1
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Shahu S, Vtyurina N, Das M, Meyer AS, Ganji M, Abbondanzieri EA. Bridging DNA contacts allow Dps from E. coli to condense DNA. Nucleic Acids Res 2024; 52:4456-4465. [PMID: 38572752 DOI: 10.1093/nar/gkae223] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/03/2023] [Revised: 03/08/2024] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
The DNA-binding protein from starved cells (Dps) plays a crucial role in maintaining bacterial cell viability during periods of stress. Dps is a nucleoid-associated protein that interacts with DNA to create biomolecular condensates in live bacteria. Purified Dps protein can also rapidly form large complexes when combined with DNA in vitro. However, the mechanism that allows these complexes to nucleate on DNA remains unclear. Here, we examine how DNA topology influences the formation of Dps-DNA complexes. We find that DNA supercoils offer the most preferred template for the nucleation of condensed Dps structures. More generally, bridging contacts between different regions of DNA can facilitate the nucleation of condensed Dps structures. In contrast, Dps shows little affinity for stretched linear DNA before it is relaxed. Once DNA is condensed, Dps forms a stable complex that can form inter-strand contacts with nearby DNA, even without free Dps present in solution. Taken together, our results establish the important role played by bridging contacts between DNA strands in nucleating and stabilizing Dps complexes.
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Affiliation(s)
- Sneha Shahu
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Anne S Meyer
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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2
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Unterauer EM, Shetab Boushehri S, Jevdokimenko K, Masullo LA, Ganji M, Sograte-Idrissi S, Kowalewski R, Strauss S, Reinhardt SCM, Perovic A, Marr C, Opazo F, Fornasiero EF, Jungmann R. Spatial proteomics in neurons at single-protein resolution. Cell 2024; 187:1785-1800.e16. [PMID: 38552614 DOI: 10.1016/j.cell.2024.02.045] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/28/2023] [Accepted: 02/29/2024] [Indexed: 04/02/2024]
Abstract
To understand biological processes, it is necessary to reveal the molecular heterogeneity of cells by gaining access to the location and interaction of all biomolecules. Significant advances were achieved by super-resolution microscopy, but such methods are still far from reaching the multiplexing capacity of proteomics. Here, we introduce secondary label-based unlimited multiplexed DNA-PAINT (SUM-PAINT), a high-throughput imaging method that is capable of achieving virtually unlimited multiplexing at better than 15 nm resolution. Using SUM-PAINT, we generated 30-plex single-molecule resolved datasets in neurons and adapted omics-inspired analysis for data exploration. This allowed us to reveal the complexity of synaptic heterogeneity, leading to the discovery of a distinct synapse type. We not only provide a resource for researchers, but also an integrated acquisition and analysis workflow for comprehensive spatial proteomics at single-protein resolution.
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Affiliation(s)
- Eduard M Unterauer
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sayedali Shetab Boushehri
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Data & Analytics, Roche Pharma Research and Early Development, Roche Innovation Center Munich, Munich, Germany; Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Kristina Jevdokimenko
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Mahipal Ganji
- Max Planck Institute of Biochemistry, Planegg, Germany; Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Shama Sograte-Idrissi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany; Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Rafal Kowalewski
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sebastian Strauss
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Susanne C M Reinhardt
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany
| | - Ana Perovic
- Max Planck Institute of Biochemistry, Planegg, Germany
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Department of Mathematics, Technical University of Munich, Munich, Germany
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany; Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany; NanoTag Biotechnologies GmbH, Göttingen, Germany
| | - Eugenio F Fornasiero
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany; Department of Life Sciences, University of Trieste, Trieste, Italy.
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Planegg, Germany; Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität, Munich, Germany.
