1
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Keyport Kik S, Christopher D, Glauninger H, Hickernell CW, Bard JAM, Lin KM, Squires AH, Ford M, Sosnick TR, Drummond DA. An adaptive biomolecular condensation response is conserved across environmentally divergent species. Nat Commun 2024; 15:3127. [PMID: 38605014 PMCID: PMC11009240 DOI: 10.1038/s41467-024-47355-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.
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Affiliation(s)
- Samantha Keyport Kik
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Dana Christopher
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Hendrik Glauninger
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Caitlin Wong Hickernell
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jared A M Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Kyle M Lin
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | | | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA.
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2
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Cook A, Dearborn MA, Anderberg TM, Vaidya K, Jureller JE, Esser-Kahn AP, Squires AH. Polymer Patterning by Laser-Induced Multipoint Initiation of Frontal Polymerization. ACS Appl Mater Interfaces 2024; 16:17973-17980. [PMID: 38418392 PMCID: PMC11009908 DOI: 10.1021/acsami.4c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 03/01/2024]
Abstract
Frontal polymerization (FP) is an approach for thermosetting plastics at a lower energy cost than an autoclave. The potential to generate simultaneous propagation of multiple polymerization fronts has been discussed as an exciting possibility. However, FP initiated at more than two points simultaneously has not been demonstrated. Multipoint initiation could enable both large-scale material fabrication and unique pattern generation. Here, the authors present laser-patterned photothermal heating as a method for simultaneous initiation of FP at multiple locations in a 2-D sample. Carbon black particles are mixed into liquid resin (dicyclopentadiene) to enhance absorption of light from a Ti:sapphire laser (800 nm) focused on a sample. The laser is time-shared by rapid steering among initiation points, generating polymerization using up to seven simultaneous points of initiation. This process results in the formation of both symmetric and asymmetric seam patterns resulting from the collision of fronts. The authors also present and validate a theoretical framework for predicting the seam patterns formed by front collisions. This framework allows the design of novel patterns via an inverse solution for determining the initiation points required to form a desired pattern. Future applications of this approach could enable rapid, energy-efficient manufacturing of novel composite-like patterned materials.
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Affiliation(s)
- Andrés
L. Cook
- Department
of Physics, University of Chicago, Chicago, Illinois 60637, United States
| | - Mason A. Dearborn
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
| | - Trevor M. Anderberg
- Department
of Physics, University of Chicago, Chicago, Illinois 60637, United States
| | - Kavya Vaidya
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
| | - Justin E. Jureller
- James
Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Aaron P. Esser-Kahn
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
- Institute
for Biophysical Dynamics, University of
Chicago, Chicago, Illinois 60637, United States
| | - Allison H. Squires
- Pritzker
School of Molecular Engineering, University
of Chicago, Chicago, Illinois 60637, United States
- Institute
for Biophysical Dynamics, University of
Chicago, Chicago, Illinois 60637, United States
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3
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Chu J, Ejaz A, Lin KM, Joseph MR, Coraor AE, Drummond DA, Squires AH. Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels. ArXiv 2024:arXiv:2307.01614v2. [PMID: 38344222 PMCID: PMC10854282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Multiplexed, real-time fluorescence detection at the single-molecule level is highly desirable to reveal the stoichiometry, dynamics, and interactions of individual molecular species within complex systems. However, traditionally fluorescence sensing is limited to 3-4 concurrently detected labels, due to low signal-to-noise, high spectral overlap between labels, and the need to avoid dissimilar dye chemistries. We have engineered a palette of several dozen fluorescent labels, called FRETfluors, for spectroscopic multiplexing at the single-molecule level. Each FRETfluor is a compact nanostructure formed from the same three chemical building blocks (DNA, Cy3, and Cy5). The composition and dye-dye geometries create a characteristic F\"orster Resonance Energy Transfer (FRET) efficiency for each construct. In addition, we varied the local DNA sequence and attachment chemistry to alter the Cy3 and Cy5 emission properties and thereby shift the emission signatures of an entire series of FRET constructs to new sectors of the multi-parameter detection space. Unique spectroscopic emission of each FRETfluor is therefore conferred by a combination of FRET and this site-specific tuning of individual fluorophore photophysics. We show single-molecule identification of a set of 27 FRETfluors in a sample mixture using a subset of constructs statistically selected to minimize classification errors, measured using an Anti-Brownian ELectrokinetic (ABEL) trap which provides precise multi-parameter spectroscopic measurements. The ABEL trap also enables discrimination between FRETfluors attached to a target (here: mRNA) and unbound FRETfluors, eliminating the need for washes or removal of excess label by purification. We show single-molecule identification of a set of 27 FRETfluors in a sample mixture using a subset of constructs selected to minimize classification errors.
