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Simon M, Prause A, Zauscher S, Gradzielski M. Self-Assembled Single-Stranded DNA Nano-Networks in Solution and at Surfaces. Biomacromolecules 2022; 23:1242-1250. [PMID: 35176851 DOI: 10.1021/acs.biomac.1c01493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We studied the directed self-assembly of two types of complementary single-stranded DNA (ssDNA) strands [i.e., poly(dA) and poly(dT)] into more complex, organized, and percolating networks in dilute solutions and at surfaces. Understanding ssDNA self-assembly into 2D networks on surfaces is important for the use of such networks in the fabrication of well-defined nanotechnological devices, as, for instance, required in nanoelectronics or for biosensing. To control the formation of 2D networks on surfaces, it is important to know whether DNA assemblies are formed already in dilute solutions or only during the drying/immobilization process at the surface, where the concentration automatically increases. Fluorescence cross-correlation spectroscopy clearly shows the presence of larger DNA complexes in mixed poly(dA) and poly(dT) solutions already at very low DNA concentrations (<1 nM), that is, well below the overlap concentration. Here, we describe for the first time such supramolecular complexes in solution and how their structure depends on the ssDNA length and concentration and ionic strength. Hence, future attempts to control such networks should also focus on network precursors in solution and not only on their immobilization on surfaces.
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Affiliation(s)
- Miriam Simon
- Stranski-Laboratorium für Physikalische und Theoretische Chemie, Institut für Chemie, Technische Universität Berlin, Berlin D-10623, Germany.,Department of Material Engineering and Material Science, Duke University, Durham, North Carolina 27708, United States.,Department of Chemical Engineering and the Russell Berrie Nanotechnolgy Institute (RBNI), Technion-Israel Institute of Technology, Haifa, Israel 3200003, Israel
| | - Albert Prause
- Stranski-Laboratorium für Physikalische und Theoretische Chemie, Institut für Chemie, Technische Universität Berlin, Berlin D-10623, Germany
| | - Stefan Zauscher
- Department of Material Engineering and Material Science, Duke University, Durham, North Carolina 27708, United States
| | - Michael Gradzielski
- Stranski-Laboratorium für Physikalische und Theoretische Chemie, Institut für Chemie, Technische Universität Berlin, Berlin D-10623, Germany
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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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Nazari ZE, Gomez Herrero J, Fojan P, Gurevich L. Formation of Conductive DNA-Based Nanowires via Conjugation of dsDNA with Cationic Peptide. NANOMATERIALS 2017; 7:nano7060128. [PMID: 28556794 PMCID: PMC5485775 DOI: 10.3390/nano7060128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 12/18/2022]
Abstract
A novel conductive DNA-based nanomaterial, DNA-peptide wire, composed of a DNA core and a peripheral peptide layer, is presented. The electrical conductivity of the wire is found to be at least three orders in magnitude higher than that of native double-stranded DNA (dsDNA). High conductivity of the wires along with a better resistance to mechanical deformations caused by interactions between the substrate and electrode surface make them appealing for a wide variety of nanoelectronic and biosensor applications.
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Affiliation(s)
- Zeinab Esmail Nazari
- Institute of Physics and Nanotechnology, Aalborg University, DK-9220 Aalborg, Denmark.
| | - Julio Gomez Herrero
- Department de Fisica de la Materia Condensada, Universidad Autonoma de Madrid, 28049 Madrid, Spain.
| | - Peter Fojan
- Institute of Physics and Nanotechnology, Aalborg University, DK-9220 Aalborg, Denmark.
| | - Leonid Gurevich
- Institute of Physics and Nanotechnology, Aalborg University, DK-9220 Aalborg, Denmark.
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Eidelshtein G, Kotlyar A, Hashemi M, Gurevich L. Aligned deposition and electrical measurements on single DNA molecules. NANOTECHNOLOGY 2015; 26:475102. [PMID: 26538384 DOI: 10.1088/0957-4484/26/47/475102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A reliable method of deposition of aligned individual dsDNA molecules on mica, silicon, and micro/nanofabricated circuits is presented. Complexes of biotinylated double stranded poly(dG)-poly(dC) DNA with avidin were prepared and deposited on mica and silicon surfaces in the absence of Mg(2+) ions. Due to its positive charge, the avidin attached to one end of the DNA anchors the complex to negatively charged substrates. Subsequent drying with a directional gas flow yields DNA molecules perfectly aligned on the surface. In the avidin-DNA complex only the avidin moiety is strongly and irreversibly bound to the surface, while the DNA counterpart interacts with the substrates much more weakly and can be lifted from the surface and realigned in any direction. Using this technique, avidin-DNA complexes were deposited across platinum electrodes on a silicon substrate. Electrical measurements on the deposited DNA molecules revealed linear IV-characteristics and exponential dependence on relative humidity.