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3
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Shahu S, Vtyurina N, Das M, Meyer AS, Ganji M, Abbondanzieri EA. Bridging DNA contacts allow Dps from E. coli to condense DNA. bioRxiv 2024:2024.01.22.576774. [PMID: 38328146 PMCID: PMC10849575 DOI: 10.1101/2024.01.22.576774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The DNA-binding protein from starved cells (Dps) plays a crucial role in maintaining bacterial cell viability during periods of stress. Dps is a nucleoid-associated protein that interacts with DNA to create biomolecular condensates in live bacteria. Purified Dps protein can also rapidly form large complexes when combined with DNA in vitro. However, the mechanism that allows these complexes to nucleate on DNA remains unclear. Here, we examine how DNA topology influences the formation of Dps-DNA complexes. We find that DNA supercoils offer the most preferred template for the nucleation of condensed Dps structures. More generally, bridging contacts between different regions of DNA can facilitate the nucleation of condensed Dps structures. In contrast, Dps shows little affinity for stretched linear DNA before it is relaxed. Once DNA is condensed, Dps forms a stable complex that can form inter-strand contacts with nearby DNA, even without free Dps present in solution. Taken together, our results establish the important role played by bridging contacts between DNA strands in nucleating and stabilizing Dps complexes.
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Affiliation(s)
- Sneha Shahu
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY, 14623
| | - Anne S. Meyer
- Department of Biology, University of Rochester, Rochester, NY, 14627
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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4
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Banerjee A, Anand M, Kalita S, Ganji M. Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures. Nat Nanotechnol 2023; 18:1474-1482. [PMID: 37591937 PMCID: PMC10716042 DOI: 10.1038/s41565-023-01485-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 12/13/2022] [Accepted: 07/10/2023] [Indexed: 08/19/2023]
Abstract
The DNA double helix structure is stabilized by base-pairing and base-stacking interactions. However, a comprehensive understanding of dinucleotide base-stacking energetics is lacking. Here we combined multiplexed DNA-based point accumulation in nanoscale topography (DNA-PAINT) imaging with designer DNA nanostructures and measured the free energy of dinucleotide base stacking at the single-molecule level. Multiplexed imaging enabled us to extract the binding kinetics of an imager strand with and without additional dinucleotide stacking interactions. The DNA-PAINT data showed that a single additional dinucleotide base stacking results in up to 250-fold stabilization for the DNA duplex nanostructure. We found that the dinucleotide base-stacking energies vary from -0.95 ± 0.12 kcal mol-1 to -3.22 ± 0.04 kcal mol-1 for C|T and A|C base-stackings, respectively. We demonstrate the application of base-stacking energetics in designing DNA-PAINT probes for multiplexed super-resolution imaging, and efficient assembly of higher-order DNA nanostructures. Our results will aid in designing functional DNA nanostructures, and DNA and RNA aptamers, and facilitate better predictions of the local DNA structure.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Simanta Kalita
- New Chemistry Unit and Chemistry and Physics of Materials Unit, The Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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5
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Abstract
Super-resolution imaging is becoming a commonly employed tool to visualize biological targets in unprecedented detail. DNA-PAINT is one of the single-molecule localization microscopy-based super-resolution imaging modalities allowing the ultra-high-resolution imaging with superior multiplexing capabilities. We discuss the importance of patterned DNA nanostructures in demonstrating the capabilities of DNA-PAINT and the design of various combinations of imager-docking strand pairs for imaging. Central to the implementation of DNA-PAINT imaging in a biological context is the generation of docking strand-conjugated binders against the target molecules. Several researchers have developed a variety of labelling probes for improving resolution while also providing multiplexing capabilities for the broader application of DNA-PAINT. This review provides a comprehensive summary of the repertoire of labelling probes used for DNA-PAINT in cells and the strategies implemented to chemically modify them with a docking strand.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
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6
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Ganji M, Schlichthaerle T, Eklund AS, Strauss S, Jungmann R. Quantitative Assessment of Labeling Probes for Super-Resolution Microscopy Using Designer DNA Nanostructures. Chemphyschem 2021; 22:911-914. [PMID: 33720501 PMCID: PMC8251534 DOI: 10.1002/cphc.202100185] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 12/22/2022]
Abstract
Improving labeling probes for state-of-the-art super-resolution microscopy is becoming of major importance. However, there is currently a lack of tools to quantitatively evaluate probe performance regarding efficiency, precision, and achievable resolution in an unbiased yet modular fashion. Herein, we introduce designer DNA origami structures combined with DNA-PAINT to overcome this issue and evaluate labeling efficiency, precision, and quantification using antibodies and nanobodies as exemplary labeling probes. Whereas current assessment of binders is mostly qualitative, e. g. based on an expected staining pattern, we herein present a quantitative analysis platform of the antigen labeling efficiency and achievable resolution, allowing researchers to choose the best performing binder. The platform can furthermore be readily adapted for discovery and precise quantification of a large variety of additional labeling probes.