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4
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Domurat-Sousa K, Poe CM, McDaniel MS, Spieglan E, Shida JF, Angelico E, Adams BW, Riviere PJL, Frisch HJ, Squires AH. Simulation of a Compton-based detector for low-dose high-resolution time-of-flight positron emission tomography. ArXiv 2024:arXiv:2305.07173v2. [PMID: 37214132 PMCID: PMC10197732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Two major challenges in time-of-flight positron emission tomography (TOF-PET) are low spatial resolution and high radioactive dose to the patient, both of which result from limitations in detection technology rather than fundamental physics. A new type of TOF-PET detector employing low-atomic number (low-Z) scintillation media and large-area, high-resolution photodetectors to record Compton scattering locations in the detector has been proposed as a promising alternative, but the minimum technical requirements for such a system have not yet been established. Here we present a simulation study evaluating the potential of a proposed low-Z detection medium, linear alkylbenzene (LAB) doped with a switchable molecular recorder, for next-generation TOF-PET detection. We developed a custom Monte Carlo simulation of full-body TOF-PET using the TOPAS Geant4 software package. By quantifying contributions and tradeoffs for energy, spatial, and timing resolution of the detector, we show that at reasonable combination of specifications, our likelihood-based identification of pairs of first interaction locations in the simulated detector identifies 87.1% of pairs with zero or negligible error, and correctly rejects 90% of all in-patient scatters. The same specifications give TOF-PET sensitivity of ~66.7% and PSF width 4.6 mm with clear contrast. A detector with these specifications provides a clear image of a brain phantom simulated at less than 1% of a standard radiotracer dose.
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5
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Ali A, Garde R, Schaffer OC, Bard JAM, Husain K, Kik SK, Davis KA, Luengo-Woods S, Igarashi MG, Drummond DA, Squires AH, Pincus D. Adaptive preservation of orphan ribosomal proteins in chaperone-dispersed condensates. Nat Cell Biol 2023; 25:1691-1703. [PMID: 37845327 PMCID: PMC10868727 DOI: 10.1038/s41556-023-01253-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Ribosome biogenesis is among the most resource-intensive cellular processes, with ribosomal proteins accounting for up to half of all newly synthesized proteins in eukaryotic cells. During stress, cells shut down ribosome biogenesis in part by halting rRNA synthesis, potentially leading to massive accumulation of aggregation-prone 'orphan' ribosomal proteins (oRPs). Here we show that, during heat shock in yeast and human cells, oRPs accumulate as reversible peri-nucleolar condensates recognized by the Hsp70 co-chaperone Sis1/DnaJB6. oRP condensates are liquid-like in cell-free lysate but solidify upon depletion of Sis1 or inhibition of Hsp70. When cells recover from heat shock, oRP condensates disperse in a Sis1- and Hsp70-dependent manner, and the oRP constituents are incorporated into functional ribosomes in the cytosol, enabling cells to efficiently resume growth. Preserving biomolecules in reversible condensates-like mRNAs in cytosolic stress granules and oRPs at the nucleolar periphery-may be a primary function of the Hsp70 chaperone system.
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Affiliation(s)
- Asif Ali
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA.
| | - Rania Garde
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Olivia C Schaffer
- Pritzker School for Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Jared A M Bard
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Kabir Husain
- Department of Physics, University of Chicago, Chicago, IL, USA
| | - Samantha Keyport Kik
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Kathleen A Davis
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Sofia Luengo-Woods
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Maya G Igarashi
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School for Molecular Engineering, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, USA
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
- Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, USA.
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6
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Squires AH. Electrokinetic manipulation of a nanowire. Nat Nanotechnol 2023; 18:1128-1129. [PMID: 37500781 DOI: 10.1038/s41565-023-01459-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Affiliation(s)
- Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.
