1
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Golubewa L, Timoshchenko I, Kulahava T. Specificity of carbon nanotube accumulation and distribution in cancer cells revealed by K-means clustering and principal component analysis of Raman spectra. Analyst 2024; 149:2680-2696. [PMID: 38497436 DOI: 10.1039/d3an02078a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Single-walled carbon nanotubes (SWCNTs) show great potential for their application as cancer therapeutic nanodrugs, but the efficiency and mechanism of their accumulation in the cell, the modulation of cell activity, and the strong dependence of the results on the type of capping molecule still hinder the transfer of SWCNTs to the clinic. In the present study, we determined the mechanism and sequence of accumulation, distribution and type discrimination of SWCNTs in glioma cells by applying K-means clustering and principal component analysis (PCA) of Raman spectra of cells exposed to SWCNTs capped with either DNA or oligonucleotides (ON). Based on the specific biochemical information uncovered by PCA and further applied to K-means, we show that the accumulation of SWCNT-DNA occurs in two phases. The first phase involves the transport of SWCNT-DNA through vesicles and its redistribution in the cytoplasm, which is reflected in two SWCNT-related clusters. The second phase begins after 18 hours of interaction between cells and SWCNT-DNA. PCA shows the appearance of two SWCNT-associated PC loadings, reflected by the addition of a new cluster of SWCNTs with a narrowed and shifted G-peak in the spectra. It is caused by the loss of DNA capping and clumping of SWCNTs and triggered by the acidic conditions in autolysosomes resulting from the fusion of transport vesicles with lysosomes. SWCNTs penetrate all cellular compartments after 42-66 hours and lead to cell death. The clumped SWCNTs are released to the outside. In contrast, SWCNT-ON is hardly accumulated in glioma cells and after 72 hours of exposure to SWCNT-ON, the accumulation of SWCNTs corresponds to the first stage without reaching the second. PCA made it possible to separate the characteristics of cellular components against the high-intensity Raman signal from nanotubes and, thus, to propose the mechanism of accumulation and metabolism of nanomaterials in living cells without the use of additional research approaches. Our results elucidate the time dependence of the accumulation of SWCNTs on the capping molecule. We expect that our results can make an important contribution to the use of these nanomaterials in the clinic.
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Affiliation(s)
- Lena Golubewa
- Department of Molecular Compounds Physics, State Research Institute Centre for Physical Sciences and Technology, Saulėtekio av. 3, Vilnius, 10257, Lithuania.
| | - Igor Timoshchenko
- Department of Computer Modelling, Physics Faculty, Belarusian State University, Nezavisimosti av. 4, Minsk, 220030, Belarus
- Laboratory of Nanoelectromagnetics, Institute for Nuclear Problems of Belarusian State University, Bobruiskaya str. 11, Minsk, 220006, Belarus
| | - Tatsiana Kulahava
- Laboratory of Nanoelectromagnetics, Institute for Nuclear Problems of Belarusian State University, Bobruiskaya str. 11, Minsk, 220006, Belarus
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2
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Budassi J, Cho N, Del Valle A, Sokolov J. Microfluidic delivery of cutting enzymes for fragmentation of surface-adsorbed DNA molecules. PLoS One 2023; 18:e0250054. [PMID: 37672538 PMCID: PMC10482287 DOI: 10.1371/journal.pone.0250054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/24/2023] [Indexed: 09/08/2023] Open
Abstract
We describe a method for fragmenting, in-situ, surface-adsorbed and immobilized DNAs on polymethylmethacrylate(PMMA)-coated silicon substrates using microfluidic delivery of the cutting enzyme DNase I. Soft lithography is used to produce silicone elastomer (Sylgard 184) gratings which form microfluidic channels for delivery of the enzyme. Bovine serum albumin (BSA) is used to reduce DNase I adsorption to the walls of the microchannels and enable diffusion of the cutting enzyme to a distance of 10mm. Due to the DNAs being immobilized, the fragment order is maintained on the surface. Possible methods of preserving the order for application to sequencing are discussed.
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Affiliation(s)
- Julia Budassi
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York, United States of America
| | - NaHyun Cho
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York, United States of America
| | - Anthony Del Valle
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York, United States of America
| | - Jonathan Sokolov
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York, United States of America
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3
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Villacorta-Rath C, Lach L, Andrade-Rodriguez N, Burrows D, Gleeson D, Trujillo-González A. Invasive terrestrial invertebrate detection in water and soil using a targeted eDNA approach. NEOBIOTA 2023. [DOI: 10.3897/neobiota.83.98898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Terrestrial invasive invertebrates can rapidly colonise new areas, causing detrimental effects on biodiversity, economy and lifestyle. Targeted environmental DNA (eDNA) methods could constitute an early detection tool given their sensitivity to small numbers of individuals. We hypothesised that terrestrial runoff would transport eDNA from the land into adjacent waterbodies and used the invasive yellow crazy ant (Anoplolepis gracilipes) as a model species to test this hypothesis. We collected water samples from four waterbodies adjacent (< 10 m from the creek edge) to infestations following rainfall events for eDNA analysis. We also collected soil samples from areas of known infestations and tested five eDNA extraction methods to determine their efficiency to extract eDNA from soil. Water samples resulted in positive yellow crazy ant eDNA amplification (20–100% field replicates across all sites), even at one site located 300 m away from where ants had been detected visually. Soil samples resulted in a higher percentage of false negatives when sampled from ant transit areas than from nest entrances. Unpurified DNA extracts from soil also resulted in false negative detections and only after applying a purification step of DNA extracts, did we detect yellow crazy ant eDNA in 40–100% of field replicates across all methods and sites. This is the first study to empirically show that eDNA from a terrestrial invertebrate can be successfully isolated and amplified from adjacent or downstream waterbodies. Our results indicate that eDNA has the potential to be a useful method for detecting terrestrial invertebrates from soil and water.
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4
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Heo W, Seo J, Lee Y, Kim Y. Fluid-driven DNA stretching for single-molecule studies on chromatin-associated proteins. Biochem Biophys Res Commun 2022; 634:122-128. [DOI: 10.1016/j.bbrc.2022.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/28/2022]
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5
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Moore G, Jimenez Sainz J, Jensen RB. DNA fiber combing protocol using in-house reagents and coverslips to analyze replication fork dynamics in mammalian cells. STAR Protoc 2022; 3:101371. [PMID: 35573479 PMCID: PMC9092994 DOI: 10.1016/j.xpro.2022.101371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
DNA fiber combing is a versatile technique that provides insight into replication fork dynamics at single-molecule resolution. DNA fibers are bound to silanized coverslips and combed, which straightens and aligns the fibers along a single axis. Here, we present a DNA fiber combing protocol that does not use commercial kits; we detail the steps to prepare all materials, reagents, and silanized coverslips. We describe the use of DLD-1 cells, but the protocol is amenable to other cell types.
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Affiliation(s)
- Gemma Moore
- Department of Therapeutic Radiology, Yale University School of Medicine, 15 York Street, New Haven, CT 06520, USA
- Corresponding author
| | - Judit Jimenez Sainz
- Department of Therapeutic Radiology, Yale University School of Medicine, 15 York Street, New Haven, CT 06520, USA
| | - Ryan B. Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, 15 York Street, New Haven, CT 06520, USA
- Corresponding author
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6
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A simple cut and stretch assay to detect antimicrobial resistance genes on bacterial plasmids by single-molecule fluorescence microscopy. Sci Rep 2022; 12:9301. [PMID: 35660772 PMCID: PMC9166776 DOI: 10.1038/s41598-022-13315-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
Antimicrobial resistance (AMR) is a fast-growing threat to global health. The genes conferring AMR to bacteria are often located on plasmids, circular extrachromosomal DNA molecules that can be transferred between bacterial strains and species. Therefore, effective methods to characterize bacterial plasmids and detect the presence of resistance genes can assist in managing AMR, for example, during outbreaks in hospitals. However, existing methods for plasmid analysis either provide limited information or are expensive and challenging to implement in low-resource settings. Herein, we present a simple assay based on CRISPR/Cas9 excision and DNA combing to detect antimicrobial resistance genes on bacterial plasmids. Cas9 recognizes the gene of interest and makes a double-stranded DNA cut, causing the circular plasmid to linearize. The change in plasmid configuration from circular to linear, and hence the presence of the AMR gene, is detected by stretching the plasmids on a glass surface and visualizing by fluorescence microscopy. This single-molecule imaging based assay is inexpensive, fast, and in addition to detecting the presence of AMR genes, it provides detailed information on the number and size of plasmids in the sample. We demonstrate the detection of several β-lactamase-encoding genes on plasmids isolated from clinical samples. Furthermore, we demonstrate that the assay can be performed using standard microbiology and clinical laboratory equipment, making it suitable for low-resource settings.