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Affiliation(s)
- Mahipal Ganji
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Current Address: Department of Biochemistry, Indian Institute of Science, CV Raman Road, 560012, Bengaluru, India
| | - Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Current Address: Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexandra S Eklund
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Sebastian Strauss
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
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7
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Ruiz J, Kandah F, Ganji M, Goswami R. The First Reported Case of COVID-19 Myocarditis Managed with Biventricular Impella Support. J Heart Lung Transplant 2021. [PMCID: PMC7979384 DOI: 10.1016/j.healun.2021.01.2079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Introduction SARS-CoV-2, responsible for COVID-19, is a pandemic that has taken the world by storm. We present the only contemporary reported case of COVID-19 myocarditis leading to recovery with utilization of biventricular impella for temporary mechanical circulatory support. No cases have been reported regarding utilization of Bi-V impella as therapy for management of SARS-CoV-2.. Case Report We present a 35 year old-woman with history of systemic sclerosis who was found to have 5 days of generalized malaise associated with fevers and cough. On arrival she was found tachycardic at 112 bpm and febrile 101.8 F. She tested positive for COVID-19 via nasal CPR. Cardiac enzymes were found elevated on admission with troponin T elevated at 0.28. On day two of hospitalization patient had spontaneous PEA arrest secondary to hypoxemia. Transthoracic echocardiogram(TTE) revealed EF <10% and RV impairment which compare to prior which had normal ejection fraction. Labs showed elevated lactic acidosis of 10. Invasive hemodynamics assessment RA 21 mmHg, PA 32/23(mean 26 mmHg) and PCWP 18 mmHg. Calculated PAPi 0.76, CO 2.1 L/min and CI of 1.2 L/min/m^2. Decision was made to place right and left sided ventricular impellas for mechanical circulatory support. She was started on IVIG for COVID-19 myocarditis along with remdesivir and solumedrol. After two weeks of continuous temporary mechanical circulatory support(TMCS), patient hemodynamics improved and she was able to be weaned from her need for TMCS. Repeat echocardiogram demonstrated recovery and remodeling with an LVEF of 60% and no significant valvular disease. She was discharge home at day 23 with no neurological deficit. Summary The use of biventricular continuous microaxial flow devices during acute COVID-19 myocarditis is key to allow ventricular rest and optimal offloading without the increased risk of surgically placed TMCS such as Centrimag or VA or VV ECMO. With recent emergency use by the FDA, its wide adaptation remains sparse. Our case demonstrates a unique approach to management of COVID-19 myocarditis. It is the only reported case in the literature utilizing biventricular Impella devices for circulatory support without the concurrent use of ECMO. Due to the success in this patient, this promising approach warrants continued investigation in the management of COVID myocarditis and cardiogenic shock.