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7
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Squires AH. Multiplexing single-molecule fluorescence measurements with spectroscopically diverse DNA-based FRET constructs. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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8
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Lavania AA, Carpenter WB, Oltrogge LM, Borden J, Perez DD, Squires AH, Dahlberg PD, Savage DF, Moerner WE. Characterizing physical properties of single carboxysomes in the Interferometric Scattering Anti-Brownian ELectrokinetic trap. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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9
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Shida JF, Spieglan E, Adams BW, Angelico E, Domurat-Sousa K, Elagin A, Frisch HJ, La Riviere P, Squires AH. Low-Dose High-Resolution TOF-PET Using Ionization-activated Multi-State Low-Z Detector Media. Nucl Instrum Methods Phys Res A 2021; 1017:165801. [PMID: 34690392 PMCID: PMC8530277 DOI: 10.1016/j.nima.2021.165801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We propose PET scanners using low atomic number media that undergo a persistent local change of state along the paths of the Compton recoil electrons. Measurement of the individual scattering locations and angles, deposited energies, and recoil electron directions allows using the kinematical constraints of the 2-body Compton scattering process to perform a statistical time-ordering of the scatterings, with a high probability of precisely identifying where the gamma first interacted in the detector. In these cases the Line-of-Response is measured with high resolution, determined by the underlying physics processes and not the detector segmentation. There are multiple such media that act through different mechanisms. As an example in which the change of state is quantum-mechanical through a change in molecular configuration, rather than thermodynamic, as in a bubble chamber, we present simulations of a two-state photoswitchable organic dye, a 'Switchillator', that is activated to a fluorescent-capable state by the ionization of the recoil electrons. The activated state is persistent, and can be optically excited multiple times to image individual activated molecules. Energy resolution is provided by counting the activated molecules. Location along the LOR is implemented by large-area time-of-flight MCP-PMT photodetectors with single photon time resolution in the tens of ps and sub-mm spatial resolution. Simulations indicate a large reduction of dose.
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Affiliation(s)
- J F Shida
- Enrico Fermi Institute, The University of Chicago, 5640 S Ellis Ave, Chicago, IL 60637
| | - E Spieglan
- Enrico Fermi Institute, The University of Chicago, 5640 S Ellis Ave, Chicago, IL 60637
| | - B W Adams
- Quantum Optics Applied Research, Naperville, IL 60564
| | - E Angelico
- Enrico Fermi Institute, The University of Chicago, 5640 S Ellis Ave, Chicago, IL 60637
| | - K Domurat-Sousa
- Enrico Fermi Institute, The University of Chicago, 5640 S Ellis Ave, Chicago, IL 60637
| | - A Elagin
- Enrico Fermi Institute, The University of Chicago, 5640 S Ellis Ave, Chicago, IL 60637
| | - H J Frisch
- Enrico Fermi Institute, The University of Chicago, 5640 S Ellis Ave, Chicago, IL 60637
| | - P La Riviere
- Department of Radiology, The University of Chicago, Billings Hospital, P220, 5841 South Maryland Avenue, MC2026, Chicago, IL 60637
| | - A H Squires
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637
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10
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Anderegg L, Doyle J, Gardel ML, Gupta A, Hallas C, Lensky Y, Love NG, Lucas BA, Mazenc E, Meisenhelder C, Pillarisetti A, Ranard D, Squires AH, Vechakul J, Vilas NB, Williams S, Wilson D, Chen TN. Heat and Humidity for Bioburden Reduction of N95 Filtering Facepiece Respirators. Applied Biosafety 2021; 26:80-89. [DOI: 10.1089/apb.20.0053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Loïc Anderegg
- Department of Physics, Harvard University, Cambridge, Massachusetts, USA
- Harvard/MIT Center for Ultracold Atoms, Cambridge, Massachusetts, USA
| | - John Doyle
- Department of Physics, Harvard University, Cambridge, Massachusetts, USA
- Harvard/MIT Center for Ultracold Atoms, Cambridge, Massachusetts, USA
| | - Margaret L. Gardel
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, USA
- Department of Physics, The University of Chicago, Chicago, Illinois, USA
| | - Amit Gupta
- Consolidated Sterilizer Systems, Billerica, Massachusetts, USA
| | - Christian Hallas
- Department of Physics, Harvard University, Cambridge, Massachusetts, USA
- Harvard/MIT Center for Ultracold Atoms, Cambridge, Massachusetts, USA
| | - Yuri Lensky
- Department of Physics, Stanford University, Stanford, California, USA
| | - Nancy G. Love
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Edward Mazenc
- Department of Physics, Stanford University, Stanford, California, USA
| | - Cole Meisenhelder
- Department of Physics, Harvard University, Cambridge, Massachusetts, USA
- Harvard/MIT Center for Ultracold Atoms, Cambridge, Massachusetts, USA
| | - Ajay Pillarisetti
- PPE Sanitizer Group, Vallejo, California, USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Daniel Ranard
- Department of Physics, Stanford University, Stanford, California, USA
| | - Allison H. Squires
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, USA
| | | | - Nathaniel B. Vilas
- Department of Physics, Harvard University, Cambridge, Massachusetts, USA
- Harvard/MIT Center for Ultracold Atoms, Cambridge, Massachusetts, USA
| | | | | | - Tyler N. Chen
- Department of Bioengineering, Stanford University, Stanford, California, USA
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11
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Abstract
This commentary profiles the research interests of my recently established research group at The University of Chicago, as well as my own research trajectory and contributions to the field of nanoscale biophysics. I describe here certain open challenges of interest that drive my group's current research efforts, along with my past efforts that have impacted these areas.