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7
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Salerno D, Marrano CA, Cassina V, Cristofalo M, Shao Q, Finzi L, Mantegazza F, Dunlap D. Nanomechanics of negatively supercoiled diaminopurine-substituted DNA. Nucleic Acids Res 2021; 49:11778-11786. [PMID: 34718727 PMCID: PMC8599871 DOI: 10.1093/nar/gkab982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Single molecule experiments have demonstrated a progressive transition from a B- to an L-form helix as DNA is gently stretched and progressively unwound. The particular sequence of a DNA segment defines both base stacking and hydrogen bonding that affect the partitioning and conformations of the two phases. Naturally or artificially modified bases alter H-bonds and base stacking and DNA with diaminopurine (DAP) replacing adenine was synthesized to produce linear fragments with triply hydrogen-bonded DAP:T base pairs. Both unmodified and DAP-substituted DNA transitioned from a B- to an L-helix under physiological conditions of mild tension and unwinding. This transition avoids writhing and the ease of this transition may prevent cumbersome topological rearrangements in genomic DNA that would require topoisomerase activity to resolve. L-DNA displayed about tenfold lower persistence length than B-DNA. However, left-handed DAP-substituted DNA was twice as stiff as unmodified L-DNA. Unmodified DNA and DAP-substituted DNA have very distinct mechanical characteristics at physiological levels of negative supercoiling and tension.
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Affiliation(s)
- Domenico Salerno
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - Claudia Adriana Marrano
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - Valeria Cassina
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - Matteo Cristofalo
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - Qing Shao
- Department of Physics, Emory University, Atlanta, GA USA
| | - Laura Finzi
- Department of Physics, Emory University, Atlanta, GA USA
| | - Francesco Mantegazza
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - David Dunlap
- Department of Physics, Emory University, Atlanta, GA USA
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8
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Hulleman CN, Thorsen RØ, Kim E, Dekker C, Stallinga S, Rieger B. Simultaneous orientation and 3D localization microscopy with a Vortex point spread function. Nat Commun 2021; 12:5934. [PMID: 34635658 PMCID: PMC8505439 DOI: 10.1038/s41467-021-26228-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 09/21/2021] [Indexed: 11/08/2022] Open
Abstract
Estimating the orientation and 3D position of rotationally constrained emitters with localization microscopy typically requires polarization splitting or a large engineered Point Spread Function (PSF). Here we utilize a compact modified PSF for single molecule emitter imaging to estimate simultaneously the 3D position, dipole orientation, and degree of rotational constraint from a single 2D image. We use an affordable and commonly available phase plate, normally used for STED microscopy in the excitation light path, to alter the PSF in the emission light path. This resulting Vortex PSF does not require polarization splitting and has a compact PSF size, making it easy to implement and combine with localization microscopy techniques. In addition to a vectorial PSF fitting routine we calibrate for field-dependent aberrations which enables orientation and position estimation within 30% of the Cramér-Rao bound limit over a 66 μm field of view. We demonstrate this technique on reorienting single molecules adhered to the cover slip, λ-DNA with DNA intercalators using binding-activated localization microscopy, and we reveal periodicity on intertwined structures on supercoiled DNA.
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Affiliation(s)
- Christiaan N Hulleman
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Rasmus Ø Thorsen
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Eugene Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Max Planck Institute of Biophysics, 60438, Frankfurt, Germany
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Sjoerd Stallinga
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands.
| | - Bernd Rieger
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands.
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9
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Yee DW, Hetts SW, Greer JR. 3D-Printed Drug Capture Materials Based on Genomic DNA Coatings. ACS APPLIED MATERIALS & INTERFACES 2021; 13:41424-41434. [PMID: 34124877 DOI: 10.1021/acsami.1c05209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The toxic side effects of chemotherapy have long limited its efficacy, prompting expensive and long-drawn efforts to develop more targeted cancer therapeutics. An alternative approach to mitigate off-target toxicity is to develop a device that can sequester chemotherapeutic agents from the veins that drain the target organ before they enter systemic circulation. This effectively localizes the chemotherapy to the target organ, minimizing any hazardous side effects. 3D printing is ideal for fabricating these devices, as the geometric control afforded allows us to precisely dictate its hemodynamic performance in vivo. However, the existing materials compatible with 3D printing do not have drug-binding capabilities. Here, we report the stable coating of genomic DNA on a 3D-printed structure for the capture of doxorubicin. Genomic DNA is an effective chemotherapeutic-agent capture material due to the intrinsic DNA-targeting mechanism of action of these drugs. Stable DNA coatings were achieved through a combination of electrostatic interactions and ultraviolet C (UVC, 254 nm) cross-linking. These UVC cross-linked DNA coatings were extremely stable-leaching on average 100 pg of genomic DNA per mm2 of 3D-printed structure over a period of 30 min. In vitro studies of these materials in phosphate buffered saline and human serum demonstrated that they were able to capture, on average, 72 and 60 ng of doxorubicin per mm2 of structure, respectively. The stability and efficacy of these genomic DNA-coated 3D-printed materials represent a significant step forward towards the translation of these devices to clinical applications for the potential improvement of chemotherapy treatment.
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Affiliation(s)
- Daryl W Yee
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, United States
| | - Steven W Hetts
- Department of Radiology and Biomedical Imaging, University of California - San Francisco, San Francisco, California 94107, United States
| | - Julia R Greer
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, California 91125, United States
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10
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Ohmatsuzawa A, Kikuchi M, Kawaguchi S, Kumaki J. Molecular Combing of Various Poly( n-Alkyl Acrylate) Chains on Mica by the Dipping Method. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:7556-7564. [PMID: 34110164 DOI: 10.1021/acs.langmuir.1c01054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
If polymer chains could be deposited on a substrate as a fully extended chain, a procedure known as "molecular combing," the chain structure could be characterized by atomic force microscopy in more detail than has been possible with the measurements available today. We show here, for the first time, that flexible polymers can be molecularly combed to fully extended chains by the dipping method. We studied the molecular combing of a series of poly(n-alkyl acrylate)s on mica from a chloroform solution by the dipping method and found that poly(n-alkyl acrylate)s with an alkyl group longer than n-octyl can be molecularly combed into straight chains under optimized conditions. With increasing alkyl lengths, the number of chains deposited decreases by four orders of magnitude, and chains become molecularly combed under a wider range of conditions. The length of the molecularly combed chains is ∼80% for poly(n-octyl acrylate) but ∼100% of the all-trans conformation for poly(n-alkyl acrylate)s with an alkyl length longer than n-nonyl.
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Affiliation(s)
- Akihiro Ohmatsuzawa
- Department of Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Moriya Kikuchi
- Department of Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Seigou Kawaguchi
- Department of Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Jiro Kumaki
- Department of Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
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11
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Maman N, Kumar P, Yadav A, Feingold M. Single Molecule Study of the Polymerization of RecA on dsDNA: The Dynamics of Individual Domains. Front Mol Biosci 2021; 8:609076. [PMID: 33842536 PMCID: PMC8025788 DOI: 10.3389/fmolb.2021.609076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/02/2021] [Indexed: 11/13/2022] Open
Abstract
In the Escherichia coli, RecA plays a central role in the recombination and repair of the DNA. For homologous recombination, RecA binds to ssDNA forming a nucleoprotein filament. The RecA-ssDNA filament searches for a homologous sequence on a dsDNA and, subsequently, RecA mediates strand exchange between the ssDNA and the dsDNA. In vitro, RecA binds to both ssDNA and dsDNA. Despite a wide range of studies of the polymerization of RecA on dsDNA, both at the single molecule level and by means of biochemical methods, important aspects of this process are still awaiting a better understanding. Specifically, a detailed, quantitative description of the nucleation and growth dynamics of the RecA-dsDNA filaments is still lacking. Here, we use Optical Tweezers together with a single molecule analysis approach to measure the dynamics of the individual RecA domains on dsDNA and the corresponding growth rates for each of their fronts. We focus on the regime where the nucleation and growth rate constants, kn and kg, are comparable, leading to a coverage of the dsDNA molecule that consists of a small number of RecA domains. For the case of essentially irreversible binding (using ATPγS instead of ATP), we find that domain growth is highly asymmetric with a ratio of about 10:1 between the fast and slow fronts growth rates.
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Affiliation(s)
- Nitzan Maman
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel.,The Ilse Katz Center for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Pramod Kumar
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Amarjeet Yadav
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel.,Department of Applied Physics, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Mario Feingold
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva, Israel.,The Ilse Katz Center for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva, Israel
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12
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Öz R, Wang JL, Guerois R, Goyal G, KK S, Ropars V, Sharma R, Koca F, Charbonnier JB, Modesti M, Strick TR, Westerlund F. Dynamics of Ku and bacterial non-homologous end-joining characterized using single DNA molecule analysis. Nucleic Acids Res 2021; 49:2629-2641. [PMID: 33590005 PMCID: PMC7969030 DOI: 10.1093/nar/gkab083] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 01/20/2021] [Accepted: 01/29/2021] [Indexed: 01/29/2023] Open
Abstract
We use single-molecule techniques to characterize the dynamics of prokaryotic DNA repair by non-homologous end-joining (NHEJ), a system comprised only of the dimeric Ku and Ligase D (LigD). The Ku homodimer alone forms a ∼2 s synapsis between blunt DNA ends that is increased to ∼18 s upon addition of LigD, in a manner dependent on the C-terminal arms of Ku. The synapsis lifetime increases drastically for 4 nt complementary DNA overhangs, independently of the C-terminal arms of Ku. These observations are in contrast to human Ku, which is unable to bridge either of the two DNA substrates. We also demonstrate that bacterial Ku binds the DNA ends in a cooperative manner for synapsis initiation and remains stably bound at DNA junctions for several hours after ligation is completed, indicating that a system for removal of the proteins is active in vivo. Together these experiments shed light on the dynamics of bacterial NHEJ in DNA end recognition and processing. We speculate on the evolutionary similarities between bacterial and eukaryotic NHEJ and discuss how an increased understanding of bacterial NHEJ can open the door for future antibiotic therapies targeting this mechanism.