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8
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Schueder F, Unterauer EM, Ganji M, Jungmann R. Front Cover: DNA‐Barcoded Fluorescence Microscopy for Spatial Omics. Proteomics 2020. [DOI: 10.1002/pmic.202070161] [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: 11/05/2022]
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9
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Schueder F, Unterauer EM, Ganji M, Jungmann R. DNA-Barcoded Fluorescence Microscopy for Spatial Omics. Proteomics 2020; 20:e1900368. [PMID: 33030780 DOI: 10.1002/pmic.201900368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/24/2020] [Indexed: 12/18/2022]
Abstract
Innovation in genomics, transcriptomics, and proteomics research has created a plethora of state-of-the-art techniques such as nucleic acid sequencing and mass-spectrometry-based proteomics with paramount impact in the life sciences. While current approaches yield quantitative abundance analysis of biomolecules on an almost routine basis, coupling this high content to spatial information in a single cell and tissue context is challenging. Here, current implementations of spatial omics are discussed and recent developments in the field of DNA-barcoded fluorescence microscopy are reviewed. Light is shed on the potential of DNA-based imaging techniques to provide a comprehensive toolbox for spatial genomics and transcriptomics and discuss current challenges, which need to be overcome on the way to spatial proteomics using high-resolution fluorescence microscopy.
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Affiliation(s)
- Florian Schueder
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Eduard M Unterauer
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Mahipal Ganji
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Ralf Jungmann
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, Munich, 80539, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
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10
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Eklund A, Ganji M, Gavins G, Seitz O, Jungmann R. Peptide-PAINT Super-Resolution Imaging Using Transient Coiled Coil Interactions. Nano Lett 2020; 20:6732-6737. [PMID: 32787168 PMCID: PMC7496730 DOI: 10.1021/acs.nanolett.0c02620] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/26/2020] [Indexed: 05/24/2023]
Abstract
Super-resolution microscopy is transforming research in the life sciences by enabling the visualization of structures and interactions on the nanoscale. DNA-PAINT is a relatively easy-to-implement single-molecule-based technique, which uses the programmable and transient interaction of dye-labeled oligonucleotides with their complements for super-resolution imaging. However, similar to many imaging approaches, it is still hampered by the subpar performance of labeling probes in terms of their large size and limited labeling efficiency. To overcome this, we here translate the programmability and transient binding nature of DNA-PAINT to coiled coil interactions of short peptides and introduce Peptide-PAINT. We benchmark and optimize its binding kinetics in a single-molecule assay and demonstrate its super-resolution capability using self-assembled DNA origami structures. Peptide-PAINT outperforms classical DNA-PAINT in terms of imaging speed and efficiency. Finally, we prove the suitability of Peptide-PAINT for cellular super-resolution imaging by visualizing the microtubule and vimentin network in fixed cells.
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Affiliation(s)
- Alexandra
S. Eklund
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max
Planck Institute of Biochemistry, Martinsried, Germany
| | - Mahipal Ganji
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max
Planck Institute of Biochemistry, Martinsried, Germany
| | - Georgina Gavins
- Institute
of Chemistry, Humboldt University, Berlin, Germany
| | - Oliver Seitz
- Institute
of Chemistry, Humboldt University, Berlin, Germany
| | - Ralf Jungmann
- Faculty
of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max
Planck Institute of Biochemistry, Martinsried, Germany
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11
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Elbatsh AMO, Kim E, Eeftens JM, Raaijmakers JA, van der Weide RH, García-Nieto A, Bravo S, Ganji M, Uit de Bos J, Teunissen H, Medema RH, de Wit E, Haering CH, Dekker C, Rowland BD. Distinct Roles for Condensin's Two ATPase Sites in Chromosome Condensation. Mol Cell 2019; 76:724-737.e5. [PMID: 31629658 PMCID: PMC6900782 DOI: 10.1016/j.molcel.2019.09.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/17/2019] [Accepted: 09/13/2019] [Indexed: 01/19/2023]
Abstract
Condensin is a conserved SMC complex that uses its ATPase machinery to structure genomes, but how it does so is largely unknown. We show that condensin's ATPase has a dual role in chromosome condensation. Mutation of one ATPase site impairs condensation, while mutating the second site results in hyperactive condensin that compacts DNA faster than wild-type, both in vivo and in vitro. Whereas one site drives loop formation, the second site is involved in the formation of more stable higher-order Z loop structures. Using hyperactive condensin I, we reveal that condensin II is not intrinsically needed for the shortening of mitotic chromosomes. Condensin II rather is required for a straight chromosomal axis and enables faithful chromosome segregation by counteracting the formation of ultrafine DNA bridges. SMC complexes with distinct roles for each ATPase site likely reflect a universal principle that enables these molecular machines to intricately control chromosome architecture.
