1
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Schirripa Spagnolo C, Moscardini A, Amodeo R, Beltram F, Luin S. Quantitative determination of fluorescence labeling implemented in cell cultures. BMC Biol 2023; 21:190. [PMID: 37697318 PMCID: PMC10496409 DOI: 10.1186/s12915-023-01685-0] [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: 11/29/2022] [Accepted: 08/18/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Labeling efficiency is a crucial parameter in fluorescence applications, especially when studying biomolecular interactions. Current approaches for estimating the yield of fluorescent labeling have critical drawbacks that usually lead them to be inaccurate or not quantitative. RESULTS We present a method to quantify fluorescent-labeling efficiency that addresses the critical issues marring existing approaches. The method operates in the same conditions of the target experiments by exploiting a ratiometric evaluation with two fluorophores used in sequential reactions. We show the ability of the protocol to extract reliable quantification for different fluorescent probes, reagents concentrations, and reaction timing and to optimize labeling performance. As paradigm, we consider the labeling of the membrane-receptor TrkA through 4'-phosphopantetheinyl transferase Sfp in living cells, visualizing the results by TIRF microscopy. This investigation allows us to find conditions for demanding single and multi-color single-molecule studies requiring high degrees of labeling. CONCLUSIONS The developed method allows the quantitative determination and the optimization of staining efficiency in any labeling strategy based on stable reactions.
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Affiliation(s)
| | - Aldo Moscardini
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127, Pisa, Italy
| | - Rosy Amodeo
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127, Pisa, Italy
- Present address: Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072, Milan, Italy
| | - Fabio Beltram
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127, Pisa, Italy
- NEST Laboratory, Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127, Pisa, Italy
| | - Stefano Luin
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127, Pisa, Italy.
- NEST Laboratory, Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127, Pisa, Italy.
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2
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Kim J, Lee S, Lee YK, Seong B, Kim HM, Kyeong S, Kim W, Ham K, Pham XH, Hahm E, Mun JY, Safaa MA, Lee YS, Jun BH, Park HS. In Vitro Tracking of Human Umbilical Vein Endothelial Cells Using Ultra-Sensitive Quantum Dot-Embedded Silica Nanoparticles. Int J Mol Sci 2023; 24:ijms24065794. [PMID: 36982869 PMCID: PMC10052325 DOI: 10.3390/ijms24065794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
The nanoscale spatiotemporal resolution of single-particle tracking (SPT) renders it a powerful method for exploring single-molecule dynamics in living cells or tissues, despite the disadvantages of using traditional organic fluorescence probes, such as the weak fluorescent signal against the strong cellular autofluorescence background coupled with a fast-photobleaching rate. Quantum dots (QDs), which enable tracking targets in multiple colors, have been proposed as an alternative to traditional organic fluorescence dyes; however, they are not ideally suitable for applying SPT due to their hydrophobicity, cytotoxicity, and blinking problems. This study reports an improved SPT method using silica-coated QD-embedded silica nanoparticles (QD2), which represent brighter fluorescence and are less toxic than single QDs. After treatment of QD2 in 10 μg/mL, the label was retained for 96 h with 83.76% of labeling efficiency, without impaired cell function such as angiogenesis. The improved stability of QD2 facilitates the visualization of in situ endothelial vessel formation without real-time staining. Cells retain QD2 fluorescence signal for 15 days at 4 °C without significant photobleaching, indicating that QD2 has overcome the limitations of SPT enabling long-term intracellular tracking. These results proved that QD2 could be used for SPT as a substitute for traditional organic fluorophores or single quantum dots, with its photostability, biocompatibility, and superior brightness.
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Affiliation(s)
- Jaehi Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Sunray Lee
- Stem Cell Niche Division, CEFO Research Center, Seoul 03150, Republic of Korea
| | - Yeon Kyung Lee
- Stem Cell Niche Division, CEFO Research Center, Seoul 03150, Republic of Korea
| | - Bomi Seong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyung-Mo Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - San Kyeong
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Wooyeon Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Kyeongmin Ham
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Xuan-Hung Pham
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Eunil Hahm
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Ji Yeon Mun
- Stem Cell Niche Division, CEFO Research Center, Seoul 03150, Republic of Korea
| | | | - Yoon-Sik Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyun-Sook Park
- Stem Cell Niche Division, CEFO Research Center, Seoul 03150, Republic of Korea
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3
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Choosing the Probe for Single-Molecule Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms232314949. [PMID: 36499276 PMCID: PMC9735909 DOI: 10.3390/ijms232314949] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
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4
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Streck S, Bohr SSR, Birch D, Rades T, Hatzakis NS, McDowell A, Mørck Nielsen H. Interactions of Cell-Penetrating Peptide-Modified Nanoparticles with Cells Evaluated Using Single Particle Tracking. ACS APPLIED BIO MATERIALS 2021; 4:3155-3165. [DOI: 10.1021/acsabm.0c01563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sarah Streck
- School of Pharmacy, University of Otago, Dunedin 9016, New Zealand
| | - Søren S.-R. Bohr
- Department of Chemistry & Nano-science Center, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Ditlev Birch
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Thomas Rades
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Nikos S. Hatzakis
- Department of Chemistry & Nano-science Center, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Arlene McDowell
- School of Pharmacy, University of Otago, Dunedin 9016, New Zealand
| | - Hanne Mørck Nielsen
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
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5
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EGFR Expression in HER2-Driven Breast Cancer Cells. Int J Mol Sci 2020; 21:ijms21239008. [PMID: 33260837 PMCID: PMC7729501 DOI: 10.3390/ijms21239008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
The epidermal growth factor receptor HER2 is overexpressed in 20% of breast cancer cases. HER2 is an orphan receptor that is activated ligand-independently by homodimerization. In addition, HER2 is able to heterodimerize with EGFR, HER3, and HER4. Heterodimerization has been proposed as a mechanism of resistance to therapy for HER2 overexpressing breast cancer. Here, a method is presented for the simultaneous detection of individual EGFR and HER2 receptors in the plasma membrane of breast cancer cells via specific labeling with quantum dot nanoparticles (QDs). Correlative fluorescence microscopy and liquid phase electron microscopy were used to analyze the plasma membrane expression levels of both receptors in individual intact cells. Fluorescent single-cell analysis of SKBR3 breast cancer cells dual-labeled for EGFR and HER2 revealed a heterogeneous expression for receptors within both the cell population as well as within individual cells. Subsequent electron microscopy of individual cells allowed the determination of individual receptors label distributions. QD-labeled EGFR was observed with a surface density of (0.5–5) × 101 QDs/µm2, whereas labeled HER2 expression was higher ranging from (2–10) × 102 QDs/µm2. Although most SKBR3 cells expressed low levels of EGFR, an enrichment was observed at large plasma membrane protrusions, and amongst a newly discovered cellular subpopulation termed EGFR-enriched cells.