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Affiliation(s)
- Robin Öz
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Jing L Wang
- Institut Jacques Monod, Université de Paris, CNRS, UMR7592, Paris, France
- Ecole Normale Supérieure, IBENS, CNRS, INSERM, PSL Research University, Paris 75005 France
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Gaurav Goyal
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Virginie Ropars
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Rajhans Sharma
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Firat Koca
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
| | - Jean-Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille 13009, France
- Equipe Labélisée, Ligue Nationale Contre le Cancer, Paris 75013, France
| | - Terence R Strick
- Institut Jacques Monod, Université de Paris, CNRS, UMR7592, Paris, France
- Ecole Normale Supérieure, IBENS, CNRS, INSERM, PSL Research University, Paris 75005 France
- Equipe Labélisée, Ligue Nationale Contre le Cancer, Paris 75013, France
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 41296, Sweden
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13
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Hu Y, Li YV. Expression of SSEA-4 and Oct-4 from somatic cells in primary mouse gastric cell culture induced by brief strong acid. Mol Cell Biochem 2021; 476:2813-2821. [PMID: 33733429 DOI: 10.1007/s11010-021-04124-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/26/2021] [Indexed: 11/29/2022]
Abstract
Environmental changes can stress and alter biology at the molecular and cellular level. For example, metal-protein interaction is a classic physic and biological property of nature, which is fundamentally influenced by acidity. Here, we report a unique cellular reprogramming phenomenon in that a brief strong acid treatment induced the expression of pluripotent stem cell (PSC) markers. We used strong acid to briefly challenge mix-cultured gastric cells, and then subcultured survived cells in a normal cell culture medium. We found that survival acid-treated cells expressed PSC markers detected by commonly used pluripotent antibodies such as SSEA-4 and Oct4. In addition, we observed that the survived cells from the acid challenge grew faster during the second and third weeks of subculture and had a relative short doubling time (DT) than the controls. PSC marker-labeled 'older' cells also presented immature cell-like morphology with some having marker Oct4 in the nucleus. Finally, the expression of the markers appeared to be sensitive to metal ion chelation. Removal of the metals during a brief acid treatment reduced pluripotent marker-positive cells, suggesting the dissociation of metals from metal-binding proteins may be a factor involved in the induction of stem cell markers. Our findings reveal that somatic cells appear to possess a plasticity feature to express pluripotent marker proteins or to select cell subpopulations that express pluripotent marker proteins when cells are transiently exposed to strong acid. It opens new directions for understanding conserved regulatory mechanisms involved in cellular survival under stressful stimulation.
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Affiliation(s)
- Yuli Hu
- Molecular & Cellular Biology Graduate Program, Departments of Biological Sciences and Biomedical Sciences, Ohio University, Athens, OH, 45701, USA
| | - Yang V Li
- Molecular & Cellular Biology Graduate Program, Departments of Biological Sciences and Biomedical Sciences, Ohio University, Athens, OH, 45701, USA. .,Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, 346 Irvine Hall, Athens, OH, 45701, USA.
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14
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Takahashi S, Oshige M, Katsura S. DNA Manipulation and Single-Molecule Imaging. Molecules 2021; 26:1050. [PMID: 33671359 PMCID: PMC7922115 DOI: 10.3390/molecules26041050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 11/22/2022] Open
Abstract
DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.
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Affiliation(s)
- Shunsuke Takahashi
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Hatoyama-cho, Hiki-gun, Saitama 350-0394, Japan;
| | - Masahiko Oshige
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
| | - Shinji Katsura
- Department of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan;
- Gunma University Center for Food Science and Wellness (GUCFW), Maebashi, Gunma 371-8510, Japan
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15
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Uppuluri L, Varapula D, Young E, Riethman H, Xiao M. Single-molecule telomere length characterization by optical mapping in nano-channel array: Perspective and review on telomere length measurement. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 82:103562. [PMID: 33310082 PMCID: PMC8500550 DOI: 10.1016/j.etap.2020.103562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 05/11/2023]
Abstract
In humans, the telomere consists of tandem 5'TTAGGG3' DNA repeats on both ends of all 46 chromosomes. Telomere shortening has been linked to aging and age-related diseases. Similarly, telomere length changes have been associated with chemical exposure, molecular-level DNA damage, and tumor development. Telomere elongation has been associated to tumor development, caused due to chemical exposure and molecular-level DNA damage. The methods used to study these effects mostly rely on average telomere length as a biomarker. The mechanisms regulating subtelomere-specific and haplotype-specific telomere lengths in humans remain understudied and poorly understood, primarily because of technical limitations in obtaining these data for all chromosomes. Recent studies have shown that it is the short telomeres that are crucial in preserving chromosome stability. The identity and frequency of specific critically short telomeres potentially is a useful biomarker for studying aging, age-related diseases, and cancer. Here, we will briefly review the role of telomere length, its measurement, and our recent single-molecule telomere length measurement assay. With this assay, one can measure individual telomere lengths as well as identify their physically linked subtelomeric DNA. This assay can also positively detect telomere loss, characterize novel subtelomeric variants, haplotypes, and previously uncharacterized recombined subtelomeres. We will also discuss its applications in aging cells and cancer cells, highlighting the utility of the single molecule telomere length assay.
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Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Dharma Varapula
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Eleanor Young
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Harold Riethman
- Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA, USA.
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA; Institute of Molecular Medicine and Infectious Disease, School of Medicine, Drexel University, Philadelphia, PA, USA.
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16
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Della Rosa G, Di Corato R, Carpi S, Polini B, Taurino A, Tedeschi L, Nieri P, Rinaldi R, Aloisi A. Tailoring of silica-based nanoporous pod by spermidine multi-activity. Sci Rep 2020; 10:21142. [PMID: 33273530 PMCID: PMC7712788 DOI: 10.1038/s41598-020-77957-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/17/2020] [Indexed: 11/20/2022] Open
Abstract
Ubiquitous in nature, polyamines (PAs) are a class of low-molecular aliphatic amines critically involved in cell growth, survival and differentiation. The polycation behavior is validated as a successful strategy in delivery systems to enhance oligonucleotide loading and cellular uptake. In this study, the chemical features and the functional roles of the PA spermidine are synergistically exploited in the synthesis and bioactive functionalization of SiO2-based structures. Inspired by biosilicification, the role of spermidine is assessed both as catalyst and template in a biomimetic one-pot synthesis of dense silica-based particles (SPs) and as a competitive agent in an interfacial reassembly strategy, to empty out SPs and generate spermidine-decorated hollow silica nanoporous pods (spd-SNPs). Spermidine bioactivity is then employed for targeting tumor cell over-expressed polyamine transport system (PTS) and for effective delivery of functional miRNA into melanoma cells. Spermidine decoration promotes spd-SNP cell internalization mediated by PTS and along with hollow structure enhances oligonucleotide loading. Accordingly, the functional delivery of the tumor suppressor miR-34a 3p resulted in intracellular accumulation of histone-complexed DNA fragments associated with apoptosis. Overall, the results highlight the potential of spd-SNP as a multi-agent anticancer therapy.
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Affiliation(s)
- Giulia Della Rosa
- Mathematics and Physics "E. De Giorgi" Department, University of Salento, Via Arnesano, 73100, Lecce, Italy
- Department of Neuroscience and Brain Technologies (NBT), Istituto Italiano di Tecnologia (IIT), Via Morego, 16163, Genova, Italy
| | - Riccardo Di Corato
- Mathematics and Physics "E. De Giorgi" Department, University of Salento, Via Arnesano, 73100, Lecce, Italy
- Center for Biomolecular Nanotechnologies (CBN), Istituto Italiano di Tecnologia (IIT), Via Barsanti, Arnesano, 73010, Lecce, Italy
- Institute for Microelectronics and Microsystems (IMM), CNR, Via Monteroni, 73100, Lecce, Italy
| | - Sara Carpi
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 56126, Pisa, Italy
- Centro Interdipartimentale di Farmacologia Marina, MARine PHARMA Center, University of Pisa, Via Bonanno Pisano, 56126, Pisa, Italy
| | - Beatrice Polini
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 56126, Pisa, Italy
| | - Antonietta Taurino
- Institute for Microelectronics and Microsystems (IMM), CNR, Via Monteroni, 73100, Lecce, Italy
| | - Lorena Tedeschi
- Oligonucleotides Laboratory, Institute of Clinical Physiology (IFC), CNR, Via Moruzzi, 56124, Pisa, Italy
| | - Paola Nieri
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano, 56126, Pisa, Italy
- Centro Interdipartimentale di Farmacologia Marina, MARine PHARMA Center, University of Pisa, Via Bonanno Pisano, 56126, Pisa, Italy
| | - Rosaria Rinaldi
- Mathematics and Physics "E. De Giorgi" Department, University of Salento, Via Arnesano, 73100, Lecce, Italy
- Institute for Microelectronics and Microsystems (IMM), CNR, Via Monteroni, 73100, Lecce, Italy
- ISUFI, University of Salento, Via Monteroni, 73100, Lecce, Italy
| | - Alessandra Aloisi
- Institute for Microelectronics and Microsystems (IMM), CNR, Via Monteroni, 73100, Lecce, Italy.