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Affiliation(s)
- Allison H Squires
- Pritzker School for Molecular Engineering, The University of Chicago, 5640 South Ellis Ave, Chicago, IL, 60637, USA.
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12
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Rudnizky S, Khamis H, Malik O, Squires AH, Meller A, Melamed P, Kaplan A. Single-molecule DNA unzipping reveals asymmetric modulation of a transcription factor by its binding site sequence and context. Nucleic Acids Res 2019; 46:1513-1524. [PMID: 29253225 PMCID: PMC5815098 DOI: 10.1093/nar/gkx1252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/11/2017] [Indexed: 12/31/2022] Open
Abstract
Most functional transcription factor (TF) binding sites deviate from their ‘consensus’ recognition motif, although their sites and flanking sequences are often conserved across species. Here, we used single-molecule DNA unzipping with optical tweezers to study how Egr-1, a TF harboring three zinc fingers (ZF1, ZF2 and ZF3), is modulated by the sequence and context of its functional sites in the Lhb gene promoter. We find that both the core 9 bp bound to Egr-1 in each of the sites, and the base pairs flanking them, modulate the affinity and structure of the protein–DNA complex. The effect of the flanking sequences is asymmetric, with a stronger effect for the sequence flanking ZF3. Characterization of the dissociation time of Egr-1 revealed that a local, mechanical perturbation of the interactions of ZF3 destabilizes the complex more effectively than a perturbation of the ZF1 interactions. Our results reveal a novel role for ZF3 in the interaction of Egr-1 with other proteins and the DNA, providing insight on the regulation of Lhb and other genes by Egr-1. Moreover, our findings reveal the potential of small changes in DNA sequence to alter transcriptional regulation, and may shed light on the organization of regulatory elements at promoters.
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Affiliation(s)
- Sergei Rudnizky
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Hadeel Khamis
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Faculty of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Omri Malik
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Allison H Squires
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Amit Meller
- Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Faculty of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
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13
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Squires AH, Dahlberg PD, Liu H, Magdaong NCM, Blankenship RE, Moerner WE. Single-molecule trapping and spectroscopy reveals photophysical heterogeneity of phycobilisomes quenched by Orange Carotenoid Protein. Nat Commun 2019; 10:1172. [PMID: 30862823 PMCID: PMC6414729 DOI: 10.1038/s41467-019-09084-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/15/2019] [Indexed: 11/09/2022] Open
Abstract
The Orange Carotenoid Protein (OCP) is a cytosolic photosensor that is responsible for non-photochemical quenching (NPQ) of the light-harvesting process in most cyanobacteria. Upon photoactivation by blue-green light, OCP binds to the phycobilisome antenna complex, providing an excitonic trap to thermally dissipate excess energy. At present, both the binding site and NPQ mechanism of OCP are unknown. Using an Anti-Brownian ELectrokinetic (ABEL) trap, we isolate single phycobilisomes in free solution, both in the presence and absence of activated OCP, to directly determine the photophysics and heterogeneity of OCP-quenched phycobilisomes. Surprisingly, we observe two distinct OCP-quenched states, with lifetimes 0.09 ns (6% of unquenched brightness) and 0.21 ns (11% brightness). Photon-by-photon Monte Carlo simulations of exciton transfer through the phycobilisome suggest that the observed quenched states are kinetically consistent with either two or one bound OCPs, respectively, underscoring an additional mechanism for excitation control in this key photosynthetic unit. Upon photoactivation the Orange Carotenoid Protein (OCP) binds to the phycobilisome and prevents damage by thermally dissipating excess energy. Here authors use an Anti-Brownian ELectrokinetic trap to determine the photophysics of single OCP-quenched phycobilisomes and observe two distinct OCP-quenched states with either one or two OCPs bound.
