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Lowe M, Glezer B, Toulan B, Hess B. Atomic force microscopy measurements and model of DNA bending caused by binding of AraC protein. J Mol Recognit 2023; 36:e2993. [PMID: 36112092 DOI: 10.1002/jmr.2993] [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: 07/22/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 12/15/2022]
Abstract
Atomic force microscopy (AFM) was used to conduct single-molecule imaging of protein/DNA complexes involved in the regulation of the arabinose operon of Escherichia coli. In the presence of arabinose, the transcription regulatory protein AraC binds to a 38 bp region consisting of the araI1 and araI2 half-sites. The domain positioning of full-length AraC, when bound to DNA, was not previously known. In this study, AraC was combined with 302 and 560 bp DNA and arabinose, deposited on a mica substrate, and imaged with AFM in air. High resolution images of 560 bp DNA, where bound protein was visible, showed that AraC induces a bend in the DNA with an angle 60° ± 12° with a median of 55°. These results are consistent with earlier gel electrophoresis measurements that measured the DNA bend angle based on migration rates. By using known domain structures of AraC, geometric constraints, and contacts determined from biochemical experiments, we developed a model of the tertiary and quaternary structure of DNA-bound AraC in the presence of arabinose. The DNA bend angle predicted by the model is in agreement with the measurement values. We discuss the results in view of other regulatory proteins that cause DNA bending and formation of the open complex to initiate transcription.
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Affiliation(s)
- Mary Lowe
- Physics Department, Loyola University Maryland, Baltimore, Maryland, USA
| | - Benjamin Glezer
- Physics Department, Loyola University Maryland, Baltimore, Maryland, USA
| | - Brendan Toulan
- Physics Department, Loyola University Maryland, Baltimore, Maryland, USA
| | - Brian Hess
- Physics Department, Loyola University Maryland, Baltimore, Maryland, USA
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2
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Main KHS, Provan JI, Haynes PJ, Wells G, Hartley JA, Pyne ALB. Atomic force microscopy-A tool for structural and translational DNA research. APL Bioeng 2021; 5:031504. [PMID: 34286171 PMCID: PMC8272649 DOI: 10.1063/5.0054294] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/07/2021] [Indexed: 12/26/2022] Open
Abstract
Atomic force microscopy (AFM) is a powerful imaging technique that allows for structural characterization of single biomolecules with nanoscale resolution. AFM has a unique capability to image biological molecules in their native states under physiological conditions without the need for labeling or averaging. DNA has been extensively imaged with AFM from early single-molecule studies of conformational diversity in plasmids, to recent examinations of intramolecular variation between groove depths within an individual DNA molecule. The ability to image dynamic biological interactions in situ has also allowed for the interaction of various proteins and therapeutic ligands with DNA to be evaluated-providing insights into structural assembly, flexibility, and movement. This review provides an overview of how innovation and optimization in AFM imaging have advanced our understanding of DNA structure, mechanics, and interactions. These include studies of the secondary and tertiary structure of DNA, including how these are affected by its interactions with proteins. The broader role of AFM as a tool in translational cancer research is also explored through its use in imaging DNA with key chemotherapeutic ligands, including those currently employed in clinical practice.
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Affiliation(s)
| | - James I. Provan
- Institute of Molecular, Cell, and Systems Biology, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | | | - Geoffrey Wells
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - John A. Hartley
- UCL Cancer Institute, University College London, London WC1E 6DD, United Kingdom
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Møller Sønderskov S, Hyldgaard Klausen L, Amland Skaanvik S, Han X, Dong M. In situ Surface Charge Density Visualization of Self-assembled DNA Nanostructures after Ion Exchange. Chemphyschem 2020; 21:1474-1482. [PMID: 32330354 PMCID: PMC7891384 DOI: 10.1002/cphc.201901168] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/14/2020] [Indexed: 12/30/2022]
Abstract
The charge density of DNA is a key parameter in strand hybridization and for the interactions occurring between DNA and molecules in biological systems. Due to the intricate structure of DNA, visualization of the surface charge density of DNA nanostructures under physiological conditions was not previously possible. Here, we perform a simultaneous analysis of the topography and surface charge density of DNA nanostructures using atomic force microscopy and scanning ion conductance microscopy. The effect of in situ ion exchange using various alkali metal ions is tested with respect to the adsorption of DNA origami onto mica, and a quantitative study of surface charge density reveals ion exchange phenomena in mica as a key parameter in DNA adsorption. This is important for structure-function studies of DNA nanostructures. The research provides an efficient approach to study surface charge density of DNA origami nanostructures and other biological molecules at a single molecule level.