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17
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Varapula D, LaBouff E, Raseley K, Uppuluri L, Ehrlich GD, Noh M, Xiao M. A micropatterned substrate for on-surface enzymatic labelling of linearized long DNA molecules. Sci Rep 2019; 9:15059. [PMID: 31636335 PMCID: PMC6803683 DOI: 10.1038/s41598-019-51507-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/02/2019] [Indexed: 12/22/2022] Open
Abstract
Optical mapping of linearized DNA molecules is a promising new technology for sequence assembly and scaffolding, large structural variant detection, and diagnostics. This is currently achieved either using nanochannel confinement or by stretching single DNA molecules on a solid surface. While the first method necessitates DNA labelling before linearization, the latter allows for modification post-linearization, thereby affording increased process flexibility. Each method is constrained by various physical and chemical limitations. One of the most common techniques for linearization of DNA uses a hydrophobic surface and a receding meniscus, termed molecular combing. Here, we report the development of a microfabricated surface that can not only comb the DNA molecules efficiently but also provides for sequence-specific enzymatic fluorescent DNA labelling. By modifying a glass surface with two contrasting functionalities, such that DNA binds selectively to one of the two regions, we can control DNA extension, which is known to be critical for sequence-recognition by an enzyme. Moreover, the surface modification provides enzymatic access to the DNA backbone, as well as minimizing non-specific fluorescent dye adsorption. These enhancements make the designed surface suitable for large-scale and high-resolution single DNA molecule studies.
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Affiliation(s)
- Dharma Varapula
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Eric LaBouff
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Kaitlin Raseley
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Lahari Uppuluri
- Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, 19104, USA
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Moses Noh
- Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, 19104, USA
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
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18
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Basak R, Liu F, Qureshi S, Gupta N, Zhang C, de Vries R, van Kan JA, Dheen ST, van der Maarel JRC. Linearization and Labeling of Single-Stranded DNA for Optical Sequence Analysis. J Phys Chem Lett 2019; 10:316-321. [PMID: 30615463 DOI: 10.1021/acs.jpclett.8b03465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Genetic profiling would benefit from linearization of ssDNA through the exposure of the unpaired bases to gene-targeting probes. This is compromised by ssDNA's high flexibility and tendency to form self-annealed structures. Here, we demonstrate that self-annealing can be avoided through controlled coating with a cationic-neutral diblock polypeptide copolymer. Coating does not preclude site-specific binding of fluorescence labeled oligonucleotides. Bottlebrush-coated ssDNA can be linearized by confinement inside a nanochannel or molecular combing. A stretch of 0.32 nm per nucleotide is achieved inside a channel with a cross-section of 100 nm and a 2-fold excess of polypeptide with respect to DNA charge. With combing, the complexes are stretched to a similar extent. Atomic force microscopy of dried complexes on silica revealed that the contour and persistence lengths are close to those of dsDNA in the B-form. Labeling is based on hybridization and not limited by restriction enzymes. Enzyme-free labeling offers new opportunities for the detection of specific sequences.
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Affiliation(s)
- Rajib Basak
- Department of Physics , National University of Singapore , Singapore 117542
| | - Fan Liu
- Department of Physics , National University of Singapore , Singapore 117542
| | - Sarfraz Qureshi
- Department of Physics , National University of Singapore , Singapore 117542
| | - Neelima Gupta
- Department of Anatomy , National University of Singapore , Singapore 117594
| | - Ce Zhang
- Institute of Photonics and Photon-Technology , Northwest University , Xi'an , China 710069
| | - Renko de Vries
- Laboratory of Physical Chemistry and Colloid Science , Wageningen University , 6708 Wageningen , The Netherlands
| | - Jeroen A van Kan
- Department of Physics , National University of Singapore , Singapore 117542
| | - S Thameem Dheen
- Department of Anatomy , National University of Singapore , Singapore 117594
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19
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Wu S, Jeffet J, Grunwald A, Sharim H, Gilat N, Torchinsky D, Zheng Q, Zirkin S, Xu L, Ebenstein Y. Microfluidic DNA combing for parallel single-molecule analysis. NANOTECHNOLOGY 2019; 30:045101. [PMID: 30485249 DOI: 10.1088/1361-6528/aaeddc] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA combing is a widely used method for stretching and immobilising DNA molecules on a surface. Fluorescent labelling of genomic information enables high-resolution optical analysis of DNA at the single-molecule level. Despite its simplicity, the application of DNA combing in diagnostic workflows is still limited, mainly due to difficulties in analysing multiple small-volume DNA samples in parallel. Here, we report a simple and versatile microfluidic DNA combing technology (μDC), which allows manipulating, stretching and imaging of multiple, microliter scale DNA samples by employing a manifold of parallel microfluidic channels. Using DNA molecules with repetitive units as molecular rulers, we demonstrate that the μDC technology allows uniform stretching of DNA molecules. The stretching ratio remains consistent along individual molecules as well as between different molecules in the various channels, allowing simultaneous quantitative analysis of different samples loaded into parallel channels. Furthermore, we demonstrate the application of μDC to characterise UVB-induced DNA damage levels in human embryonic kidney cells and the spatial correlation between DNA damage sites. Our results point out the potential application of μDC for quantitative and comparative single-molecule studies of genomic features. The extremely simple design of μDC makes it suitable for integration into other microfluidic platforms to facilitate high-throughput DNA analysis in biological research and medical point-of-care applications.
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Affiliation(s)
- Shuyi Wu
- Center for Nano and Micro Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, People's Republic of China
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20
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One-step DNA purification and amplification on an integrated plastic microdevice for on-site identification of foodborne pathogens. Anal Chim Acta 2018; 1040:63-73. [DOI: 10.1016/j.aca.2018.06.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/06/2018] [Accepted: 06/18/2018] [Indexed: 11/16/2022]
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21
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He M, Zhou Y, Cui W, Yang Y, Zhang H, Chen X, Pang W, Duan X. An on-demand femtoliter droplet dispensing system based on a gigahertz acoustic resonator. LAB ON A CHIP 2018; 18:2540-2546. [PMID: 30043817 DOI: 10.1039/c8lc00540k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
On-demand droplet dispensing systems are indispensable tools in bioanalytical fields, such as microarray fabrication. Biomaterial solutions can be very limited and expensive, so minimizing the use of solution per spot produced is highly desirable. Here, we proposed a novel droplet dispensing method which utilizes a gigahertz (GHz) acoustic resonator to deposit well-defined droplets on-demand. This ultra-high frequency acoustic resonator induces a highly localized and strong body force at the solid-liquid interface, which pushes the liquid to generate a stable and sharp "liquid needle" and further delivers droplets to the target substrate surface by transient contact. This approach is between contact and non-contact methods, thus avoiding some issues of traditional methods (such as nozzle clogging or satellite spots). We demonstrated the feasibility of this approach by fabricating high quality DNA and protein microarrays on glass and flexible substrates. Notably, the spot size can be delicately controlled down to a few microns (femtoliter in volume). Because of the CMOS compatibility, we expect this technique to be readily applied to advanced biofabrication processes.
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Affiliation(s)
- Meihang He
- State Key Laboratory of Precision Measuring Technology & Instruments, Tianjin University, Tianjin 300072, China.
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22
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Eisenbeis J, Saffarzadeh M, Peisker H, Jung P, Thewes N, Preissner KT, Herrmann M, Molle V, Geisbrecht BV, Jacobs K, Bischoff M. The Staphylococcus aureus Extracellular Adherence Protein Eap Is a DNA Binding Protein Capable of Blocking Neutrophil Extracellular Trap Formation. Front Cell Infect Microbiol 2018; 8:235. [PMID: 30038902 PMCID: PMC6047304 DOI: 10.3389/fcimb.2018.00235] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/19/2018] [Indexed: 01/07/2023] Open
Abstract
The extracellular adherence protein (Eap) of Staphylococcus aureus is a secreted protein known to exert a number of adhesive and immunomodulatory properties. Here we describe the intrinsic DNA binding activity of this multifunctional secretory factor. By using atomic force microscopy, we provide evidence that Eap can bind and aggregate DNA. While the origin of the DNA substrate (e.g., eukaryotic, bacterial, phage, and artificial DNA) seems to not be of major importance, the DNA structure (e.g., linear or circular) plays a critical role with respect to the ability of Eap to bind and condense DNA. Further functional assays corroborated the nature of Eap as a DNA binding protein, since Eap suppressed the formation of "neutrophil extracellular traps" (NETs), composed of DNA-histone scaffolds, which are thought to function as a neutrophil-mediated extracellular trapping mechanism. The DNA binding and aggregation activity of Eap may thereby protect S. aureus against a specific anti-microbial defense reaction from the host.