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Affiliation(s)
- Ahmed M O Elbatsh
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Eugene Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jorine M Eeftens
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jonne A Raaijmakers
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Robin H van der Weide
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alberto García-Nieto
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Sol Bravo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Mahipal Ganji
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jelmi Uit de Bos
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Christian H Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
| | - Benjamin D Rowland
- Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands.
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12
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Wade O, Woehrstein JB, Nickels PC, Strauss S, Stehr F, Stein J, Schueder F, Strauss MT, Ganji M, Schnitzbauer J, Grabmayr H, Yin P, Schwille P, Jungmann R. 124-Color Super-resolution Imaging by Engineering DNA-PAINT Blinking Kinetics. Nano Lett 2019; 19:2641-2646. [PMID: 30864449 PMCID: PMC6463241 DOI: 10.1021/acs.nanolett.9b00508] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [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: 02/04/2019] [Revised: 02/20/2019] [Indexed: 05/20/2023]
Abstract
Optical super-resolution techniques reach unprecedented spatial resolution down to a few nanometers. However, efficient multiplexing strategies for the simultaneous detection of hundreds of molecular species are still elusive. Here, we introduce an entirely new approach to multiplexed super-resolution microscopy by designing the blinking behavior of targets with engineered binding frequency and duration in DNA-PAINT. We assay this kinetic barcoding approach in silico and in vitro using DNA origami structures, show the applicability for multiplexed RNA and protein detection in cells, and finally experimentally demonstrate 124-plex super-resolution imaging within minutes.
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Affiliation(s)
- Orsolya
K. Wade
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Johannes B. Woehrstein
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Philipp C. Nickels
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Sebastian Strauss
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Florian Stehr
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Johannes Stein
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Florian Schueder
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Maximilian T. Strauss
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Mahipal Ganji
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Joerg Schnitzbauer
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Heinrich Grabmayr
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Peng Yin
- Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02138, United States
- Department
of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Petra Schwille
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ralf Jungmann
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
- E-mail: . Phone: +49
89 8578 3410
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13
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Schlichthaerle T, Ganji M, Auer A, Kimbu Wade O, Jungmann R. Bacterially Derived Antibody Binders as Small Adapters for DNA-PAINT Microscopy. Chembiochem 2019; 20:1032-1038. [PMID: 30589198 DOI: 10.1002/cbic.201800743] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/21/2022]
Abstract
Current optical super-resolution implementations are capable of resolving features spaced just a few nanometers apart. However, translating this spatial resolution to cellular targets is limited by the large size of traditionally employed primary and secondary antibody reagents. Recent advancements in small and efficient protein binders for super-resolution microscopy, such as nanobodies or aptamers, provide an exciting avenue for the future; however, their widespread availability is still limited. To address this issue, here we report the combination of bacterial-derived binders commonly used in antibody purification with DNA-based point accumulation for imaging in nanoscale topography (DNA-PAINT) microscopy. The small sizes of these protein binders, relative to secondary antibodies, make them an attractive labeling alternative for emerging superresolution techniques. We present here a labeling protocol for DNA conjugation of bacterially derived proteins A and G for DNA-PAINT, having assayed their intracellular performance by targeting primary antibodies against tubulin, TOM20, and the epidermal growth factor receptor (EGFR) and quantified the increases in obtainable resolution.