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Affiliation(s)
| | - Lasse Hyldgaard Klausen
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University, Denmark
- Department of ChemistryStanford University333 Campus DriveStanfordCA 94305USA
| | | | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and EnvironmentSchool of Chemistry and Chemical EngineeringHarbin Institute of Technology, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University, Denmark
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Mikheikin A, Olsen A, Leslie K, Russell-Pavier F, Yacoot A, Picco L, Payton O, Toor A, Chesney A, Gimzewski JK, Mishra B, Reed J. DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle. Nat Commun 2017; 8:1665. [PMID: 29162844 PMCID: PMC5698298 DOI: 10.1038/s41467-017-01891-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/24/2017] [Indexed: 01/26/2023] Open
Abstract
Progress in whole-genome sequencing using short-read (e.g., <150 bp), next-generation sequencing technologies has reinvigorated interest in high-resolution physical mapping to fill technical gaps that are not well addressed by sequencing. Here, we report two technical advances in DNA nanotechnology and single-molecule genomics: (1) we describe a labeling technique (CRISPR-Cas9 nanoparticles) for high-speed AFM-based physical mapping of DNA and (2) the first successful demonstration of using DVD optics to image DNA molecules with high-speed AFM. As a proof of principle, we used this new “nanomapping” method to detect and map precisely BCL2–IGH translocations present in lymph node biopsies of follicular lymphoma patents. This HS-AFM “nanomapping” technique can be complementary to both sequencing and other physical mapping approaches. Physical mapping of DNA can be used to detect structural variants and for whole-genome haplotype assembly. Here, the authors use CRISPR-Cas9 and high-speed atomic force microscopy to ‘nanomap’ single molecules of DNA.
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Affiliation(s)
- Andrey Mikheikin
- Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA
| | - Anita Olsen
- Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA
| | - Kevin Leslie
- Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA
| | - Freddie Russell-Pavier
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, Middlesex, UK.,Interface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Andrew Yacoot
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, Middlesex, UK
| | - Loren Picco
- Interface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Oliver Payton
- Interface Analysis Centre, H. H. Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Amir Toor
- Department of Internal Medicine, VCU School of Medicine, Richmond, 23284, VA, USA.,VCU Massey Cancer Center, Richmond, 23284, VA, USA
| | - Alden Chesney
- VCU Massey Cancer Center, Richmond, 23284, VA, USA.,Department of Pathology, VCU School of Medicine, Richmond, 23284, VA, USA
| | - James K Gimzewski
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, 90095, CA, USA
| | - Bud Mishra
- Departments of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, 10012, NY, USA
| | - Jason Reed
- Department of Physics, Virginia Commonwealth University, Richmond, 23284, VA, USA. .,VCU Massey Cancer Center, Richmond, 23284, VA, USA.
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Sumino A, Uchihashi T, Oiki S. Oriented Reconstitution of the Full-Length KcsA Potassium Channel in a Lipid Bilayer for AFM Imaging. J Phys Chem Lett 2017; 8:785-793. [PMID: 28139934 DOI: 10.1021/acs.jpclett.6b03058] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Here, we have developed a method of oriented reconstitution of the KcsA potassium channel amenable to high-resolution AFM imaging. The solubilized full-length KcsA channels with histidine-tagged (His-tag) C-terminal ends were attached to a Ni2+-coated mica surface, and then detergent-destabilized liposomes were added to fill the interchannel space. AFM revealed that the membrane-embedded KcsA channels were oriented with their extracellular faces upward, seen as a tetrameric square shape. This orientation was corroborated by the visible binding of a peptide scorpion toxin, agitoxin-2. To observe the cytoplasmic side of the channel, a His-tag was inserted into the extracellular loop, and the oppositely oriented channels provided wholly different images. In either orientation, the channels were individually dispersed at acidic pH, whereas they were self-assembled at neutral pH, indicating that the oriented channels are allowed to diffuse in the membrane. This method is readily applicable to membrane proteins in general for AFM imaging.