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Affiliation(s)
- Janina Eisenbeis
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Mona Saffarzadeh
- Department of Biochemistry, Medical Faculty, Justus-Liebig-University, Giessen, Germany
| | - Henrik Peisker
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Philipp Jung
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Nicolas Thewes
- Experimental Physics, Saarland University, Saarbrücken, Germany
| | - Klaus T. Preissner
- Department of Biochemistry, Medical Faculty, Justus-Liebig-University, Giessen, Germany
| | - Mathias Herrmann
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Virginie Molle
- Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Centre National de la Recherche Scientifique, UMR 5235, Université de Montpellier, Montpellier, France
| | - Brian V. Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, United States
| | - Karin Jacobs
- Experimental Physics, Saarland University, Saarbrücken, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
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23
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Shimanuki C, Matsuta Y, Fujita R, Kumaki J. Molecular Combing of a Flexible Polymer Chain by Simple Spin-Casting. ACS OMEGA 2018; 3:3983-3990. [PMID: 31458636 PMCID: PMC6641330 DOI: 10.1021/acsomega.8b00325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 03/29/2018] [Indexed: 06/10/2023]
Abstract
If polymer chains could be fixed on a substrate as a fully elongated chain, a procedure known as "molecular combing", the chain structure could be analyzed more precisely than has been possible with the characterization techniques available today. Although the molecular combing of a rigid biomolecule, DNA, has been attained for the mapping of genetic information, that of flexible chains has never been achieved as yet. We show here that poly(n-nonyl acrylate) (PNA) can be molecularly combed on mica by a simple spin-casting method, and that the chain lengths were in good agreement with that of the all-trans conformation. One of the key factors for successful molecular combing was found to be the weak adsorption of PNA on mica, indicating that flexible polymers may be molecularly combed by adjusting their affinity to the substrate. The molecular combing of polymer chains may open a new way not only to characterize the chain structures more precisely but also to fabricate new nanomaterials based on polymers.
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Affiliation(s)
- Chisato Shimanuki
- Department
of Polymer Science and Engineering, Faculty of Engineering, Department of Polymer
Science and Engineering, Graduate School of Engineering and Science, and Department of
Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Yuuma Matsuta
- Department
of Polymer Science and Engineering, Faculty of Engineering, Department of Polymer
Science and Engineering, Graduate School of Engineering and Science, and Department of
Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Ryo Fujita
- Department
of Polymer Science and Engineering, Faculty of Engineering, Department of Polymer
Science and Engineering, Graduate School of Engineering and Science, and Department of
Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
| | - Jiro Kumaki
- Department
of Polymer Science and Engineering, Faculty of Engineering, Department of Polymer
Science and Engineering, Graduate School of Engineering and Science, and Department of
Organic Materials Science, Graduate School of Organic Materials Science, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
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24
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Yadav H, Sharma P. A simple and novel DNA combing methodology for Fiber-FISH and optical mapping. Genomics 2018; 111:567-578. [PMID: 29550497 DOI: 10.1016/j.ygeno.2018.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 02/02/2023]
Abstract
Single molecule analysis can help us study genomics efficiently. It involves studying single DNA molecules for genomic studies. DNA combing is one of such techniques which allowed us to study single DNA molecules for multiple uses. DNA combing technology can be used to perform Fiber-FISH and optical mapping. Physical mapping of genomes can be studied by restriction digestion of combed DNA on glass slides. Restriction fragments can be arranged into optical maps by gathering fluorescent intensity data by CCD camera and image analysis by softwares. Physical mapping and DNA segment rearrangements can be studied by Fiber-FISH which involves application of probes on genomic DNA combed over glass slides. We developed a novel methodology involving combing solution optimization, denatured combed DNA and performed restriction digestion of combed DNA. Thus we provided an efficient and robust combing platform for its application in Fiber-FISH and optical mapping.
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Affiliation(s)
- Hemendra Yadav
- Department of Botany, University of Rajasthan, Jaipur, India.
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25
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Tassler S, Wölk C, Janich C, Dobner B, Brezesinski G. Lysine-based amino-functionalized lipids for gene transfection: the protonation state in monolayers at the air-liquid interface. Phys Chem Chem Phys 2018; 19:20271-20280. [PMID: 28726909 DOI: 10.1039/c7cp03107f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cationic lipids are considered as non-viral carriers for genetic material used in gene therapy. They have no carcinogenic potential and cause low immune response compared to existing viral systems. The protonation degree of these cationic lipids is a crucial parameter for the binding behavior of polynucleotides (e.g., DNA). Newly synthesized peptide-mimic lysine-based amino-functionalized lipids have been investigated in 2D models as monolayers at the air-liquid interface. Standard surface pressure - area isotherms have been measured to prove the layer stability. Total reflection X-ray fluorescence (TRXF) has been used as a surface sensitive analytical method to estimate the amount of counterions at the head groups. Using a standard sample as a reference, the protonation degree of these cationic lipids can be quantified on buffers with different pH values. It is found that the protonation degree depends linearly on the packing density of the lipid monolayer.
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Affiliation(s)
- Stephanie Tassler
- Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, Am Mühlenberg 1, 14476 Potsdam, Germany.
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26
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Analysis of Fission Yeast Single DNA Molecules on the Megabase Scale Using DNA Combing. Methods Mol Biol 2018; 1721:9-24. [PMID: 29423843 DOI: 10.1007/978-1-4939-7546-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
DNA combing enables the quantitative analysis of DNA replication, DNA recombination, DNA-protein interaction, and DNA methylation along genomic single DNA molecules at 1 kb resolution. However, DNA combing has been restricted to short 200-500 kb long DNA fragments, which introduces significant bias in data analysis. An improved DNA combing methodology that allows to routinely image Mb-scale single DNA molecules and occasionally up to full-length fission yeast chromosomes is presented in this chapter. DNA combing of Mb-scale single DNA molecules can be applied to accurately measure the dynamic properties of DNA replication such as the rate of origin firing, replication fork velocity, fork directionality and the frequency of fork blockage. In addition, Mb-scale single DNA molecules enable the quantitative analysis of complex genomic rearrangements including gross chromosomal translocations, repetitive DNA sequences, large deletions, and duplications, which are difficult to investigate with deep sequencing strategies.
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27
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Yadav H, Sharma P. Enhanced post wash retention of combed DNA molecules by varying multiple combing parameters. Anal Biochem 2017; 536:45-50. [PMID: 28821423 DOI: 10.1016/j.ab.2017.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/07/2017] [Accepted: 08/14/2017] [Indexed: 01/01/2023]
Abstract
Recent advances in genomics have created a need for efficient techniques for deciphering information hidden in various genomes. Single molecule analysis is one such technique to understand molecular processes at single molecule level. Fiber- FISH performed with the help of DNA combing can help us in understanding genetic rearrangements and changes in genome at single DNA molecule level. For performing Fiber-FISH we need high retention of combed DNA molecules post wash as Fiber-FISH requires profuse washing. We optimized combing process involving combing solution, method of DNA mounting on glass slides and coating of glass slides to enhance post-wash retention of DNA molecules. It was found that average number of DNA molecules observed post-wash per field of view was maximum with our optimized combing solution. APTES coated glass slides showed lesser retention than PEI surface but fluorescent intensity was higher in case of APTES coated surface. Capillary method used to mount DNA on glass slides also showed lesser retention but straight DNA molecules were observed as compared to force flow method.
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Affiliation(s)
- Hemendra Yadav
- Department of Botany, University of Rajasthan, Jaipur, India.
| | - Pulkit Sharma
- Bioinventree Pvt Ltd., SB 17 Bhawani Singh Road, Bapunagar, Jaipur 302015 India
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Brun C, Elchinger PH, Nonglaton G, Tidiane-Diagne C, Tiron R, Thuaire A, Gasparutto D, Baillin X. Metallic Conductive Nanowires Elaborated by PVD Metal Deposition on Suspended DNA Bundles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1700956. [PMID: 28677894 DOI: 10.1002/smll.201700956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Metallic conductive nanowires (NWs) with DNA bundle core are achieved, thanks to an original process relying on double-stranded DNA alignment and physical vapor deposition (PVD) metallization steps involving a silicon substrate. First, bundles of DNA are suspended with a repeatable process between 2 µm high parallel electrodes with separating gaps ranging from 800 nm to 2 µm. The process consists in the drop deposition of a DNA lambda-phage solution on the electrodes followed by a naturally evaporation step. The deposition process is controlled by the DNA concentration within the buffer solution, the drop volume, and the electrode hydrophobicity. The suspended bundles are finally metallized with various thicknesses of titanium and gold by a PVD e-beam evaporation process. The achieved NWs have a width ranging from a few nanometers up to 100 nm. The electrical behavior of the achieved 60 and 80 nm width metallic NWs is shown to be Ohmic and their intrinsic resistance is estimated according to different geometrical models of the NW section area. For the 80 nm width NWs, a resistance of about few ohms is established, opening exploration fields for applications in microelectronics.