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6
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Le P, Vaidya R, Smith LD, Han Z, Zahid MU, Winter J, Sarkar S, Chung HJ, Perez-Pinera P, Selvin PR, Smith AM. Optimizing Quantum Dot Probe Size for Single-Receptor Imaging. ACS NANO 2020; 14:8343-8358. [PMID: 32525656 PMCID: PMC7872344 DOI: 10.1021/acsnano.0c02390] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Quantum dots (QDs) are nanocrystals with bright fluorescence and long-term photostability, attributes particularly beneficial for single-molecule imaging and molecular counting in the life sciences. The size of a QD nanocrystal determines its physicochemical and photophysical properties, both of which dictate the success of imaging applications. Larger nanocrystals typically have better optical properties, with higher brightness, red-shifted emission, reduced blinking, and greater stability. However, larger nanocrystals introduce molecular-labeling biases due to steric hindrance and nonspecific binding. Here, we systematically analyze the impact of nanocrystal size on receptor labeling in live and fixed cells. We designed three (core)shell QDs with red emission (600-700 nm) and crystalline sizes of 3.2, 5.5, and 8.3 nm. After coating with the same multidentate polymer, hydrodynamic sizes were 9.2 nm (QD9.2), 13.3 nm (QD13.3), and 17.4 nm (QD17.4), respectively. The QDs were conjugated to streptavidin and applied as probes for biotinylated neurotransmitter receptors. QD9.2 exhibited the highest labeling specificity for receptors in the narrow synaptic cleft (∼20-30 nm) in living neurons. However, for dense receptor labeling for molecular counting in live and fixed HeLa cells, QD13.3 yielded the highest counts. Nonspecific binding rose sharply for hydrodynamic sizes larger than 13.3 nm, with QD17.4 exhibiting particularly diminished specificity. Our comparisons further highlight needs to continue engineering the smallest QDs to increase single-molecule intensity, suppress blinking frequency, and inhibit nonspecific labeling in fixed and permeabilized cells. These results lay a foundation for designing QD probes with further reduced sizes to achieve unbiased labeling for quantitative and single-molecule imaging.
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Affiliation(s)
- Phuong Le
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Rohit Vaidya
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lucas D Smith
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zhiyuan Han
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mohammad U Zahid
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jackson Winter
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Suresh Sarkar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hee Jung Chung
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, Urbana, Illinois 61801 United States
| | - Paul R Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Departments of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, Urbana, Illinois 61801 United States
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7
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Alkyltransferase-like protein clusters scan DNA rapidly over long distances and recruit NER to alkyl-DNA lesions. Proc Natl Acad Sci U S A 2020; 117:9318-9328. [PMID: 32273391 DOI: 10.1073/pnas.1916860117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alkylation of guanine bases in DNA is detrimental to cells due to its high mutagenic and cytotoxic potential and is repaired by the alkyltransferase AGT. Additionally, alkyltransferase-like proteins (ATLs), which are structurally similar to AGTs, have been identified in many organisms. While ATLs are per se catalytically inactive, strong evidence has suggested that ATLs target alkyl lesions to the nucleotide excision repair system (NER). Using a combination of single-molecule and ensemble approaches, we show here recruitment of UvrA, the initiating enzyme of prokaryotic NER, to an alkyl lesion by ATL. We further characterize lesion recognition by ATL and directly visualize DNA lesion search by highly motile ATL and ATL-UvrA complexes on DNA at the molecular level. Based on the high similarity of ATLs and the DNA-interacting domain of AGTs, our results provide important insight in the lesion search mechanism, not only by ATL but also by AGT, thus opening opportunities for controlling the action of AGT for therapeutic benefit during chemotherapy.
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8
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Huang T, Phelps C, Wang J, Lin LJ, Bittel A, Scott Z, Jacques S, Gibbs SL, Gray JW, Nan X. Simultaneous Multicolor Single-Molecule Tracking with Single-Laser Excitation via Spectral Imaging. Biophys J 2019; 114:301-310. [PMID: 29401428 DOI: 10.1016/j.bpj.2017.11.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/11/2017] [Accepted: 11/13/2017] [Indexed: 11/18/2022] Open
Abstract
Single-molecule tracking (SMT) offers rich information on the dynamics of underlying biological processes, but multicolor SMT has been challenging due to spectral cross talk and a need for multiple laser excitations. Here, we describe a single-molecule spectral imaging approach for live-cell tracking of multiple fluorescent species at once using a single-laser excitation. Fluorescence signals from all the molecules in the field of view are collected using a single objective and split between positional and spectral channels. Images of the same molecule in the two channels are then combined to determine both the location and the identity of the molecule. The single-objective configuration of our approach allows for flexible sample geometry and the use of a live-cell incubation chamber required for live-cell SMT. Despite a lower photon yield, we achieve excellent spatial (20-40 nm) and spectral (10-15 nm) resolutions comparable to those obtained with dual-objective, spectrally resolved Stochastic Optical Reconstruction Microscopy. Furthermore, motions of the fluorescent molecules did not cause loss of spectral resolution owing to the dual-channel spectral calibration. We demonstrate SMT in three (and potentially more) colors using spectrally proximal fluorophores and single-laser excitation, and show that trajectories of each species can be reliably extracted with minimal cross talk.
