5
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Demirer GS, Zhang H, Goh NS, Pinals RL, Chang R, Landry MP. Carbon nanocarriers deliver siRNA to intact plant cells for efficient gene knockdown. SCIENCE ADVANCES 2020; 6:eaaz0495. [PMID: 32637592 PMCID: PMC7314522 DOI: 10.1126/sciadv.aaz0495] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 05/08/2020] [Indexed: 05/19/2023]
Abstract
Posttranscriptional gene silencing (PTGS) is a powerful tool to understand and control plant metabolic pathways, which is central to plant biotechnology. PTGS is commonly accomplished through delivery of small interfering RNA (siRNA) into cells. Standard plant siRNA delivery methods (Agrobacterium and viruses) involve coding siRNA into DNA vectors and are only tractable for certain plant species. Here, we develop a nanotube-based platform for direct delivery of siRNA and show high silencing efficiency in intact plant cells. We demonstrate that nanotubes successfully deliver siRNA and silence endogenous genes, owing to effective intracellular delivery and nanotube-induced protection of siRNA from nuclease degradation. This study establishes that nanotubes could enable a myriad of plant biotechnology applications that rely on RNA delivery to intact cells.
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Affiliation(s)
- Gozde S. Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Natalie S. Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rebecca L. Pinals
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Roger Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Markita P. Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94702, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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6
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Hendler-Neumark A, Bisker G. Fluorescent Single-Walled Carbon Nanotubes for Protein Detection. SENSORS (BASEL, SWITZERLAND) 2019; 19:E5403. [PMID: 31817932 PMCID: PMC6960995 DOI: 10.3390/s19245403] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/02/2019] [Accepted: 12/05/2019] [Indexed: 01/06/2023]
Abstract
Nanosensors have a central role in recent approaches to molecular recognition in applications like imaging, drug delivery systems, and phototherapy. Fluorescent nanoparticles are particularly attractive for such tasks owing to their emission signal that can serve as optical reporter for location or environmental properties. Single-walled carbon nanotubes (SWCNTs) fluoresce in the near-infrared part of the spectrum, where biological samples are relatively transparent, and they do not photobleach or blink. These unique optical properties and their biocompatibility make SWCNTs attractive for a variety of biomedical applications. Here, we review recent advancements in protein recognition using SWCNTs functionalized with either natural recognition moieties or synthetic heteropolymers. We emphasize the benefits of the versatile applicability of the SWCNT sensors in different systems ranging from single-molecule level to in-vivo sensing in whole animal models. Finally, we discuss challenges, opportunities, and future perspectives.
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Affiliation(s)
| | - Gili Bisker
- Department of Biomedical Engineering, Faculty of Engineering, Tel-Aviv University, Tel Aviv 6997801, Israel;
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7
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Jeong S, Yang D, Beyene AG, Del Bonis-O’Donnell JT, Gest AMM, Navarro N, Sun X, Landry MP. High-throughput evolution of near-infrared serotonin nanosensors. SCIENCE ADVANCES 2019; 5:eaay3771. [PMID: 31897432 PMCID: PMC6920020 DOI: 10.1126/sciadv.aay3771] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/30/2019] [Indexed: 05/11/2023]
Abstract
Imaging neuromodulation with synthetic probes is an emerging technology for studying neurotransmission. However, most synthetic probes are developed through conjugation of fluorescent signal transducers to preexisting recognition moieties such as antibodies or receptors. We introduce a generic platform to evolve synthetic molecular recognition on the surface of near-infrared fluorescent single-wall carbon nanotube (SWCNT) signal transducers. We demonstrate evolution of molecular recognition toward neuromodulator serotonin generated from large libraries of ~6.9 × 1010 unique ssDNA sequences conjugated to SWCNTs. This probe is reversible and produces a ~200% fluorescence enhancement upon exposure to serotonin with a K d = 6.3 μM, and shows selective responsivity over serotonin analogs, metabolites, and receptor-targeting drugs. Furthermore, this probe remains responsive and reversible upon repeat exposure to exogenous serotonin in the extracellular space of acute brain slices. Our results suggest that evolution of nanosensors could be generically implemented to develop other neuromodulator probes with synthetic molecular recognition.