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Affiliation(s)
- Gennady Eidelshtein
- Department of Biochemistry and Molecular Biology, George S Wise Faculty of Life Sciences and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
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Haidara H. Wetting-mediated collective tubulation and pearling in confined vesicular drops of DDAB solutions. SOFT MATTER 2014; 10:9460-9469. [PMID: 25343282 DOI: 10.1039/c4sm01579g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Whether driven by external mechanical stresses (shear flow) or induced by membrane-active peptides and/or proteins, the collective growth of tubules in membranous fluids has seldom been reported. The pearling destabilization of these membranous tubules which requires an activation of the shape distortion, often induced by optical tweezers, membrane-active biomolecules or an electrical field, has also rarely been observed under mild experimental conditions. Here we report such events of collective tubulation and pearling destabilization in sessile drops of a didodecyl-dimethylammonium bromide (DDAB) vesicular solution that are confined by a surrounding oil medium. Based on the wetting dynamics and the features of the tubulation process, we show that the growth of the tubules here relies on a mechanism of "pinning-induced pulling" from the retracting drop, rather than the classical hydrodynamic fingering instability. We show that the whole tubulation process is driven by a strong coupling between the bulk properties of the ternary (DAAB/water/oil) system and the dynamics of wetting. Finally, we discuss the pearling destabilization of these tubules under vanishing static interface tension and quite mild tensile force arising from their pulling. We show that under those mild conditions, shape disturbances readily grow, either as pearling waves moving toward the drop-reservoir or as Rayleigh-type peristaltic modulations. Besides revealing singular non-Rayleigh pearling modes, this work also brings new insights into the flow dynamics in membranous tubules anchored to an infinite reservoir.
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Affiliation(s)
- Hamidou Haidara
- Institut de Science des Matériaux de Mulhouse (IS2M), UMR 7361-CNRS/Université de Haute Alsace, 15 rue Jean Starcky, 68057 Mulhouse Cedex, France.
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Kiss B, Kellermayer MSZ. Stretching desmin filaments with receding meniscus reveals large axial tensile strength. J Struct Biol 2014; 186:472-80. [PMID: 24746912 DOI: 10.1016/j.jsb.2014.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 04/06/2014] [Accepted: 04/08/2014] [Indexed: 11/25/2022]
Abstract
Desmin forms the intermediate filament system of muscle cells where it plays important role in maintaining mechanical integrity and elasticity. Although the importance of intermediate-filament elasticity in cellular mechanics is being increasingly recognized, the molecular basis of desmin's elasticity is not fully understood. We explored desmin elasticity by molecular combing with forces calculated to be as large as 4nN. Average filament contour length increased 1.55-fold axial on average. Molecular combing together with EGTA-treatment caused the fragmentation of the filament into short, 60 to 120-nm-long and 4-nm-wide structures. The fragments display a surface periodicity of 38nm, suggesting that they are composed of laterally attached desmin dimers. The axis of the fragments may deviate significantly from that of the overstretched filament, indicating that they have a large orientational freedom in spite of being axially interconnected. The emergence of protofibril fragments thus suggests that the interconnecting head or tail domains of coiled-coil desmin dimers are load-bearing elements during axial stretch.
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Affiliation(s)
- Balázs Kiss
- Department of Biophysics and Radiation Biology, MTA-SE Molecular Biophysics Research Group, Semmelweis University, 1094 Budapest, Tűzoltó u. 37-47, Hungary.
| | - Miklós S Z Kellermayer
- Department of Biophysics and Radiation Biology, MTA-SE Molecular Biophysics Research Group, Semmelweis University, 1094 Budapest, Tűzoltó u. 37-47, Hungary
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Charlot B, Bardin F, Sanchez N, Roux P, Teixeira S, Schwob E. Elongated unique DNA strand deposition on microstructured substrate by receding meniscus assembly and capillary force. BIOMICROFLUIDICS 2014; 8:014103. [PMID: 24753724 PMCID: PMC3977786 DOI: 10.1063/1.4863575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 01/16/2014] [Indexed: 05/07/2023]
Abstract
Ordered deposition of elongated DNA molecules was achieved by the forced dewetting of a DNA solution droplet over a microstructured substrate. This technique allows trapping, uncoiling, and deposition of DNA fragments without the need of a physicochemical anchoring of the molecule and results in the combing of double stranded DNA from the edge of microwells on a polydimethylsiloxane (PDMS) substrate. The technique involves scanning a droplet of DNA solution caught between a movable blade and a PDMS substrate containing an array of microwells. The deposition and elongation appears when the receding meniscus dewets microwells, the latter acting here as a perturbation in the dewetting line forcing the water film to break locally. Thus, DNA molecules can be deposited in an ordered manner and elongated conformation based solely on a physical phenomenon, allowing uncoiled DNA molecules to be observed in all their length. However, the exact mechanism that governs the deposition of DNA strands is not well understood. This paper is an analysis of the physical phenomenon occurring in the deposition process and is based on observations made with the use of high frame/second rate video microscopy.
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Affiliation(s)
- B Charlot
- IES CNRS, Université Montpellier 2, France
| | - F Bardin
- IES CNRS, Université Montpellier 2, France ; Université de Nîmes, France
| | | | - P Roux
- SANOFI, Montpellier, France
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