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Affiliation(s)
- Tao Huang
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Carey Phelps
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Jing Wang
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Li-Jung Lin
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Amy Bittel
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Zubenelgenubi Scott
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Steven Jacques
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Summer L Gibbs
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Joe W Gray
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Xiaolin Nan
- Department of Biomedical Engineering, OHSU Center for Spatial Systems Biomedicine, and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon.
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9
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Pan H, Bilinovich SM, Kaur P, Riehn R, Wang H, Williams DC. CpG and methylation-dependent DNA binding and dynamics of the methylcytosine binding domain 2 protein at the single-molecule level. Nucleic Acids Res 2017. [PMID: 28637186 PMCID: PMC5587734 DOI: 10.1093/nar/gkx548] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The methylcytosine-binding domain 2 (MBD2) protein recruits the nucleosome remodeling and deacetylase complex (NuRD) to methylated DNA to modify chromatin and regulate transcription. Importantly, MBD2 functions within CpG islands that contain 100s to 1000s of potential binding sites. Since NuRD physically rearranges nucleosomes, the dynamic mobility of this complex is directly related to function. In these studies, we use NMR and single-molecule atomic force microscopy and fluorescence imaging to study DNA binding dynamics of MBD2. Single-molecule fluorescence tracking on DNA tightropes containing regions with CpG-rich and CpG-free regions reveals that MBD2 carries out unbiased 1D diffusion on CpG-rich DNA but subdiffusion on CpG-free DNA. In contrast, the protein stably and statically binds to methylated CpG (mCpG) regions. The intrinsically disordered region (IDR) on MBD2 both reduces exchange between mCpG sites along the DNA as well as the dissociation from DNA, acting like an anchor that restricts the dynamic mobility of the MBD domain. Unexpectedly, MBD2 binding to methylated CpGs induces DNA bending that is augmented by the IDR region of the protein. These results suggest that MBD2 targets NuRD to unmethylated or methylated CpG islands where its distinct dynamic binding modes help maintain open or closed chromatin, respectively.
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Affiliation(s)
- Hai Pan
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Stephanie M Bilinovich
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Parminder Kaur
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Hong Wang
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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10
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Limitations of Qdot labelling compared to directly-conjugated probes for single particle tracking of B cell receptor mobility. Sci Rep 2017; 7:11379. [PMID: 28900238 PMCID: PMC5595841 DOI: 10.1038/s41598-017-11563-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/18/2017] [Indexed: 12/25/2022] Open
Abstract
Single-particle tracking (SPT) is a powerful method for exploring single-molecule dynamics in living cells with nanoscale spatiotemporal resolution. Photostability and bright fluorescence make quantum dots (Qdots) a popular choice for SPT. However, their large size could potentially alter the mobility of the molecule of interest. To test this, we labelled B cell receptors on the surface of B-lymphocytes with monovalent Fab fragments of antibodies that were either linked to Qdots via streptavidin or directly conjugated to the small organic fluorophore Cy3. Imaging of receptor mobility by total internal reflection fluorescence microscopy (TIRFM), followed by quantitative single-molecule diffusion and confinement analysis, definitively showed that Qdots sterically hinder lateral mobility regardless of the substrate to which the cells were adhered. Qdot labelling also drastically altered the frequency with which receptors transitioned between apparent slow- and fast-moving states and reduced the size of apparent confinement zones. Although we show that Qdot-labelled probes can detect large differences in receptor mobility, they fail to resolve subtle differences in lateral diffusion that are readily detectable using Cy3-labelled Fabs. Our findings highlight the utility and limitations of using Qdots for TIRFM and wide-field-based SPT, and have significant implications for interpreting SPT data.
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11
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Meiri A, Ebeling CG, Martineau J, Zalevsky Z, Gerton JM, Menon R. Interference based localization of single emitters. OPTICS EXPRESS 2017; 25:17174-17191. [PMID: 28789212 PMCID: PMC5557332 DOI: 10.1364/oe.25.017174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/26/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
The ability to localize precisely a single optical emitter is important for particle tracking applications and super resolution microscopy. It is known that for a traditional microscope the ability to localize such an emitter is limited by the photon count. Here we analyze the ability to improve such localization by imposing interference fringes. We show here that a simple grating interferometer can introduce such improvement in certain circumstances and analyze what is required to increase the localization precision further.
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Affiliation(s)
- Amihai Meiri
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Carl G. Ebeling
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Martineau
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Zeev Zalevsky
- Faculty of Engineering, Bar-Ilan University, Ramat-Gan, Israel
| | - Jordan M. Gerton
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Rajesh Menon
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT 84112, USA
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12
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Kong M, Beckwitt EC, Springall L, Kad NM, Van Houten B. Single-Molecule Methods for Nucleotide Excision Repair: Building a System to Watch Repair in Real Time. Methods Enzymol 2017; 592:213-257. [PMID: 28668122 DOI: 10.1016/bs.mie.2017.03.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-molecule approaches to solving biophysical problems are powerful tools that allow static and dynamic real-time observations of specific molecular interactions of interest in the absence of ensemble-averaging effects. Here, we provide detailed protocols for building an experimental system that employs atomic force microscopy and a single-molecule DNA tightrope assay based on oblique angle illumination fluorescence microscopy. Together with approaches for engineering site-specific lesions into DNA substrates, these complementary biophysical techniques are well suited for investigating protein-DNA interactions that involve target-specific DNA-binding proteins, such as those engaged in a variety of DNA repair pathways. In this chapter, we demonstrate the utility of the platform by applying these techniques in the studies of proteins participating in nucleotide excision repair.
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Affiliation(s)
- Muwen Kong
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States
| | - Emily C Beckwitt
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States
| | - Luke Springall
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Neil M Kad
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Bennett Van Houten
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States; University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States.