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Affiliation(s)
- Sanghwa Jeong
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Darwin Yang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Abraham G. Beyene
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Anneliese M. M. Gest
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicole Navarro
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xiaoqi Sun
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Markita P. Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute (IGI), Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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8
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Budhathoki-Uprety J, Shah J, Korsen JA, Wayne AE, Galassi TV, Cohen JR, Harvey JD, Jena PV, Ramanathan LV, Jaimes EA, Heller DA. Synthetic molecular recognition nanosensor paint for microalbuminuria. Nat Commun 2019; 10:3605. [PMID: 31399600 PMCID: PMC6689023 DOI: 10.1038/s41467-019-11583-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/19/2019] [Indexed: 01/16/2023] Open
Abstract
Microalbuminuria is an important clinical marker of several cardiovascular, metabolic, and other diseases such as diabetes, hypertension, atherosclerosis, and cancer. The accurate detection of microalbuminuria relies on albumin quantification in the urine, usually via an immunoturbidity assay; however, like many antibody-based assessments, this method may not be robust enough to function in global health applications, point-of-care assays, or wearable devices. Here, we develop an antibody-free approach using synthetic molecular recognition by constructing a polymer to mimic fatty acid binding to the albumin, informed by the albumin crystal structure. A single-walled carbon nanotube, encapsulated by the polymer, as the transduction element produces a hypsochromic (blue) shift in photoluminescence upon the binding of albumin in clinical urine samples. This complex, incorporated into an acrylic material, results in a nanosensor paint that enables the detection of microalbuminuria in patient samples and comprises a rapid point-of-care sensor robust enough to be deployed in resource-limited settings.
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Affiliation(s)
- Januka Budhathoki-Uprety
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
- Department of Textile Engineering, Chemistry, and Science, North Carolina State University, Raleigh, NC, 27695, United States
| | - Janki Shah
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
| | - Joshua A Korsen
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
- Weill Cornell Medical College, New York, NY, 10065, United States
| | - Alysandria E Wayne
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
- Washington University in St. Louis, St. Louis, MO, 63130, United States
| | - Thomas V Galassi
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
- Weill Cornell Medical College, New York, NY, 10065, United States
| | - Joseph R Cohen
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
| | - Jackson D Harvey
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
- Weill Cornell Medical College, New York, NY, 10065, United States
| | - Prakrit V Jena
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
| | | | - Edgar A Jaimes
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States
- Weill Cornell Medical College, New York, NY, 10065, United States
| | - Daniel A Heller
- Memorial Sloan Kettering Cancer Center, New York, NY, 10065, United States.
- Weill Cornell Medical College, New York, NY, 10065, United States.
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9
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Lui A, Wang J, Chio L, Landry MP. Synthetic probe development for measuring single or few-cell activity and efflux. Methods Enzymol 2019; 628:19-41. [PMID: 31668229 PMCID: PMC10461879 DOI: 10.1016/bs.mie.2019.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Studying the single cell protein secretome offers the opportunity to understand how a phenotypically heterogeneous population of individual cells contribute to ensemble physiology and signaling. Polarized secretion events such as neurotransmitter release and cytokine signaling necessitates spatiotemporal information to elucidate structure-function relationships. Polymer functionalized single-walled carbon nanotube protein sensor arrays allow microscopic imaging of secreted protein footprints and enable the study of the spatiotemporal heterogeneity of protein secretion at the single-cell level. The protocols for carbon nanotube sensor creation, sensor array preparation, and imaging secreted proteins in both prokaryotic and mammalian cells are presented in this chapter. Secreted RAP1 and HIV-1 integrase proteins were used as proof-of-concept examples. Additionally, we discuss potential variety of protein and non-protein analyte effluxes that can be imaged using this platform, as well as current and future perspectives related to sensor development and deployment.
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Affiliation(s)
- Alison Lui
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Jeffrey Wang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Linda Chio
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, United States; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States; California Institute for Quantitative Biosciences (QB3), Berkeley, CA, United States; Chan-Zuckerberg Biohub, San Francisco, CA, United States.
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10
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Demirer GS, Zhang H, Matos JL, Goh NS, Cunningham FJ, Sung Y, Chang R, Aditham AJ, Chio L, Cho MJ, Staskawicz B, Landry MP. High aspect ratio nanomaterials enable delivery of functional genetic material without DNA integration in mature plants. NATURE NANOTECHNOLOGY 2019; 14:456-464. [PMID: 30804481 PMCID: PMC10461892 DOI: 10.1038/s41565-019-0382-5] [Citation(s) in RCA: 247] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/18/2019] [Indexed: 05/19/2023]
Abstract
Genetic engineering of plants is at the core of sustainability efforts, natural product synthesis and crop engineering. The plant cell wall is a barrier that limits the ease and throughput of exogenous biomolecule delivery to plants. Current delivery methods either suffer from host-range limitations, low transformation efficiencies, tissue damage or unavoidable DNA integration into the host genome. Here, we demonstrate efficient diffusion-based biomolecule delivery into intact plants of several species with pristine and chemically functionalized high aspect ratio nanomaterials. Efficient DNA delivery and strong protein expression without transgene integration is accomplished in Nicotiana benthamiana (Nb), Eruca sativa (arugula), Triticum aestivum (wheat) and Gossypium hirsutum (cotton) leaves and arugula protoplasts. We find that nanomaterials not only facilitate biomolecule transport into plant cells but also protect polynucleotides from nuclease degradation. Our work provides a tool for species-independent and passive delivery of genetic material, without transgene integration, into plant cells for diverse biotechnology applications.