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Affiliation(s)
- Christophe Brun
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Pierre-Henri Elchinger
- Université Grenoble Alpes, F-38000, Grenoble, France
- Laboratory of Plant & Cell Physiology, CEA/DRF/BIG, CNRS UMR5168, INRA UMR 1417, F-38054, Grenoble, France
| | - Guillaume Nonglaton
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Cheikh Tidiane-Diagne
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Raluca Tiron
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Aurélie Thuaire
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
| | - Didier Gasparutto
- Université Grenoble Alpes, F-38000, Grenoble, France
- INAC/SyMMES, UMR 5819 CEA CNRS UGA, MINATEC Campus, F-38054, Grenoble, France
| | - Xavier Baillin
- Université Grenoble Alpes, F-38000, Grenoble, France
- CEA, LETI, MINATEC Campus, F-38054, Grenoble, France
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Iyer DR, Rhind N. Replication fork slowing and stalling are distinct, checkpoint-independent consequences of replicating damaged DNA. PLoS Genet 2017; 13:e1006958. [PMID: 28806726 PMCID: PMC5570505 DOI: 10.1371/journal.pgen.1006958] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/24/2017] [Accepted: 08/04/2017] [Indexed: 11/30/2022] Open
Abstract
In response to DNA damage during S phase, cells slow DNA replication. This slowing is orchestrated by the intra-S checkpoint and involves inhibition of origin firing and reduction of replication fork speed. Slowing of replication allows for tolerance of DNA damage and suppresses genomic instability. Although the mechanisms of origin inhibition by the intra-S checkpoint are understood, major questions remain about how the checkpoint regulates replication forks: Does the checkpoint regulate the rate of fork progression? Does the checkpoint affect all forks, or only those encountering damage? Does the checkpoint facilitate the replication of polymerase-blocking lesions? To address these questions, we have analyzed the checkpoint in the fission yeast Schizosaccharomyces pombe using a single-molecule DNA combing assay, which allows us to unambiguously separate the contribution of origin and fork regulation towards replication slowing, and allows us to investigate the behavior of individual forks. Moreover, we have interrogated the role of forks interacting with individual sites of damage by using three damaging agents-MMS, 4NQO and bleomycin-that cause similar levels of replication slowing with very different frequency of DNA lesions. We find that the checkpoint slows replication by inhibiting origin firing, but not by decreasing fork rates. However, the checkpoint appears to facilitate replication of damaged templates, allowing forks to more quickly pass lesions. Finally, using a novel analytic approach, we rigorously identify fork stalling events in our combing data and show that they play a previously unappreciated role in shaping replication kinetics in response to DNA damage.
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Affiliation(s)
- Divya Ramalingam Iyer
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Nicholas Rhind
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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Wan M, Sun D, Wang S, Wu J, Yang Y, Wang K, He Q, Wang G, Bai J. Influence of concentration on distribution properties of stretched-DNA in the MEC studied with fluorescence imaging and drop shape analyzing. Colloids Surf B Biointerfaces 2017; 151:11-18. [PMID: 27939693 DOI: 10.1016/j.colsurfb.2016.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/19/2016] [Accepted: 12/01/2016] [Indexed: 11/28/2022]
Abstract
Stretching and manipulating DNA efficiently is significant for exploring the properties and applications of single DNA molecules. Here, the influence of concentrations of buffer and DNA on properties of stretched DNA molecules in the molecular evaporation combing (MEC) is investigated systematically with the single molecule fluorescence imaging microscopy and the high-precision drop shape analyzing technology. The stretched degree and uniformity of combed DNA molecules decrease as the buffer concentration are increased from 7 to 20mM. When the buffer concentration changes from 12 to 15mM, the stretched DNA molecules are apt to form a ringlike pattern. During the MEC process, there exist two kinds of evaporation modes, i.e., the constant contact angle mode and the constant contact radius mode. The former only takes effect in the lower concentration of buffer and DNA, enabling the uniform stretching. While the latter plays the leading role in the higher concentration, promoting the formation of the ringlike pattern of DNA molecules.
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Affiliation(s)
- Mengjiao Wan
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China; School of Physics, Northwest University, Xi'an 710069, Shaanxi, China
| | - Dan Sun
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Shuang Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Jianguo Wu
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yuanyuan Yang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Kaige Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China.
| | - Qingli He
- School of Physics, Northwest University, Xi'an 710069, Shaanxi, China
| | - Guiren Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China; Mechanical Engineering Department & Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Jintao Bai
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China; School of Physics, Northwest University, Xi'an 710069, Shaanxi, China
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31
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Igarashi C, Murata A, Itoh Y, Subekti DRG, Takahashi S, Kamagata K. DNA Garden: A Simple Method for Producing Arrays of Stretchable DNA for Single-Molecule Fluorescence Imaging of DNA-Binding Proteins. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20160298] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chihiro Igarashi
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Agato Murata
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Yuji Itoh
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Dwiky Rendra Graha Subekti
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Satoshi Takahashi
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
| | - Kiyoto Kamagata
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578
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32
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Microfluidic DNA Stretching Device for Single-Molecule Diagnostics. Methods Mol Biol 2017. [PMID: 28044290 DOI: 10.1007/978-1-4939-6734-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The method described here enables the automatic stretching and patterning of single DNA molecules onto a solid surface. It does not require chemical modification of the DNA or surface modification of the substrate. To detect a signal variation caused by sequence-specific dye binding or partial melting, it is crucial that the DNA molecules are arrayed in a parallel direction inside the narrow microscopic field. The method uses zigzag-shaped microgrooves in a densely-arranged molecular patterning apparatus in a microfluidic channel. By syringing through the microchannel, over 1500 DNA molecules can be arrayed simultaneously in the microgrooves. It will therefore serve as a template preparation for DNA molecular diagnosis by high-resolution imaging.
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33
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Brun C. DNA for Nanopackaging: A Promising Bottom-Up Approach. IEEE NANOTECHNOLOGY MAGAZINE 2017. [DOI: 10.1109/mnano.2016.2633679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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34
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Lacroix J, Pélofy S, Blatché C, Pillaire MJ, Huet S, Chapuis C, Hoffmann JS, Bancaud A. Analysis of DNA Replication by Optical Mapping in Nanochannels. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5963-5970. [PMID: 27624455 DOI: 10.1002/smll.201503795] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 06/21/2016] [Indexed: 06/06/2023]
Abstract
DNA replication is essential to maintain genome integrity in S phase of the cell division cycle. Accumulation of stalled replication forks is a major source of genetic instability, and likely constitutes a key driver of tumorigenesis. The mechanisms of regulation of replication fork progression have therefore been extensively investigated, in particular with DNA combing, an optical mapping technique that allows the stretching of single molecules and the mapping of active region for DNA synthesis by fluorescence microscopy. DNA linearization in nanochannels has been successfully used to probe genomic information patterns along single chromosomes, and has been proposed to be a competitive alternative to DNA combing. Yet this conjecture remains to be confirmed experimentally. Here, two complementary techniques are established to detect the genomic distribution of tracks of newly synthesized DNA in human cells by optical mapping in nanochannels. Their respective advantages and limitations are compared, and applied them to detect deregulations of the replication program induced by the antitumor drug hydroxyurea. The developments here thus broaden the field of applications accessible to nanofluidic technologies, and can be used in the future as part for molecular diagnostics in the context of high throughput cancer drug screening.
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Affiliation(s)
- Joris Lacroix
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Sandrine Pélofy
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Charline Blatché
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
| | - Marie-Jeanne Pillaire
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
- Equipe "Labellisée LA LIGUE CONTRE LE CANCER 2013" - Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, 2 Avenue Hubert Curien, CS 53717, 31037, Toulouse, France
| | - Sébastien Huet
- CNRS, UMR 6061, Institut Génétique et Développement de Rennes, F-35043, Rennes, France
- Université Rennes 1, UEB, UMR 6290, Faculté de Médecine, F-35043, Rennes, France
| | - Catherine Chapuis
- CNRS, UMR 6061, Institut Génétique et Développement de Rennes, F-35043, Rennes, France
- Université Rennes 1, UEB, UMR 6290, Faculté de Médecine, F-35043, Rennes, France
| | - Jean-Sébastien Hoffmann
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
- Equipe "Labellisée LA LIGUE CONTRE LE CANCER 2013" - Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, 2 Avenue Hubert Curien, CS 53717, 31037, Toulouse, France
| | - Aurélien Bancaud
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400, Toulouse, France
- Univ de Toulouse, LAAS, F-31400, Toulouse, France
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35
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Wang J, Barnett JT, Pollard MR, Kad NM. Integrating Optical Tweezers, DNA Tightropes, and Single-Molecule Fluorescence Imaging: Pitfalls and Traps. Methods Enzymol 2016; 582:171-192. [PMID: 28062034 DOI: 10.1016/bs.mie.2016.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Fluorescence imaging is one of the cornerstone techniques for understanding how single molecules search for their targets on DNA. By tagging individual proteins, it is possible to track their position with high accuracy. However, to understand how proteins search for targets, it is necessary to elongate the DNA to avoid protein localization ambiguities. Such structures known as "DNA tightropes" are tremendously powerful for imaging target location; however, they lack information about how force and load affect protein behavior. The use of optically trapped microstructures offers the means to apply and measure force effects. Here we describe a system that we recently developed to enable individual proteins to be directly manipulated on DNA tightropes. Proteins bound to DNA can be conjugated with Qdot fluorophores for visualization and also directly manipulated by an optically trapped, manufactured microstructure. Together this offers a new approach to understanding the physical environment of molecules, and the combination with DNA tightropes presents opportunities to study complex biological phenomena.