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13
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Lagerholm BC, Andrade DM, Clausen MP, Eggeling C. Convergence of lateral dynamic measurements in the plasma membrane of live cells from single particle tracking and STED-FCS. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2017; 50:063001. [PMID: 28458397 PMCID: PMC5390782 DOI: 10.1088/1361-6463/aa519e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 11/15/2016] [Accepted: 12/05/2016] [Indexed: 05/06/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) in combination with the super-resolution imaging method STED (STED-FCS), and single-particle tracking (SPT) are able to directly probe the lateral dynamics of lipids and proteins in the plasma membrane of live cells at spatial scales much below the diffraction limit of conventional microscopy. However, a major disparity in interpretation of data from SPT and STED-FCS remains, namely the proposed existence of a very fast (unhindered) lateral diffusion coefficient, ⩾5 µm2 s-1, in the plasma membrane of live cells at very short length scales, ≈⩽ 100 nm, and time scales, ≈1-10 ms. This fast diffusion coefficient has been advocated in several high-speed SPT studies, for lipids and membrane proteins alike, but the equivalent has not been detected in STED-FCS measurements. Resolving this ambiguity is important because the assessment of membrane dynamics currently relies heavily on SPT for the determination of heterogeneous diffusion. A possible systematic error in this approach would thus have vast implications in this field. To address this, we have re-visited the analysis procedure for SPT data with an emphasis on the measurement errors and the effect that these errors have on the measurement outputs. We subsequently demonstrate that STED-FCS and SPT data, following careful consideration of the experimental errors of the SPT data, converge to a common interpretation which for the case of a diffusing phospholipid analogue in the plasma membrane of live mouse embryo fibroblasts results in an unhindered, intra-compartment, diffusion coefficient of ≈0.7-1.0 µm2 s-1, and a compartment size of about 100-150 nm.
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Affiliation(s)
- B Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Débora M Andrade
- Centre for Neural Circuits and Behaviour, University of Oxford, Mansfield Road, Oxford OX1 3SR, UK
| | - Mathias P Clausen
- MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, Odense M DK-5230, Denmark
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Christian Eggeling
- Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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14
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Lin J, Countryman P, Chen H, Pan H, Fan Y, Jiang Y, Kaur P, Miao W, Gurgel G, You C, Piehler J, Kad NM, Riehn R, Opresko PL, Smith S, Tao YJ, Wang H. Functional interplay between SA1 and TRF1 in telomeric DNA binding and DNA-DNA pairing. Nucleic Acids Res 2016; 44:6363-76. [PMID: 27298259 PMCID: PMC5291270 DOI: 10.1093/nar/gkw518] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/30/2016] [Indexed: 12/23/2022] Open
Abstract
Proper chromosome alignment and segregation during mitosis depend on cohesion between sister chromatids. Cohesion is thought to occur through the entrapment of DNA within the tripartite ring (Smc1, Smc3 and Rad21) with enforcement from a fourth subunit (SA1/SA2). Surprisingly, cohesin rings do not play a major role in sister telomere cohesion. Instead, this role is replaced by SA1 and telomere binding proteins (TRF1 and TIN2). Neither the DNA binding property of SA1 nor this unique telomere cohesion mechanism is understood. Here, using single-molecule fluorescence imaging, we discover that SA1 displays two-state binding on DNA: searching by one-dimensional (1D) free diffusion versus recognition through subdiffusive sliding at telomeric regions. The AT-hook motif in SA1 plays dual roles in modulating non-specific DNA binding and subdiffusive dynamics over telomeric regions. TRF1 tethers SA1 within telomeric regions that SA1 transiently interacts with. SA1 and TRF1 together form longer DNA–DNA pairing tracts than with TRF1 alone, as revealed by atomic force microscopy imaging. These results suggest that at telomeres cohesion relies on the molecular interplay between TRF1 and SA1 to promote DNA–DNA pairing, while along chromosomal arms the core cohesin assembly might also depend on SA1 1D diffusion on DNA and sequence-specific DNA binding.
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Affiliation(s)
- Jiangguo Lin
- School of Bioscience and Engineering, South China University of Technology, Guangzhou, Guangdong 510006, P.R. China Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Preston Countryman
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Haijiang Chen
- Department of BioSciences, Rice University, Houston, TX 77005, USA Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - Hai Pan
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Yanlin Fan
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Yunyun Jiang
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Wang Miao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450014, P.R. China
| | - Gisele Gurgel
- Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Changjiang You
- Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany
| | - Neil M Kad
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Robert Riehn
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh, PA 15213, USA
| | - Susan Smith
- Kimmel Center for Biology and Medicine at the Skirball Institute, Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Yizhi Jane Tao
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
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15
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Ma L, Tu C, Le P, Chitoor S, Lim SJ, Zahid MU, Teng KW, Ge P, Selvin PR, Smith AM. Multidentate Polymer Coatings for Compact and Homogeneous Quantum Dots with Efficient Bioconjugation. J Am Chem Soc 2016; 138:3382-94. [PMID: 26863113 DOI: 10.1021/jacs.5b12378] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Quantum dots are fluorescent nanoparticles used to detect and image proteins and nucleic acids. Compared with organic dyes and fluorescent proteins, these nanocrystals have enhanced brightness, photostability, and wavelength tunability, but their larger size limits their use. Recently, multidentate polymer coatings have yielded stable quantum dots with small hydrodynamic dimensions (≤10 nm) due to high-affinity, compact wrapping around the nanocrystal. However, this coating technology has not been widely adopted because the resulting particles are frequently heterogeneous and clustered, and conjugation to biological molecules is difficult to control. In this article we develop new polymeric ligands and optimize coating and bioconjugation methodologies for core/shell CdSe/Cd(x)Zn(1-x)S quantum dots to generate homogeneous and compact products. We demonstrate that "ligand stripping" to rapidly displace nonpolar ligands with hydroxide ions allows homogeneous assembly with multidentate polymers at high temperature. The resulting aqueous nanocrystals are 7-12 nm in hydrodynamic diameter, have quantum yields similar to those in organic solvents, and strongly resist nonspecific interactions due to short oligoethylene glycol surfaces. Compared with a host of other methods, this technique is superior for eliminating small aggregates identified through chromatographic and single-molecule analysis. We also demonstrate high-efficiency bioconjugation through azide-alkyne click chemistry and self-assembly with hexa-histidine-tagged proteins that eliminate the need for product purification. The conjugates retain specificity of the attached biomolecules and are exceptional probes for immunofluorescence and single-molecule dynamic imaging. These results are expected to enable broad utilization of compact, biofunctional quantum dots for studying crowded macromolecular environments such as the neuronal synapse and cellular cytoplasm.