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Affiliation(s)
- Gozde S Demirer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Huan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Juliana L Matos
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute (IGI), Berkeley, CA, USA
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Francis J Cunningham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Younghun Sung
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Roger Chang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Abhishek J Aditham
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Linda Chio
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Myeong-Je Cho
- Innovative Genomics Institute (IGI), Berkeley, CA, USA
| | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute (IGI), Berkeley, CA, USA
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Innovative Genomics Institute (IGI), Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
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11
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Beyene AG, Alizadehmojarad AA, Dorlhiac G, Goh N, Streets AM, Král P, Vuković L, Landry MP. Ultralarge Modulation of Fluorescence by Neuromodulators in Carbon Nanotubes Functionalized with Self-Assembled Oligonucleotide Rings. NANO LETTERS 2018; 18:6995-7003. [PMID: 30350638 PMCID: PMC6771428 DOI: 10.1021/acs.nanolett.8b02937] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Noncovalent interactions between single-stranded DNA (ssDNA) oligonucleotides and single wall carbon nanotubes (SWNTs) have provided a unique class of tunable chemistries for a variety of applications. However, mechanistic insight into both the photophysical and intermolecular phenomena underlying their utility is lacking, which results in obligate heuristic approaches for producing ssDNA-SWNT based technologies. In this work, we present an ultrasensitive "turn-on" nanosensor for neuromodulators dopamine and norepinephrine with strong relative change in fluorescence intensity (Δ F/ F0) of up to 3500%, a signal appropriate for in vivo neuroimaging, and uncover the photophysical principles and intermolecular interactions that govern the molecular recognition and fluorescence modulation of this nanosensor synthesized from the spontaneous self-assembly of (GT)6 ssDNA rings on SWNTs. The fluorescence modulation of the ssDNA-SWNT conjugate is shown to exhibit remarkable sensitivity to the ssDNA sequence chemistry, length, and surface density, providing a set of parameters with which to tune nanosensor dynamic range, analyte selectivity and strength of fluorescence turn-on. We employ classical and quantum mechanical molecular dynamics simulations to rationalize our experimental findings. Calculations show that (GT)6 ssDNA form ordered rings around (9,4) SWNTs, inducing periodic surface potentials that modulate exciton recombination lifetimes. Further evidence is presented to elucidate how dopamine analyte binding modulates SWNT fluorescence. We discuss the implications of our findings for SWNT-based molecular imaging applications.
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Affiliation(s)
- Abraham G. Beyene
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720
| | - Ali A. Alizadehmojarad
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX 79968
| | - Gabriel Dorlhiac
- Berkeley Biophysics Program, University of California, Berkeley, Berkeley, CA 94720
| | - Natalie Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720
| | - Aaron M. Streets
- Berkeley Biophysics Program, University of California, Berkeley, Berkeley, CA 94720
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720
- Chan-Zuckerberg Biohub, San Francisco, CA 94158
| | - Petr Král
- Department of Chemistry, Physics, and Biopharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 79968
| | - Lela Vuković
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX 79968
| | - Markita P. Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720
- Chan-Zuckerberg Biohub, San Francisco, CA 94158
- California Institute for Quantitative Biosciences (qb3), University of California, Berkeley, Berkeley, CA 94720
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12
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Beyene AG, McFarlane IR, Pinals RL, Landry MP. Stochastic Simulation of Dopamine Neuromodulation for Implementation of Fluorescent Neurochemical Probes in the Striatal Extracellular Space. ACS Chem Neurosci 2017; 8:2275-2289. [PMID: 28714693 PMCID: PMC10494912 DOI: 10.1021/acschemneuro.7b00193] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Imaging the dynamic behavior of neuromodulatory neurotransmitters in the extracelluar space that arise from individual quantal release events would constitute a major advance in neurochemical imaging. Spatial and temporal resolution of these highly stochastic neuromodulatory events requires concurrent advances in the chemical development of optical nanosensors selective for neuromodulators in concert with advances in imaging methodologies to capture millisecond neurotransmitter release. Herein, we develop and implement a stochastic model to describe dopamine dynamics in the extracellular space (ECS) of the brain dorsal striatum to guide the design and implementation of fluorescent neurochemical probes that record neurotransmitter dynamics in the ECS. Our model is developed from first-principles and simulates release, diffusion, and reuptake of dopamine in a 3D simulation volume of striatal tissue. We find that in vivo imaging of neuromodulation requires simultaneous optimization of dopamine nanosensor reversibility and sensitivity: dopamine imaging in the striatum or nucleus accumbens requires nanosensors with an optimal dopamine dissociation constant (Kd) of 1 μM, whereas Kds above 10 μM are required for dopamine imaging in the prefrontal cortex. Furthermore, as a result of the probabilistic nature of dopamine terminal activity in the striatum, our model reveals that imaging frame rates of 20 Hz are optimal for recording temporally resolved dopamine release events. Our work provides a modeling platform to probe how complex neuromodulatory processes can be studied with fluorescent nanosensors and enables direct evaluation of nanosensor chemistry and imaging hardware parameters. Our stochastic model is generic for evaluating fluorescent neurotransmission probes, and is broadly applicable to the design of other neurotransmitter fluorophores and their optimization for implementation in vivo.