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Affiliation(s)
- Allison H Squires
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Peter D Dahlberg
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Haijun Liu
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Nikki Cecil M Magdaong
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Robert E Blankenship
- Departments of Biology and Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
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14
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Squires AH, Dahlberg PD, Liu H, Blankenship RE, Moerner W. Single-Molecule Measurements of Quenching and Photophysical Heterogeneity in Phycobiliproteins. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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15
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Dahlberg PD, Squires AH, Sartor AM, Liu H, Blankenship RE, Moerner W. Cryogenic Dissection of the Phycobilisome's Electronic Structure. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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16
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Squires AH, Wang Q, Moerner W. Direct Single-Molecule Measurements of Phycocyanobilin Photophysics in Monomeric C-Phycocyanin. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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17
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Squires AH, Gilboa T, Torfstein C, Varongchayakul N, Meller A. Single-Molecule Characterization of DNA-Protein Interactions Using Nanopore Biosensors. Methods Enzymol 2016; 582:353-385. [PMID: 28062042 DOI: 10.1016/bs.mie.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Detection and characterization of nucleic acid-protein interactions, particularly those involving DNA and proteins such as transcription factors, enzymes, and DNA packaging proteins, remain significant barriers to our understanding of genetic regulation. Nanopores are an extremely sensitive and versatile sensing platform for label-free detection of single biomolecules. Analyte molecules are drawn to and through a nanoscale aperture by an electrophoretic force, which acts upon their native charge while in the sensing region of the pore. When the nanopore's diameter is only slightly larger than the biopolymer's cross section (typically a few nm); the latter must translocate through the pore in a linear fashion due to the constricted geometry in this region. These features allow nanopores to interrogate protein-nucleic acids in multiple sensing modes: first, by scanning and mapping the locations of binding sites along an analyte molecule, and second, by probing the strength of the bond between a protein and nucleic acid, using the native charge of the nucleic acid to apply an electrophoretic force to the complex while the protein is geometrically prevented from passing through the nanopore. In this chapter, we describe progress toward nanopore sensing of protein-nucleic acid complexes in the context of both mapping binding sites and performing force spectroscopy to determine the strength of interactions. We conclude by reviewing the strengths and challenges of the nanopore technique in the context of studying DNA-protein interactions.
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Affiliation(s)
- A H Squires
- Stanford University, Stanford, CA, United States
| | | | | | | | - A Meller
- The Technion, Haifa, Israel; Boston University, Boston, MA, United States.
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Abstract
In clinical settings, rapid and accurate characterization of pathogens is essential for effective treatment of patients; however, subtle genetic changes in pathogens which elude traditional phenotypic typing may confer dangerous pathogenic properties such as toxicity, antibiotic resistance, or virulence. Existing options for molecular typing techniques characterize the critical genomic changes that distinguish harmful and benign strains, yet the well-established approaches, in particular those that rely on electrophoretic separation of nucleic acid fragments on a gel, have room for only incremental future improvements in speed, cost, and complexity. Solid-state nanopores are an emerging class of single-molecule sensors that can electrophoretically characterize charged biopolymers, and which offer significant advantages in terms of sample and reagent requirements, readout speed, parallelization, and automation. We present here the first application of nanopores for single-molecule molecular typing using length based "fingerprints" of critical sites in bacterial genomes. This technique is highly adaptable for detection of different types of genetic variation; as we illustrate using prototypical examples including Mycobacterium tuberculosis and methicillin-resistant Streptococcus aureus, the solid-state nanopore diagnostic platform may be used to detect large insertions or deletions, small insertions or deletions, and even single-nucleotide variations in bacterial DNA. We further show that Bayesian classification of test samples can provide highly confident pathogen typing results based on only a few tens of independent single-molecule events, making this method extremely sensitive and statistically robust.