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Affiliation(s)
| | - Chunlai Tu
- School of Physical Science and Technology, ShanghaiTech University , 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
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16
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Lim SJ, McDougle DR, Zahid MU, Ma L, Das A, Smith AM. Lipoprotein Nanoplatelets: Brightly Fluorescent, Zwitterionic Probes with Rapid Cellular Entry. J Am Chem Soc 2015; 138:64-7. [PMID: 26687504 DOI: 10.1021/jacs.5b11225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Semiconductor nanoplatelets (NPLs) are planar nanocrystals that have recently attracted considerable attention due to their quantum-well-like physics, atomically precise thickness, and unique photophysical properties such as narrow-band fluorescence emission. These attributes are of potential interest for applications in biomolecular and cellular imaging, but it has been challenging to colloidally stabilize these nanocrystals in biological media due to their large dimensions and tendency to aggregate. Here we introduce a new colloidal material that is a hybrid between a NPL and an organic nanodisc composed of phospholipids and lipoproteins. The phospholipids adsorb to flat surfaces on the NPL, and lipoproteins bind to sharp edges to enable monodisperse NPL encapsulation with long-term stability in biological buffers and high-salt solutions. The lipoprotein NPLs (L-NPLs) are highly fluorescent, with brightness comparable to that of wavelength-matched quantum dots at both the ensemble and single-molecule levels. They also exhibit a unique feature of rapid internalization into living cells, after which they retain their fluorescence. These unique properties suggest that L-NPLs are particularly well suited for applications in live-cell single-molecule imaging and multiplexed cellular labeling.
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Affiliation(s)
| | - Daniel R McDougle
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign , Urbana, Illinois 61802, United States
| | | | | | - Aditi Das
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign , Urbana, Illinois 61802, United States
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17
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Manzo C, Garcia-Parajo MF. A review of progress in single particle tracking: from methods to biophysical insights. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:124601. [PMID: 26511974 DOI: 10.1088/0034-4885/78/12/124601] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Optical microscopy has for centuries been a key tool to study living cells with minimum invasiveness. The advent of single molecule techniques over the past two decades has revolutionized the field of cell biology by providing a more quantitative picture of the complex and highly dynamic organization of living systems. Amongst these techniques, single particle tracking (SPT) has emerged as a powerful approach to study a variety of dynamic processes in life sciences. SPT provides access to single molecule behavior in the natural context of living cells, thereby allowing a complete statistical characterization of the system under study. In this review we describe the foundations of SPT together with novel optical implementations that nowadays allow the investigation of single molecule dynamic events with increasingly high spatiotemporal resolution using molecular densities closer to physiological expression levels. We outline some of the algorithms for the faithful reconstruction of SPT trajectories as well as data analysis, and highlight biological examples where the technique has provided novel insights into the role of diffusion regulating cellular function. The last part of the review concentrates on different theoretical models that describe anomalous transport behavior and ergodicity breaking observed from SPT studies in living cells.
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Affiliation(s)
- Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
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18
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Lim SJ, Zahid MU, Le P, Ma L, Entenberg D, Harney AS, Condeelis J, Smith AM. Brightness-equalized quantum dots. Nat Commun 2015; 6:8210. [PMID: 26437175 PMCID: PMC4594210 DOI: 10.1038/ncomms9210] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 07/29/2015] [Indexed: 11/17/2022] Open
Abstract
As molecular labels for cells and tissues, fluorescent probes have shaped our understanding of biological structures and processes. However, their capacity for quantitative analysis is limited because photon emission rates from multicolour fluorophores are dissimilar, unstable and often unpredictable, which obscures correlations between measured fluorescence and molecular concentration. Here we introduce a new class of light-emitting quantum dots with tunable and equalized fluorescence brightness across a broad range of colours. The key feature is independent tunability of emission wavelength, extinction coefficient and quantum yield through distinct structural domains in the nanocrystal. Precise tuning eliminates a 100-fold red-to-green brightness mismatch of size-tuned quantum dots at the ensemble and single-particle levels, which substantially improves quantitative imaging accuracy in biological tissue. We anticipate that these materials engineering principles will vastly expand the optical engineering landscape of fluorescent probes, facilitate quantitative multicolour imaging in living tissue and improve colour tuning in light-emitting devices. Quantum dots with different size emit light at different wavelengths but also different brightness, which complicates analysis of fluorescence images. Here, the authors synthesize multicolour brightness-equalized quantum dots by controlling the composition and structure of core-shell HgCdSeS-CdZnS nanocrystals.
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Affiliation(s)
- Sung Jun Lim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Mohammad U Zahid
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Phuong Le
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Liang Ma
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - David Entenberg
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA.,Integrated Imaging Program, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
| | - Allison S Harney
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA.,Integrated Imaging Program, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA.,Department of Radiology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
| | - John Condeelis
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA.,Integrated Imaging Program, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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19
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Miotke L, Maity A, Ji H, Brewer J, Astakhova K. Enzyme-Free Detection of Mutations in Cancer DNA Using Synthetic Oligonucleotide Probes and Fluorescence Microscopy. PLoS One 2015; 10:e0136720. [PMID: 26312489 PMCID: PMC4552304 DOI: 10.1371/journal.pone.0136720] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/07/2015] [Indexed: 11/19/2022] Open
Abstract
Background Rapid reliable diagnostics of DNA mutations are highly desirable in research and clinical assays. Current development in this field goes simultaneously in two directions: 1) high-throughput methods, and 2) portable assays. Non-enzymatic approaches are attractive for both types of methods since they would allow rapid and relatively inexpensive detection of nucleic acids. Modern fluorescence microscopy is having a huge impact on detection of biomolecules at previously unachievable resolution. However, no straightforward methods to detect DNA in a non-enzymatic way using fluorescence microscopy and nucleic acid analogues have been proposed so far. Methods and Results Here we report a novel enzyme-free approach to efficiently detect cancer mutations. This assay includes gene-specific target enrichment followed by annealing to oligonucleotides containing locked nucleic acids (LNAs) and finally, detection by fluorescence microscopy. The LNA containing probes display high binding affinity and specificity to DNA containing mutations, which allows for the detection of mutation abundance with an intercalating EvaGreen dye. We used a second probe, which increases the overall number of base pairs in order to produce a higher fluorescence signal by incorporating more dye molecules. Indeed we show here that using EvaGreen dye and LNA probes, genomic DNA containing BRAF V600E mutation could be detected by fluorescence microscopy at low femtomolar concentrations. Notably, this was at least 1000-fold above the potential detection limit. Conclusion Overall, the novel assay we describe could become a new approach to rapid, reliable and enzyme-free diagnostics of cancer or other associated DNA targets. Importantly, stoichiometry of wild type and mutant targets is conserved in our assay, which allows for an accurate estimation of mutant abundance when the detection limit requirement is met. Using fluorescence microscopy, this approach presents the opportunity to detect DNA at single-molecule resolution and directly in the biological sample of choice.