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Affiliation(s)
- Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Mahipal Ganji
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Alexander Auer
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Orsolya Kimbu Wade
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.,Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
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14
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Abstract
The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes (extended intertwined DNA structures formed upon supercoiling) on individual DNA molecules. Remarkably, our experiments show that the DNA sequence directly encodes the structure of supercoiled DNA by pinning plectonemes at specific sequences. We develop a physical model that predicts that sequence-dependent intrinsic curvature is the key determinant of pinning strength and demonstrate this simple model provides very good agreement with the data. Analysis of several prokaryotic genomes indicates that plectonemes localize directly upstream of promoters, which we experimentally confirm for selected promotor sequences. Our findings reveal a hidden code in the genome that helps to spatially organize the chromosomal DNA.
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Affiliation(s)
- Sung Hyun Kim
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Mahipal Ganji
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Eugene Kim
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Jaco van der Torre
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Elio Abbondanzieri
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Cees Dekker
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
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15
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Ketterer P, Ananth AN, Laman Trip DS, Mishra A, Bertosin E, Ganji M, van der Torre J, Onck P, Dietz H, Dekker C. DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex. Nat Commun 2018; 9:902. [PMID: 29500415 PMCID: PMC5834454 DOI: 10.1038/s41467-018-03313-w] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [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: 11/06/2017] [Accepted: 02/02/2018] [Indexed: 11/09/2022] Open
Abstract
The nuclear pore complex (NPC) is the gatekeeper for nuclear transport in eukaryotic cells. A key component of the NPC is the central shaft lined with intrinsically disordered proteins (IDPs) known as FG-Nups, which control the selective molecular traffic. Here, we present an approach to realize artificial NPC mimics that allows controlling the type and copy number of FG-Nups. We constructed 34 nm-wide 3D DNA origami rings and attached different numbers of NSP1, a model yeast FG-Nup, or NSP1-S, a hydrophilic mutant. Using (cryo) electron microscopy, we find that NSP1 forms denser cohesive networks inside the ring compared to NSP1-S. Consistent with this, the measured ionic conductance is lower for NSP1 than for NSP1-S. Molecular dynamics simulations reveal spatially varying protein densities and conductances in good agreement with the experiments. Our technique provides an experimental platform for deciphering the collective behavior of IDPs with full control of their type and position.
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Affiliation(s)
- Philip Ketterer
- Physik Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, Garching bei München, D-85748, Germany
| | - Adithya N Ananth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Diederik S Laman Trip
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Ankur Mishra
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Eva Bertosin
- Physik Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, Garching bei München, D-85748, Germany
| | - Mahipal Ganji
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Patrick Onck
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Hendrik Dietz
- Physik Department and Institute for Advanced Study, Technische Universität München, Am Coulombwall 4a, Garching bei München, D-85748, Germany.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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16
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Ganji M, Shaltiel IA, Bisht S, Kim E, Kalichava A, Haering CH, Dekker C. Real-time imaging of DNA loop extrusion by condensin. Science 2018; 360:102-105. [PMID: 29472443 DOI: 10.1126/science.aar7831] [Citation(s) in RCA: 428] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 02/06/2018] [Indexed: 12/30/2022]
Abstract
It has been hypothesized that SMC protein complexes such as condensin and cohesin spatially organize chromosomes by extruding DNA into large loops. We directly visualized the formation and processive extension of DNA loops by yeast condensin in real time. Our findings constitute unambiguous evidence for loop extrusion. We observed that a single condensin complex is able to extrude tens of kilobase pairs of DNA at a force-dependent speed of up to 1500 base pairs per second, using the energy of adenosine triphosphate hydrolysis. Condensin-induced loop extrusion was strictly asymmetric, which demonstrates that condensin anchors onto DNA and reels it in from only one side. Active DNA loop extrusion by SMC complexes may provide the universal unifying principle for genome organization.