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Affiliation(s)
- Allison H Squires
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, United States of America
| | - Evrim Atas
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, United States of America
| | - Amit Meller
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215, United States of America.,Department of Biomedical Engineering, The Technion-Israel Institute of Technology, Haifa, 32000, Israel
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Assad O, Di Fiori N, Squires AH, Meller A. Two color DNA barcode detection in photoluminescence suppressed silicon nitride nanopores. Nano Lett 2015; 15:745-52. [PMID: 25522780 PMCID: PMC4296929 DOI: 10.1021/nl504459c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/16/2014] [Indexed: 05/20/2023]
Abstract
Optical sensing of solid-state nanopores is a relatively new approach that can enable high-throughput, multicolor readout from a collection of nanopores. It is therefore highly attractive for applications such as nanopore-based DNA sequencing and genotyping using DNA barcodes. However, to date optical readout has been plagued by the need to achieve sufficiently high signal-to-noise ratio (SNR) for single fluorophore sensing, while still maintaining millisecond resolution. One of the main factors degrading the optical SNR in solid-state nanopores is the high photoluminescence (PL) background emanating from the silicon nitride (SiNx) membrane in which pores are commonly fabricated. Focusing on the optical properties of SiNx nanopores we show that the local membrane PL intensity is substantially reduced, and its spectrum is shifted toward shorter wavelengths with increasing e-beam dose. This phenomenon, which is correlated with a marked photocurrent enhancement in these nanopores, is utilized to perform for the first time single molecule fluorescence detection using both green and red laser excitations. Specifically, the reduction in PL and the concurrent measurement of the nanopore photocurrent enhancement allow us to maximize the background suppression and to detect a dual color, five-unit DNA barcode with high SNR levels.
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Affiliation(s)
- Ossama
N. Assad
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 United States
| | - Nicolas Di Fiori
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 United States
| | - Allison H. Squires
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 United States
| | - Amit Meller
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 United States
- Department
of Biomedical Engineering, Technion −
Israel Institute of Technology, Haifa, Israel 32000
- E-mail:
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Anderson BN, Assad ON, Gilboa T, Squires AH, Bar D, Meller A. Probing solid-state nanopores with light for the detection of unlabeled analytes. ACS Nano 2014; 8:11836-45. [PMID: 25363680 PMCID: PMC4334260 DOI: 10.1021/nn505545h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Nanopore sensing has enabled label-free single-molecule measurements on a wide variety of analytes, including DNA, RNA, and protein complexes. Much progress has been made toward biotechnological applications; however, electrically probing the ion current introduces nonideal noise components. Here we further develop a method to couple an ionic current to a photon-by-photon counting of fluorescent signal from Ca(2+)-sensitive dyes and demonstrate label-free optical detection of biopolymer translocation through solid-state nanopores using TIRF and confocal microscopy. We show that by fine adjustment of the CaCl2 gradient, EGTA concentration, and voltage, the optical signals can be localized to the immediate vicinity of the pore. Consequently, the noise spectral density distribution in the optical signal exhibits a nearly flat distribution throughout the entire frequency range. With the use of high-speed photon counting devices in confocal microscopy and higher photon count rates using stronger light sources, we can improve the signal-to-noise ratio of signal acquisition, while the use of wide-field imaging in TIRF can allow for simultaneous quantitative imaging of large arrays of nanopores.
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Affiliation(s)
- Brett N. Anderson
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
| | - Ossama N. Assad
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Tal Gilboa
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Allison H. Squires
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
| | - Daniel Bar
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Amit Meller
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
- Address correspondence to
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Squires AH, Meller A. Solid-State Nanopore Modifications for Improved Resolution of DNA Translocations. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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MacKechnie HL, Squires AH, Platts M, Pruzanski W. Thymoma, myasthenia gravis, erythroblastopenic anemia and systemic lupus erythematosus in one patient. Can Med Assoc J 1973; 109:733-8. [PMID: 4126868 PMCID: PMC1947065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A 50-year-old woman who initially had myasthenia gravis subsequently presented with thymoma, erythroblastopenic anemia and systemic lupus erythematosus during 17 years of follow-up. In a review of the literature no similar documented cases were found, although 14 patients were reported with three of the above diseases, two also having positive LE cell tests. An association of several autoimmune disorders in one patient may be more frequent than was previously believed.
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Hooey MA, Crookston JH, Squires AH. Myeloproliferative disease complicated by megaloblastic anemia and hyperuricemia. Can Med Assoc J 1965; 93:935-7. [PMID: 5829412 PMCID: PMC1928979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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