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Affiliation(s)
- Laura Miotke
- The Division of Oncology, Stanford School of Medicine, Stanford University, Stanford, California, United States of America
| | - Arindam Maity
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
- Dr B C Roy College of Pharmacy and AHS, Durgapur, West Bengal, India
| | - Hanlee Ji
- The Division of Oncology, Stanford School of Medicine, Stanford University, Stanford, California, United States of America
| | - Jonathan Brewer
- Memphys Center for Biomembrane Physics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Kira Astakhova
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
- * E-mail:
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20
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Ebeling CG, Meiri A, Martineau J, Zalevsky Z, Gerton JM, Menon R. Increased localization precision by interference fringe analysis. NANOSCALE 2015; 7:10430-7. [PMID: 25999093 PMCID: PMC4827330 DOI: 10.1039/c5nr01927c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report a novel optical single-emitter-localization methodology that uses the phase induced by path length differences in a Mach-Zehnder interferometer to improve localization precision. Using information theory, we demonstrate that the localization capability of a modified Fourier domain signal generated by photon interference enables a more precise localization compared to a standard Gaussian intensity distribution of the corresponding point-spread function. The calculations were verified by numerical simulations and an exemplary experiment, where the centers of metal nanoparticles were localized to a precision of 3 nm.
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Affiliation(s)
- Carl G. Ebeling
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Amihai Meiri
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Martineau
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Zeev Zalevsky
- Faculty of Engineering, Bar-llan University, Ramat-Gan, Israel
| | - Jordan M. Gerton
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Rajesh Menon
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT 84112, USA
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21
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Hanne J, Falk HJ, Görlitz F, Hoyer P, Engelhardt J, Sahl SJ, Hell SW. STED nanoscopy with fluorescent quantum dots. Nat Commun 2015; 6:7127. [PMID: 25980788 PMCID: PMC4479004 DOI: 10.1038/ncomms8127] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 04/02/2015] [Indexed: 11/14/2022] Open
Abstract
The widely popular class of quantum-dot molecular labels could so far not be utilized as standard fluorescent probes in STED (stimulated emission depletion) nanoscopy. This is because broad quantum-dot excitation spectra extend deeply into the spectral bands used for STED, thus compromising the transient fluorescence silencing required for attaining super-resolution. Here we report the discovery that STED nanoscopy of several red-emitting commercially available quantum dots is in fact successfully realized by the increasingly popular 775 nm STED laser light. A resolution of presently ∼ 50 nm is demonstrated for single quantum dots, and sub-diffraction resolution is further shown for imaging of quantum-dot-labelled vimentin filaments in fibroblasts. The high quantum-dot photostability enables repeated STED recordings with >1,000 frames. In addition, we have evidence that the tendency of quantum-dot labels to blink is largely suppressed by combined action of excitation and STED beams. Quantum-dot STED significantly expands the realm of application of STED nanoscopy, and, given the high stability of these probes, holds promise for extended time-lapse imaging.
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Affiliation(s)
- Janina Hanne
- German Cancer Research Center (DKFZ), Optical Nanoscopy Division, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Henning J. Falk
- German Cancer Research Center (DKFZ), Optical Nanoscopy Division, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Frederik Görlitz
- German Cancer Research Center (DKFZ), Optical Nanoscopy Division, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Patrick Hoyer
- German Cancer Research Center (DKFZ), Optical Nanoscopy Division, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Johann Engelhardt
- German Cancer Research Center (DKFZ), Optical Nanoscopy Division, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Steffen J. Sahl
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
| | - Stefan W. Hell
- German Cancer Research Center (DKFZ), Optical Nanoscopy Division, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany
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22
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Albrecht D, Winterflood CM, Ewers H. Dual color single particle tracking via nanobodies. Methods Appl Fluoresc 2015; 3:024001. [DOI: 10.1088/2050-6120/3/2/024001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Vu TQ, Lam WY, Hatch EW, Lidke DS. Quantum dots for quantitative imaging: from single molecules to tissue. Cell Tissue Res 2015; 360:71-86. [PMID: 25620410 DOI: 10.1007/s00441-014-2087-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/04/2014] [Indexed: 10/24/2022]
Abstract
Since their introduction to biological imaging, quantum dots (QDs) have progressed from a little known, but attractive, technology to one that has gained broad application in many areas of biology. The versatile properties of these fluorescent nanoparticles have allowed investigators to conduct biological studies with extended spatiotemporal capabilities that were previously not possible. In this review, we focus on QD applications that provide enhanced quantitative information concerning protein dynamics and localization, including single particle tracking and immunohistochemistry, and finish by examining the prospects of upcoming applications, such as correlative light and electron microscopy and super-resolution. Advances in single molecule imaging, including multi-color and three-dimensional QD tracking, have provided new insights into the mechanisms of cell signaling and protein trafficking. New forms of QD tracking in vivo have allowed the observation of biological processes at molecular level resolution in the physiological context of the whole animal. Further methodological development of multiplexed QD-based immunohistochemistry assays should enable more quantitative analysis of key proteins in tissue samples. These advances highlight the unique quantitative data sets that QDs can provide to further our understanding of biological and disease processes.