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Affiliation(s)
- Ayumi Sumino
- PRESTO, Japan Science and Technology Agency (JST) , 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui , 23-3 Matsuokashimoaizuki, Yoshida-gun, Fukui 910-1193, Japan
| | - Takayuki Uchihashi
- Department of Physics, Kanazawa University , Kakuma-machi, Kanazawa 920-1192, Japan
- Bio-AFM Frontier Research Center , Kanazawa 920-1192, Japan
| | - Shigetoshi Oiki
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui , 23-3 Matsuokashimoaizuki, Yoshida-gun, Fukui 910-1193, Japan
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Ke S, Chen C, Fu N, Zhou H, Ye M, Lin P, Yuan W, Zeng X, Chen L, Huang H. Transparent Indium Tin Oxide Electrodes on Muscovite Mica for High-Temperature-Processed Flexible Optoelectronic Devices. ACS APPLIED MATERIALS & INTERFACES 2016; 8:28406-28411. [PMID: 27726330 DOI: 10.1021/acsami.6b09166] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Sn-doped In2O3 (ITO) electrodes were deposited on transparent and flexible muscovite mica. The use of mica substrate makes a high-temperature annealing process (up to 500 °C) possible. ITO/mica retains its low electric resistivity even after continuous bending of 1000 times on account of the unique layered structure of mica. When used as a transparent flexible heater, ITO/mica shows an extremely fast ramping (<15 s) up to a high temperature of over 438 °C. When used as a transparent electrode, ITO/mica permits a high-temperature annealing (450 °C) approach to fabricate flexible perovskite solar cells (PSCs) with high efficiency.
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Affiliation(s)
- Shanming Ke
- State Key Laboratory of Solidification Processing, Northwestern Polytechnical University , Xi'an 710072, P. R. China
| | | | - Nianqing Fu
- School of Materials Science and Engineering, South China University of Technology , Guangzhou 510640, PR China
| | | | | | | | | | | | - Lang Chen
- Department of Physics, South University of Science and Technology of China , Shenzhen, 518055, PR China
| | - Haitao Huang
- Department of Applied Physics and Materials Research Center, The Hong Kong Polytechnic University , Hung Hom, Kowloon, Hong Kong, PR China
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Pillers MA, Shute R, Farchone A, Linder KP, Doerfler R, Gavin C, Goss V, Lieberman M. Preparation of Mica and Silicon Substrates for DNA Origami Analysis and Experimentation. J Vis Exp 2015:e52972. [PMID: 26274888 PMCID: PMC4545022 DOI: 10.3791/52972] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The designed nature and controlled, one-pot synthesis of DNA origami provides exciting opportunities in many fields, particularly nanoelectronics. Many of these applications require interaction with and adhesion of DNA nanostructures to a substrate. Due to its atomically flat and easily cleaned nature, mica has been the substrate of choice for DNA origami experiments. However, the practical applications of mica are relatively limited compared to those of semiconductor substrates. For this reason, a straightforward, stable, and repeatable process for DNA origami adhesion on derivatized silicon oxide is presented here. To promote the adhesion of DNA nanostructures to silicon oxide surface, a self-assembled monolayer of 3-aminopropyltriethoxysilane (APTES) is deposited from an aqueous solution that is compatible with many photoresists. The substrate must be cleaned of all organic and metal contaminants using Radio Corporation of America (RCA) cleaning processes and the native oxide layer must be etched to ensure a flat, functionalizable surface. Cleanrooms are equipped with facilities for silicon cleaning, however many components of DNA origami buffers and solutions are often not allowed in them due to contamination concerns. This manuscript describes the set-up and protocol for in-lab, small-scale silicon cleaning for researchers who do not have access to a cleanroom or would like to incorporate processes that could cause contamination of a cleanroom CMOS clean bench. Additionally, variables for regulating coverage are discussed and how to recognize and avoid common sample preparation problems is described.