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Affiliation(s)
- J Wang
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | - J T Barnett
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom
| | | | - N M Kad
- School of Biosciences, University of Kent, Canterbury, Kent, United Kingdom.
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36
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Giri D, Li Z, Ashraf KM, Collinson MM, Higgins DA. Molecular Combing of λ-DNA using Self-Propelled Water Droplets on Wettability Gradient Surfaces. ACS APPLIED MATERIALS & INTERFACES 2016; 8:24265-24272. [PMID: 27541167 DOI: 10.1021/acsami.6b08607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Surface wettability gradients were used to elongate and align double stranded λ-DNA. Gradients were prepared by vapor phase deposition of octyltrichlorosilane (C8-silane) and fluorinated octyltrichlorosilane (F-silane) precursors. Gradient formation was confirmed by water contact angle and ellipsometric film thickness measurements. Placement of a droplet of aqueous DNA solution on the hydrophobic end of each gradient led to spontaneous motion of the droplet toward the hydrophilic end and deposition of the DNA. Fluorescence imaging of surface-adsorbed YOYO-1 labeled DNA molecules revealed that they are elongated and aligned perpendicular to the droplet-surface contact line at all positions along the gradient, consistent with a dominant role played by surface tension forces in elongating the DNA. The density of adsorbed DNA was found to be greatest on the C8-silane gradient at its hydrophobic end. DNA density decreased toward the hydrophilic end, while the length of the elongated DNA was less dependent on position. The elongation of DNA molecules by spontaneous droplet motion on chemical gradient surfaces has possible applications in DNA barcoding and studies of DNA-protein interactions.
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Affiliation(s)
- Dipak Giri
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
| | - Zi Li
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
| | - Kayesh M Ashraf
- Department of Chemistry, Virginia Commonwealth University , Richmond, Virginia 23284-2006, United States
| | - Maryanne M Collinson
- Department of Chemistry, Virginia Commonwealth University , Richmond, Virginia 23284-2006, United States
| | - Daniel A Higgins
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
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37
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Wah JLT, David C, Rudiuk S, Baigl D, Estevez-Torres A. Observing and Controlling the Folding Pathway of DNA Origami at the Nanoscale. ACS NANO 2016; 10:1978-87. [PMID: 26795025 DOI: 10.1021/acsnano.5b05972] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
DNA origami is a powerful method to fold DNA into rationally designed nanostructures that holds great promise for bionanotechnology. However, the folding mechanism has yet to be fully resolved, principally due to a lack of data with single molecule resolution. To address this issue, we have investigated in detail, using atomic force microscopy, the morphological evolution of hundreds of individual rectangular origamis in solution as a function of temperature. Significant structural changes were observed between 65 and 55 °C both for folding and melting, and six structural intermediates were identified. Under standard conditions, folding was initiated at the edges of the rectangle and progressed toward the center. Melting occurred through the reverse pathway until the structures were significantly disrupted but ended through a different pathway involving out-of-equilibrium chainlike structures. Increasing the relative concentration of center to edge staples dramatically modified the folding pathway to a mechanism progressing from the center toward the edges. These results indicate that the folding pathway is determined by thermodynamics and suggest a way of controlling it.
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Affiliation(s)
- Jonathan Lee Tin Wah
- Laboratoire Jean Perrin, Université Pierre et Marie Curie , 4 place Jussieu, 75005 Paris, France
- CNRS, UMR 8237, 75005 Paris, France
| | - Christophe David
- Laboratoire de photonique et de nanostructures, CNRS, route de Nozay, 91460 Marcoussis, France
| | - Sergii Rudiuk
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 Rue Lhomond, 75005 Paris, France
- Sorbonne Universités , UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Damien Baigl
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 Rue Lhomond, 75005 Paris, France
- Sorbonne Universités , UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - André Estevez-Torres
- Laboratoire Jean Perrin, Université Pierre et Marie Curie , 4 place Jussieu, 75005 Paris, France
- CNRS, UMR 8237, 75005 Paris, France
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38
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Molecular Combing of Single DNA Molecules on the 10 Megabase Scale. Sci Rep 2016; 6:19636. [PMID: 26781994 PMCID: PMC4726065 DOI: 10.1038/srep19636] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/14/2015] [Indexed: 02/06/2023] Open
Abstract
DNA combing allows the investigation of DNA replication on genomic single DNA molecules, but the lengths that can be analysed have been restricted to molecules of 200-500 kb. We have improved the DNA combing procedure so that DNA molecules can be analysed up to the length of entire chromosomes in fission yeast and up to 12 Mb fragments in human cells. Combing multi-Mb-scale DNA molecules revealed previously undetected origin clusters in fission yeast and shows that in human cells replication origins fire stochastically forming clusters of fired origins with an average size of 370 kb. We estimate that a single human cell forms around 3200 clusters at mid S-phase and fires approximately 100,000 origins to complete genome duplication. The procedure presented here will be adaptable to other organisms and experimental conditions.
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39
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Directly interrogating single quantum dot labelled UvrA2 molecules on DNA tightropes using an optically trapped nanoprobe. Sci Rep 2015; 5:18486. [PMID: 26691010 PMCID: PMC4686980 DOI: 10.1038/srep18486] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 11/18/2015] [Indexed: 02/06/2023] Open
Abstract
In this study we describe a new methodology to physically probe individual complexes formed between proteins and DNA. By combining nanoscale, high speed physical force measurement with sensitive fluorescence imaging we investigate the complex formed between the prokaryotic DNA repair protein UvrA2 and DNA. This approach uses a triangular, optically-trapped “nanoprobe” with a nanometer scale tip protruding from one vertex. By scanning this tip along a single DNA strand suspended between surface-bound micron-scale beads, quantum-dot tagged UvrA2 molecules bound to these ‘”DNA tightropes” can be mechanically interrogated. Encounters with UvrA2 led to deflections of the whole nanoprobe structure, which were converted to resistive force. A force histogram from all 144 detected interactions generated a bimodal distribution centered on 2.6 and 8.1 pN, possibly reflecting the asymmetry of UvrA2’s binding to DNA. These observations successfully demonstrate the use of a highly controllable purpose-designed and built synthetic nanoprobe combined with fluorescence imaging to study protein-DNA interactions at the single molecule level.
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40
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Kang SH, Hwang WS, Lin Z, Kwon SH, Hong SW. A Robust Highly Aligned DNA Nanowire Array-Enabled Lithography for Graphene Nanoribbon Transistors. NANO LETTERS 2015; 15:7913-7920. [PMID: 26569342 DOI: 10.1021/acs.nanolett.5b02946] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Because of its excellent charge carrier mobility at the Dirac point, graphene possesses exceptional properties for high-performance devices. Of particular interest is the potential use of graphene nanoribbons or graphene nanomesh for field-effect transistors. Herein, highly aligned DNA nanowire arrays were crafted by flow-assisted self-assembly of a drop of DNA aqueous solution on a flat polymer substrate. Subsequently, they were exploited as "ink" and transfer-printed on chemical vapor deposited (CVD)-grown graphene substrate. The oriented DNA nanowires served as the lithographic resist for selective removal of graphene, forming highly aligned graphene nanoribbons. Intriguingly, these graphene nanoribbons can be readily produced over a large area (i.e., millimeter scale) with a high degree of feature-size controllability and a low level of defects, rendering the fabrication of flexible two terminal devices and field-effect transistors.
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Affiliation(s)
| | - Wan Sik Hwang
- Department of Materials Engineering, Korea Aerospace University , Goyang 412-791, Republic of Korea
| | - Zhiqun Lin
- School of Materials Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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Vargas-Lara F, Stavis SM, Strychalski EA, Nablo BJ, Geist J, Starr FW, Douglas JF. Dimensional reduction of duplex DNA under confinement to nanofluidic slits. SOFT MATTER 2015; 11:8273-8284. [PMID: 26353028 DOI: 10.1039/c5sm01580d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
There has been much interest in the dimensional properties of double-stranded DNA (dsDNA) confined to nanoscale environments as a problem of fundamental importance in both biological and technological fields. This has led to a series of measurements by fluorescence microscopy of single dsDNA molecules under confinement to nanofluidic slits. Despite the efforts expended on such experiments and the corresponding theory and simulations of confined polymers, a consistent description of changes of the radius of gyration of dsDNA under strong confinement has not yet emerged. Here, we perform molecular dynamics (MD) simulations to identify relevant factors that might account for this inconsistency. Our simulations indicate a significant amplification of excluded volume interactions under confinement at the nanoscale due to the reduction of the effective dimensionality of the system. Thus, any factor influencing the excluded volume interaction of dsDNA, such as ionic strength, solution chemistry, and even fluorescent labels, can greatly influence the dsDNA size under strong confinement. These factors, which are normally less important in bulk solutions of dsDNA at moderate ionic strengths because of the relative weakness of the excluded volume interaction, must therefore be under tight control to achieve reproducible measurements of dsDNA under conditions of dimensional reduction. By simulating semi-flexible polymers over a range of parameter values relevant to the experimental systems and exploiting past theoretical treatments of the dimensional variation of swelling exponents and prefactors, we have developed a novel predictive relationship for the in-plane radius of gyration of long semi-flexible polymers under slit-like confinement. Importantly, these analytic expressions allow us to estimate the properties of dsDNA for the experimentally and biologically relevant range of contour lengths that is not currently accessible by state-of-the-art MD simulations.