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Affiliation(s)
- Tania Q Vu
- Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, Ore., USA,
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24
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Jauffred L, Kyrsting A, Arnspang EC, Reihani SNS, Oddershede LB. Sub-diffraction positioning of a two-photon excited and optically trapped quantum dot. NANOSCALE 2014; 6:6997-7003. [PMID: 24839080 DOI: 10.1039/c4nr01319k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Colloidal quantum dots are luminescent long-lived probes that can be two-photon excited and manipulated by a single laser beam. Therefore, quantum dots can be used for simultaneous single molecule visualization and force manipulation using an infra-red laser. Here, we show that even a single optically trapped quantum dot, performing restricted Brownian motion within the focal volume, can be two-photon excited by the trapping laser beam and its luminescence can be detected by a camera. After two-photon excitation for a time long enough, the emitted light from the quantum dot is shown to blueshift. A quantum dot is much smaller than a diffraction limited laser focus and by mapping out the intensity of the focal volume and overlaying this with the positions visited by a quantum dot, a quantum dot is shown often to explore regions of the focal volume where the intensity is too low to render two-photon absorption likely. This is in accordance with the observation that a trapped quantum dot is only fluorescing 5-10 percent of the time. The results are important for realizing nano-scale quantum dot control and visualization and for correct interpretation of experiments using two-photon excited quantum dots as markers.
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25
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Clausen MP, Arnspang EC, Ballou B, Bear JE, Lagerholm BC. Simultaneous multi-species tracking in live cells with quantum dot conjugates. PLoS One 2014; 9:e97671. [PMID: 24892555 PMCID: PMC4043679 DOI: 10.1371/journal.pone.0097671] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 04/23/2014] [Indexed: 11/18/2022] Open
Abstract
Quantum dots are available in a range of spectrally separated emission colors and with a range of water-stabilizing surface coatings that offers great flexibility for enabling bio-specificity. In this study, we have taken advantage of this flexibility to demonstrate that it is possible to perform a simultaneous investigation of the lateral dynamics in the plasma membrane of i) the transmembrane epidermal growth factor receptor, ii) the glucosylphospatidylinositol-anchored protein CD59, and iii) ganglioside GM1-cholera toxin subunit B clusters in a single cell. We show that a large number of the trajectories are longer than 50 steps, which we by simulations show to be sufficient for robust single trajectory analysis. This analysis shows that the populations of the diffusion coefficients are heterogeneously distributed for all three species, but differ between the different species. We further show that the heterogeneity is decreased upon treating the cells with methyl-β-cyclodextrin.
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Affiliation(s)
- Mathias P. Clausen
- MEMPHYS – Center for Biomembrane Physics and Danish Molecular Biomedical Imaging Center (DaMBIC), University of Southern Denmark, Odense M, Denmark
| | - Eva C. Arnspang
- MEMPHYS – Center for Biomembrane Physics and Danish Molecular Biomedical Imaging Center (DaMBIC), University of Southern Denmark, Odense M, Denmark
| | - Byron Ballou
- Molecular Biosensor and Imaging Center (MBIC), Mellon Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - James E. Bear
- Lineberger Comprehensive Cancer Center and Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - B. Christoffer Lagerholm
- MEMPHYS – Center for Biomembrane Physics and Danish Molecular Biomedical Imaging Center (DaMBIC), University of Southern Denmark, Odense M, Denmark
- * E-mail:
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Valley CC, Lidke KA, Lidke DS. The spatiotemporal organization of ErbB receptors: insights from microscopy. Cold Spring Harb Perspect Biol 2014; 6:cshperspect.a020735. [PMID: 24370847 DOI: 10.1101/cshperspect.a020735] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Signal transduction is regulated by protein-protein interactions. In the case of the ErbB family of receptor tyrosine kinases (RTKs), the precise nature of these interactions remains a topic of debate. In this review, we describe state-of-the-art imaging techniques that are providing new details into receptor dynamics, clustering, and interactions. We present the general principles of these techniques, their limitations, and the unique observations they provide about ErbB spatiotemporal organization.
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Affiliation(s)
- Christopher C Valley
- Department of Pathology and the Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico 87131
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Arnspang EC, Schwartzentruber J, Clausen MP, Wiseman PW, Lagerholm BC. Bridging the gap between single molecule and ensemble methods for measuring lateral dynamics in the plasma membrane. PLoS One 2013; 8:e78096. [PMID: 24324577 PMCID: PMC3850922 DOI: 10.1371/journal.pone.0078096] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 09/17/2013] [Indexed: 11/22/2022] Open
Abstract
The lateral dynamics of proteins and lipids in the mammalian plasma membrane are heterogeneous likely reflecting both a complex molecular organization and interactions with other macromolecules that reside outside the plane of the membrane. Several methods are commonly used for characterizing the lateral dynamics of lipids and proteins. These experimental and data analysis methods differ in equipment requirements, labeling complexities, and further oftentimes give different results. It would therefore be very convenient to have a single method that is flexible in the choice of fluorescent label and labeling densities from single molecules to ensemble measurements, that can be performed on a conventional wide-field microscope, and that is suitable for fast and accurate analysis. In this work we show that k-space image correlation spectroscopy (kICS) analysis, a technique which was originally developed for analyzing lateral dynamics in samples that are labeled at high densities, can also be used for fast and accurate analysis of single molecule density data of lipids and proteins labeled with quantum dots (QDs). We have further used kICS to investigate the effect of the label size and by comparing the results for a biotinylated lipid labeled at high densities with Atto647N-strepatvidin (sAv) or sparse densities with sAv-QDs. In this latter case, we see that the recovered diffusion rate is two-fold greater for the same lipid and in the same cell-type when labeled with Atto647N-sAv as compared to sAv-QDs. This data demonstrates that kICS can be used for analysis of single molecule data and furthermore can bridge between samples with a labeling densities ranging from single molecule to ensemble level measurements.