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Affiliation(s)
- Mahipal Ganji
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Indra A Shaltiel
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shveta Bisht
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eugene Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Ana Kalichava
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Christian H Haering
- Cell Biology and Biophysics Unit, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands.
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17
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18
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Affiliation(s)
- M. Ganji
- Department of Statistics, University of Mohaghegh Ardabili, Ardabil, Iran
| | - F. Gharari
- Department of Statistics, University of Mohaghegh Ardabili, Ardabil, Iran
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19
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Hyun Kim S, Ganji M, van der Torre J, Abbondanzieri E, Dekker C. DNA Sequence can Pin the Position of DNA Supercoils. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1182] [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: 10/20/2022] Open
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20
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Ganji M, Docter M, Le Grice SFJ, Abbondanzieri EA. DNA binding proteins explore multiple local configurations during docking via rapid rebinding. Nucleic Acids Res 2016; 44:8376-84. [PMID: 27471033 PMCID: PMC5041478 DOI: 10.1093/nar/gkw666] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/12/2016] [Indexed: 12/15/2022] Open
Abstract
Finding the target site and associating in a specific orientation are essential tasks for DNA-binding proteins. In order to make the target search process as efficient as possible, proteins should not only rapidly diffuse to the target site but also dynamically explore multiple local configurations before diffusing away. Protein flipping is an example of this second process that has been observed previously, but the underlying mechanism of flipping remains unclear. Here, we probed the mechanism of protein flipping at the single molecule level, using HIV-1 reverse transcriptase (RT) as a model system. In order to test the effects of long-range attractive forces on flipping efficiency, we varied the salt concentration and macromolecular crowding conditions. As expected, increased salt concentrations weaken the binding of RT to DNA while increased crowding strengthens the binding. Moreover, when we analyzed the flipping kinetics, i.e. the rate and probability of flipping, at each condition we found that flipping was more efficient when RT bound more strongly. Our data are consistent with a view that DNA bound proteins undergo multiple rapid re-binding events, or short hops, that allow the protein to explore other configurations without completely dissociating from the DNA.
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Affiliation(s)
- Mahipal Ganji
- Kavli Institute of Nanoscience, Department of Bionanoscience, TU Delft, 2629HZ, Delft, The Netherlands
| | - Margreet Docter
- Kavli Institute of Nanoscience, Department of Bionanoscience, TU Delft, 2629HZ, Delft, The Netherlands
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Elio A Abbondanzieri
- Kavli Institute of Nanoscience, Department of Bionanoscience, TU Delft, 2629HZ, Delft, The Netherlands
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21
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Ganji M, Kim SH, van der Torre J, Abbondanzieri E, Dekker C. Intercalation-Based Single-Molecule Fluorescence Assay To Study DNA Supercoil Dynamics. Nano Lett 2016; 16:4699-4707. [PMID: 27356180 DOI: 10.1021/acs.nanolett.6b02213] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [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: 06/06/2023]
Abstract
DNA supercoiling crucially affects cellular processes such as DNA replication, gene expression, and chromatin organization. However, mechanistic understanding of DNA supercoiling and the related DNA-processing enzymes has remained limited, mainly due to the lack of convenient experimental tools to probe these phenomena. Here, we report a novel high-throughput single-molecule assay for real-time visualization of supercoiled DNA molecules, named ISD (Intercalation-induced Supercoiling of DNA). We use an intercalating dye to induce supercoiling of surface-attached DNA molecules as well as to visualize coiled-loop structures (i.e., plectonemes) formed on DNA. The technique is solely based on epifluorescence microscopy and requires no mechanical manipulation of the DNA molecules. This new assay allows to track positions and sizes of individual plectonemes and characterize their position-dependent dynamics such as nucleation, termination, and diffusion. We describe the ISD technique and demonstrate its potential by establishing that plectonemes are pinned to a local 10-nucleotide long mispaired sequence along a double-stranded DNA molecule.