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Affiliation(s)
- Fernando Vargas-Lara
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Samuel M Stavis
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Elizabeth A Strychalski
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Brian J Nablo
- Semiconductor and Dimensional Metrology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Jon Geist
- Semiconductor and Dimensional Metrology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Francis W Starr
- Department of Physics and Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Jack F Douglas
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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Li B, Zhang C, Jiang B, Han W, Lin Z. Flow-Enabled Self-Assembly of Large-Scale Aligned Nanowires. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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43
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Li B, Zhang C, Jiang B, Han W, Lin Z. Flow-Enabled Self-Assembly of Large-Scale Aligned Nanowires. Angew Chem Int Ed Engl 2015; 54:4250-4. [DOI: 10.1002/anie.201412388] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Indexed: 11/12/2022]
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Deen J, Sempels W, De Dier R, Vermant J, Dedecker P, Hofkens J, Neely RK. Combing of genomic DNA from droplets containing picograms of material. ACS NANO 2015; 9:809-816. [PMID: 25561163 PMCID: PMC4344373 DOI: 10.1021/nn5063497] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/05/2015] [Indexed: 05/30/2023]
Abstract
Deposition of linear DNA molecules is a critical step in many single-molecule genomic approaches including DNA mapping, fiber-FISH, and several emerging sequencing technologies. In the ideal situation, the DNA that is deposited for these experiments is absolutely linear and uniformly stretched, thereby enabling accurate distance measurements. However, this is rarely the case, and furthermore, current approaches for the capture and linearization of DNA on a surface tend to require complex surface preparation and large amounts of starting material to achieve genomic-scale mapping. This makes them technically demanding and prevents their application in emerging fields of genomics, such as single-cell based analyses. Here we describe a simple and extremely efficient approach to the deposition and linearization of genomic DNA molecules. We employ droplets containing as little as tens of picograms of material and simply drag them, using a pipet tip, over a polymer-coated coverslip. In this report we highlight one particular polymer, Zeonex, which is remarkably efficient at capturing DNA. We characterize the method of DNA capture on the Zeonex surface and find that the use of droplets greatly facilitates the efficient deposition of DNA. This is the result of a circulating flow in the droplet that maintains a high DNA concentration at the interface of the surface/solution. Overall, our approach provides an accessible route to the study of genomic structural variation from samples containing no more than a handful of cells.
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Affiliation(s)
- Jochem Deen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Wouter Sempels
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Raf De Dier
- Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46, Heverlee 3001, Belgium
| | - Jan Vermant
- Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46, Heverlee 3001, Belgium
- Department of Materials, ETH Zürich, Vladimir Prelog Weg 5, CH 8093 Zürich, Switzerland
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Robert K. Neely
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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Yasaki H, Onoshima D, Yasui T, Yukawa H, Kaji N, Baba Y. Microfluidic transfer of liquid interface for parallel stretching and stamping of terminal-unmodified single DNA molecules in zigzag-shaped microgrooves. LAB ON A CHIP 2015; 15:135-140. [PMID: 25318047 DOI: 10.1039/c4lc00990h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The molecular stretching of DNA is an indispensable tool for the optical exploration of base sequences and epigenomic changes of DNA at a single molecule level. In stretching terminal-unmodified DNA molecules parallel to each other on solid substrate, the receding meniscus assembly and capillary force through the dewetting process are quite useful. These can be achieved by pulling the substrate out of the DNA solution or sliding a droplet of DNA solution between a pair of substrates. However, currently used methods do not allow control over liquid interface motion and single-molecule DNA positioning. Here, we show a microfluidic device for stretching DNA molecules by syringing through microgrooves. The device can trap single DNA molecules at vertices of the microgrooves, which were designed as parallel zigzag lines. Different zigzag pattern depths, sizes, and shapes were studied to evaluate the adsorption possibility of DNA on the surface. The microfluidic transfer of the liquid interface stretched over 1500 DNA molecules simultaneously. The stretched DNA molecules could be stamped to a silanized surface. The device will therefore serve as a template preparation for high-resolution DNA imaging studies.
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Affiliation(s)
- Hirotoshi Yasaki
- Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
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Bialic M, Coulon V, Drac M, Gostan T, Schwob E. Analyzing the dynamics of DNA replication in Mammalian cells using DNA combing. Methods Mol Biol 2015; 1300:67-78. [PMID: 25916705 DOI: 10.1007/978-1-4939-2596-4_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
How cells duplicate their chromosomes is a key determinant of cell identity and genome stability. DNA replication can initiate from more than 100,000 sites distributed along mammalian chromosomes, yet a given cell uses only a subset of these origins due to inefficient origin activation and regulation by developmental or environmental cues. An impractical consequence of cell-to-cell variations in origin firing is that population-based techniques do not accurately describe how chromosomes are replicated in single cells. DNA combing is a biophysical DNA fiber stretching method which permits visualization of ongoing DNA synthesis along Mb-sized single-DNA molecules purified from cells that were previously pulse-labeled with thymidine analogues. This allows quantitative measurements of several salient features of chromosome replication dynamics, such as fork velocity, fork asymmetry, inter-origin distances, and global instant fork density. In this chapter we describe how to obtain this information from asynchronous cultures of mammalian cells.
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Affiliation(s)
- Marta Bialic
- Institute of Molecular Genetics, CNRS UMR5535 & Université Montpellier, 1919 route de Mende, Montpellier, 34293, France
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Hosseinidoust Z, Olsson AL, Tufenkji N. Going viral: Designing bioactive surfaces with bacteriophage. Colloids Surf B Biointerfaces 2014; 124:2-16. [DOI: 10.1016/j.colsurfb.2014.05.036] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/25/2014] [Accepted: 05/26/2014] [Indexed: 12/22/2022]
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Hughes CD, Simons M, Mackenzie CE, Van Houten B, Kad NM. Single molecule techniques in DNA repair: a primer. DNA Repair (Amst) 2014; 20:2-13. [PMID: 24819596 DOI: 10.1016/j.dnarep.2014.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
Abstract
A powerful new approach has become much more widespread and offers insights into aspects of DNA repair unattainable with billions of molecules. Single molecule techniques can be used to image, manipulate or characterize the action of a single repair protein on a single strand of DNA. This allows search mechanisms to be probed, and the effects of force to be understood. These physical aspects can dominate a biochemical reaction, where at the ensemble level their nuances are obscured. In this paper we discuss some of the many technical advances that permit study at the single molecule level. We focus on DNA repair to which these techniques are actively being applied. DNA repair is also a process that encompasses so much of what single molecule studies benefit--searching for targets, complex formation, sequential biochemical reactions and substrate hand-off to name just a few. We discuss how single molecule biophysics is poised to transform our understanding of biological systems, in particular DNA repair.
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Affiliation(s)
- Craig D Hughes
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Michelle Simons
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Cassidy E Mackenzie
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Neil M Kad
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
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49
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Liu R, Wong ST, Lau PPZ, Tomczak N. Stretching and imaging of single DNA chains on a hydrophobic polymer surface made of amphiphilic alternating comb-copolymer. ACS APPLIED MATERIALS & INTERFACES 2014; 6:2479-2485. [PMID: 24472014 DOI: 10.1021/am404907c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Functionalization of amine derivatized glass slides with a poly(maleic anhydride)-based comb-copolymer to facilitate stretching, aligning, and imaging of individual dsDNA chains is presented. The polymer-coated surface is hydrophobic due to the presence of the long alkyl side chains along the polymer backbone. The surface is also characterized by low roughness and a globular morphology. Stretched and aligned bacteriophage λ-DNA chains were obtained using a robust method based on stretching by a receding water meniscus at pH 7.8 without the need for small droplet volumes or precoating the surface with additional layers of (bio)molecules. Although the dye to DNA base pairs ratio did not influence substantially the stretching length distributions, a clear peak at stretching lengths close to the contour length of the dsDNA is visible at larger staining ratios.
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Affiliation(s)
- Rongrong Liu
- Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602
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50
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Zarkov A, Stoynov S, Nedelcheva-Veleva M. Novel glass slide preparation system for single DNA molecules analysis. BIOTECHNOL BIOTEC EQ 2014; 28:112-117. [PMID: 26019496 PMCID: PMC4434140 DOI: 10.1080/13102818.2014.901687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Here we propose an easy to build up and apply glass slide preparation system for single DNA molecules stretching. It is based on fast and simple coating of a solid glass with a cocktail of acrylic monomers that are easily polymerized via ultraviolet illumination. The acrylated slides are used to successfully stretch DNA molecules in a broader pH range compared to that of the commonly used amino-silanes. Moreover, the single DNA molecules that are stretched on the acrylated slides give a brighter and more photostable signal when visualized under a fluorescent microscope.
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