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Affiliation(s)
- Eva C. Arnspang
- Department of Physics, Chemistry and Pharmacy, MEMPHYS-Center for Biomembrane Physics & DaMBIC – Danish Molecular Biomedical Imaging Center, University of Southern Denmark, Odense, Denmark
| | | | - Mathias P. Clausen
- Department of Physics, Chemistry and Pharmacy, MEMPHYS-Center for Biomembrane Physics & DaMBIC – Danish Molecular Biomedical Imaging Center, University of Southern Denmark, Odense, Denmark
| | - Paul W. Wiseman
- Department of Physics and Department of Chemistry, McGill University, Montreal, Canada
| | - B. Christoffer Lagerholm
- Department of Physics, Chemistry and Pharmacy, MEMPHYS-Center for Biomembrane Physics & DaMBIC – Danish Molecular Biomedical Imaging Center, University of Southern Denmark, Odense, Denmark
- * E-mail:
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28
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Lin J, Countryman P, Buncher N, Kaur P, E L, Zhang Y, Gibson G, You C, Watkins SC, Piehler J, Opresko PL, Kad NM, Wang H. TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres. Nucleic Acids Res 2013; 42:2493-504. [PMID: 24271387 PMCID: PMC3936710 DOI: 10.1093/nar/gkt1132] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Human telomeres are maintained by the shelterin protein complex in which TRF1 and TRF2 bind directly to duplex telomeric DNA. How these proteins find telomeric sequences among a genome of billions of base pairs and how they find protein partners to form the shelterin complex remains uncertain. Using single-molecule fluorescence imaging of quantum dot-labeled TRF1 and TRF2, we study how these proteins locate TTAGGG repeats on DNA tightropes. By virtue of its basic domain TRF2 performs an extensive 1D search on nontelomeric DNA, whereas TRF1’s 1D search is limited. Unlike the stable and static associations observed for other proteins at specific binding sites, TRF proteins possess reduced binding stability marked by transient binding (∼9–17 s) and slow 1D diffusion on specific telomeric regions. These slow diffusion constants yield activation energy barriers to sliding ∼2.8–3.6 κBT greater than those for nontelomeric DNA. We propose that the TRF proteins use 1D sliding to find protein partners and assemble the shelterin complex, which in turn stabilizes the interaction with specific telomeric DNA. This ‘tag-team proofreading’ represents a more general mechanism to ensure a specific set of proteins interact with each other on long repetitive specific DNA sequences without requiring external energy sources.
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Affiliation(s)
- Jiangguo Lin
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA, Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA, Electric and Computer Engineering Department, University of North Carolina at Charlotte, Charlotte, NC 28223, USA, Department of Industrial and System Engineering, North Carolina State University, Raleigh, NC 27695, USA, Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA, Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076, Osnabrück, Germany and School of Biological Sciences, University of Essex, Colchester, Essex CO4 3SQ UK
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29
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Clausen MP, Lagerholm BC. Visualization of plasma membrane compartmentalization by high-speed quantum dot tracking. NANO LETTERS 2013; 13:2332-7. [PMID: 23647479 DOI: 10.1021/nl303151f] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In this study, we have imaged plasma membrane molecules labeled with quantum dots in live cells using a conventional wide-field microscope with high spatial precision at sampling frequencies of 1.75 kHz. Many of the resulting single molecule trajectories are sufficiently long (up to several thousand steps) to allow for robust single trajectory analysis. This analysis indicates that a majority of the investigated molecules are transiently confined in nanoscopic compartments with a mean size of (100–150 nm)(2) for a mean duration of 50–100 ms.
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Affiliation(s)
- Mathias P Clausen
- MEMPHYS − Center for Biomembrane Physics and DaMBIC − Danish Molecular Biomedical Imaging Center, University of Southern Denmark, DK-5230 Odense M, Denmark
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30
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Multi-color quantum dot tracking using a high-speed hyperspectral line-scanning microscope. PLoS One 2013; 8:e64320. [PMID: 23717596 PMCID: PMC3661486 DOI: 10.1371/journal.pone.0064320] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/11/2013] [Indexed: 12/12/2022] Open
Abstract
Many cellular signaling processes are initiated by dimerization or oligomerization of membrane proteins. However, since the spatial scale of these interactions is below the diffraction limit of the light microscope, the dynamics of these interactions have been difficult to study on living cells. We have developed a novel high-speed hyperspectral microscope (HSM) to perform single particle tracking of up to 8 spectrally distinct species of quantum dots (QDs) at 27 frames per second. The distinct emission spectra of the QDs allows localization with ∼10 nm precision even when the probes are clustered at spatial scales below the diffraction limit. The capabilities of the HSM are demonstrated here by application of multi-color single particle tracking to observe membrane protein behavior, including: 1) dynamic formation and dissociation of Epidermal Growth Factor Receptor dimers; 2) resolving antigen induced aggregation of the high affinity IgE receptor, FcεR1; 3) four color QD tracking while simultaneously visualizing GFP-actin; and 4) high-density tracking for fast diffusion mapping.
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31
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Chen EH, Gaathon O, Trusheim ME, Englund D. Wide-field multispectral super-resolution imaging using spin-dependent fluorescence in nanodiamonds. NANO LETTERS 2013; 13:2073-2077. [PMID: 23547791 DOI: 10.1021/nl400346k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recent advances in fluorescence microscopy have enabled spatial resolution below the diffraction limit by localizing multiple temporally or spectrally distinguishable fluorophores. Here, we introduce a super-resolution technique that deterministically controls the brightness of uniquely addressable, photostable emitters. We modulate the fluorescence brightness of negatively charged nitrogen-vacancy (NV(-)) centers in nanodiamonds through magnetic resonance techniques. Using a CCD camera, this "deterministic emitter switch microscopy" (DESM) technique enables super-resolution imaging with localization down to 12 nm across a 35 × 35 μm(2) area. DESM is particularly well suited for biological applications such as multispectral particle tracking since fluorescent nanodiamonds are not only cytocompatible but also nonbleaching and bright. We observe fluorescence count rates exceeding 1.5 × 10(6) photons per second from single NV(-) centers at saturation. When combined with emerging NV(-)-based techniques for sensing magnetic and electric fields, DESM opens the door to rapid, super-resolution imaging for tracking and sensing applications in the life and physical sciences.
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Affiliation(s)
- Edward H Chen
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
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Rasmussen TE, Jauffred L, Brewer J, Vogel S, Torbensen ER, Lagerholm BC, Oddershede L, Arnspang EC. Single Molecule Applications of Quantum Dots. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/jmp.2013.411a2002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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