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Affiliation(s)
- Mahipal Ganji
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology , Van der Maasweg 9, Delft, 2629HZ, The Netherlands
| | - Sung Hyun Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology , Van der Maasweg 9, Delft, 2629HZ, The Netherlands
| | - Jaco van der Torre
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology , Van der Maasweg 9, Delft, 2629HZ, The Netherlands
| | - Elio Abbondanzieri
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology , Van der Maasweg 9, Delft, 2629HZ, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology , Van der Maasweg 9, Delft, 2629HZ, The Netherlands
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22
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Hyun Kim S, Ganji M, van J, Torre D, Abbondanzieri E, Dekker C. The Occurrence of Plectonemes in Supercoiled DNA Depends on DNA Sequence. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.3013] [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: 10/22/2022] Open
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23
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Ganji M, Docter M, Le Grice SF, Abbondanzieri E. Flipping by DNA Bound Proteins Occurs through Rapid Rebinding. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2752] [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: 10/22/2022] Open
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24
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Ghanadzadeh H, Fallahi S, Ganji M. Liquid–Liquid Equilibrium Calculation for Ternary Aqueous Mixtures of Ethanol and Acetic Acid with 2-Ethyl-1-hexanol Using the GMDH-Type Neural Network. Ind Eng Chem Res 2011. [DOI: 10.1021/ie101425w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- H. Ghanadzadeh
- Department of Chemical Engineering, University of Guilan, Rasht, Iran
| | - S. Fallahi
- Department of Mathematics, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - M. Ganji
- Department of Mathematics, Faculty of Sciences, University of Guilan, Rasht, Iran
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Ghaninejad H, Ehsani AH, Ghiasi M, Noormohammadpour P, Najafi E, Naderi G, Ganji M, Mirnezami M, Nezami R, Kiani P. Benign and malignant skin lesions in renal transplant recipients. Indian J Dermatol 2009; 54:247-50. [PMID: 20161856 PMCID: PMC2810691 DOI: 10.4103/0019-5154.55634] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [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: 11/04/2022] Open
Abstract
BACKGROUND Skin lesions - benign and malignant - occur frequently in organ transplant recipients receiving long-term immunosuppressive therapy. These patients are at greater risk of skin cancers. AIMS To study dermatologic problems in renal transplant recipients (RTRs). METHODS One hundred patients (53 men and 47 women) were consecutively examined for benign and malignant skin complications since transplantation in Razi Hospital in Tehran Medical University. The main immunosuppressive therapy regimen in these patients was a combination of prednisolone, azathioprine, and cyclosporine. RESULTS The early and most common complication was cosmetic side effects that occurred in 98% patients. Skin infections occurred in 83% of the patients and most of them were viral infections (65%), especially of human papilloma viruses (HPVs) in 40% of the patients. We found six cases of malignancy in these patients in that four cases were skin cancers, including one case of SCC, one BCC, and two cases of Kaposi's sarcoma. Dermatologic problems occur most frequently in RTRs, especially skin cancers which have higher frequency in these patients than general population, particularly, Kaposi sarcoma. Sun exposure has an important role in developing epithelial skin cancers following transplantation. The age of developing skin cancer in these patients was early than normal population. CONCLUSION Our results emphasize the importance of dermatologic examinations and monitoring RTRs to obtain an early diagnosis and treatment of cutaneous manifestations.
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Affiliation(s)
- H Ghaninejad
- From the Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - A H Ehsani
- From the Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - M Ghiasi
- From the Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - P Noormohammadpour
- From the Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - E Najafi
- From the Department of Nephrology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - G Naderi
- From the Department of Nephrology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - M Ganji
- From the Department of Nephrology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - M Mirnezami
- From the Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - R Nezami
- From the Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran.
| | - P Kiani
- From the Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran.
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