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Affiliation(s)
| | - Rebecca Shute
- Department of Chemistry and Biochemistry, University of Notre Dame
| | - Adam Farchone
- Department of Chemical and Biomolecular Engineering, University of Notre Dame
| | - Keenan P Linder
- Department of Chemistry, Physics, and Engineering Studies, Chicago State University
| | - Rose Doerfler
- Department of Chemical and Biomolecular Engineering, University of Notre Dame
| | - Corey Gavin
- Department of Technology, Ivy Tech Community College, South Bend, Indiana
| | - Valerie Goss
- Department of Chemistry, Physics, and Engineering Studies, Chicago State University
| | - Marya Lieberman
- Department of Chemistry and Biochemistry, University of Notre Dame
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Zhang F, Zhang P, Hou J, Yun X, Li W, Du Q, Chen Y. Large scale anomalous patterns of muscovite mica discovered by atomic force microscopy. ACS APPLIED MATERIALS & INTERFACES 2015; 7:8699-8705. [PMID: 25839085 DOI: 10.1021/acsami.5b00984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Muscovite mica is a widely used substrate because of its flatness. The large scale anomalous patterns of muscovite have been discovered by atomic force microscopy (AFM). These patterns distribute around the defects of the muscovite surface. By using different imaging modes and analyzing functions of AFM, these extraordinary patterns are thoroughly characterized, and it was revealed that some selected regularly aligned patterns mimic 2-D orthorhombic crystal systems surrounding the regular structure. However, such patterned nanostructures have no effects on the template-assisted self-assembly (or epitaxial growth) of a disease-related peptide GAV-9.
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Affiliation(s)
- Feng Zhang
- School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Ping Zhang
- School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Jiahua Hou
- School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Xiaoling Yun
- School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Wanrong Li
- School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Qiqige Du
- School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
| | - Youjun Chen
- School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China
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Billingsley DJ, Lee AJ, Johansson NAB, Walton A, Stanger L, Crampton N, Bonass WA, Thomson NH. Patchiness of ion-exchanged mica revealed by DNA binding dynamics at short length scales. NANOTECHNOLOGY 2014; 25:025704. [PMID: 24334563 DOI: 10.1088/0957-4484/25/2/025704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The binding of double-stranded (ds) DNA to mica can be controlled through ion-exchanging the mica with divalent cations. Measurements of the end-to-end distance of linear DNA molecules discriminate whether the binding mechanism occurs through 2D surface equilibration or kinetic trapping. A range of linear dsDNA fragments have been used to investigate length dependences of binding. Mica, ion-exchanged with Ni(II) usually gives rise to kinetically trapped DNA molecules, however, short linear fragments (<800 bp) are seen to deviate from the expected behaviour. This indicates that ion-exchanged mica is heterogeneous, and contains patches or domains, separating different ionic species. These results correlate with imaging of dsDNA under aqueous buffer on Ni(II)-mica and indicate that binding domains are of the order of 100 nm in diameter. Shorter DNA fragments behave intermediate to the two extreme cases of 2D equilibration and kinetic trapping. Increasing the incubation time of Ni(II) on mica, from minutes to hours, brings the conformations of the shorter DNA fragments closer to the theoretical value for kinetic trapping, indicating that long timescale kinetics play a role in ion-exchange. X-ray photoelectron spectroscopy (XPS) was used to confirm that the relative abundance of Ni(II) ions on the mica surface increases with time. These findings can be used to enhance spatial control of binding of DNA to inorganic surfaces with a view to patterning high densities arrays.
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Affiliation(s)
- D J Billingsley
- School of Physics and Astronomy, University of Leeds, Woodhouse Lane, Leeds, West Yorkshire LS2 9JT, UK. Department of Oral Biology, School of Dentistry, University of Leeds, Woodhouse Lane, Leeds, West Yorkshire LS2 9LU, UK
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