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Affiliation(s)
- Abraham G. Beyene
- Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Ian R. McFarlane
- Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Rebecca L. Pinals
- Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Markita P. Landry
- Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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Landry MP, Ando H, Chen A, Cao J, Kottadiel VI, Chio L, Yang D, Dong J, Lu T, Strano M. Single-molecule detection of protein efflux from microorganisms using fluorescent single-walled carbon nanotube sensor arrays. NATURE NANOTECHNOLOGY 2017; 12:368-377. [PMID: 28114298 PMCID: PMC6438169 DOI: 10.1038/nnano.2016.284] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 12/01/2016] [Indexed: 05/14/2023]
Abstract
A distinct advantage of nanosensor arrays is their ability to achieve ultralow detection limits in solution by proximity placement to an analyte. Here, we demonstrate label-free detection of individual proteins from Escherichia coli (bacteria) and Pichia pastoris (yeast) immobilized in a microfluidic chamber, measuring protein efflux from single organisms in real time. The array is fabricated using non-covalent conjugation of an aptamer-anchor polynucleotide sequence to near-infrared emissive single-walled carbon nanotubes, using a variable chemical spacer shown to optimize sensor response. Unlabelled RAP1 GTPase and HIV integrase proteins were selectively detected from various cell lines, via large near-infrared fluorescent turn-on responses. We show that the process of E. coli induction, protein synthesis and protein export is highly stochastic, yielding variability in protein secretion, with E. coli cells undergoing division under starved conditions producing 66% fewer secreted protein products than their non-dividing counterparts. We further demonstrate the detection of a unique protein product resulting from T7 bacteriophage infection of E. coli, illustrating that nanosensor arrays can enable real-time, single-cell analysis of a broad range of protein products from various cell types.
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Affiliation(s)
- Markita Patricia Landry
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720
- California Institute for Quantitative Biosciences (qb3), University of California-Berkeley, Berkeley, CA 94720
| | - Hiroki Ando
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Allen Chen
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Biophysics Program, Harvard University, Cambridge, Massachusetts 02138
| | - Jicong Cao
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Vishal Isaac Kottadiel
- The Rowland Institute at Harvard University, Cambridge, Massachusetts 02142
- Department of Biology, The Catholic University of America, Washington, District of Columbia 20064
| | - Linda Chio
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720
| | - Darwin Yang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720
| | - Juyao Dong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02138
| | - Timothy Lu
- Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Michael Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02138
- Corresponding Author: (M.S.S.)
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Abstract
Surface engineering of nanoparticles has recently emerged as a promising technique for synthetic molecular recognition of biological analytes. In particular, the use of synthetic heteropolymers adsorbed onto the surface of a nanoparticle can yield selective detection of a molecular target. Synthetic molecular recognition has unique advantages in leveraging the photostability, versatility, and exceptional chemical stability of nanomaterials. In particular, single-walled carbon nanotubes (SWNT) exhibit a large Stokes shift and near infrared emission for maximum biological sample transparency. Optical biosensors with high signal transduction and molecular specificity can be synthesized with amphiphilic heteropolymers grafted to SWNT, and discovered by high-throughput screening. Herein, we describe the development and the characterization of surface-engineered nanoparticles, or "synthetic antibodies," for protein detection.
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Affiliation(s)
- Linda Chio
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Darwin Yang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Markita Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
- Landry Lab, California Institute for Quantitative Biosciences, QB3, University of California, #3220, 476 Stanley Hall, Berkeley, CA, 94720, USA.
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