1
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Majzner K, Deckert-Gaudig T, Baranska M, Deckert V. DOX-DNA Interactions on the Nanoscale: In Situ Studies Using Tip-Enhanced Raman Scattering. Anal Chem 2024; 96:8905-8913. [PMID: 38771097 PMCID: PMC11154666 DOI: 10.1021/acs.analchem.3c05372] [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: 11/27/2023] [Revised: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024]
Abstract
Chemotherapeutic anthracyclines, like doxorubicin (DOX), are drugs endowed with cytostatic activity and are widely used in antitumor therapy. Their molecular mechanism of action involves the formation of a stable anthracycline-DNA complex, which prevents cell division and results in cell death. It is known that elevated DOX concentrations induce DNA chain loops and overlaps. Here, for the first time, tip-enhanced Raman scattering was used to identify and localize intercalated DOX in isolated double-stranded calf thymus DNA, and the correlated near-field spectroscopic and morphologic experiments locate the DOX molecules in the DNA and provide further information regarding specific DOX-nucleobase interactions. Thus, the study provides a tool specifically for identifying intercalation markers and generally analyzing drug-DNA interactions. The structure of such complexes down to the molecular level provides mechanistic information about cytotoxicity and the development of potential anticancer drugs.
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Affiliation(s)
- Katarzyna Majzner
- Department
of Chemical Physics, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Tanja Deckert-Gaudig
- Friedrich
Schiller University Jena, Institute of Physical Chemistry and Abbe
Center of Photonics, Helmholtzweg 4, Jena 07743, Germany
- Leibniz
Insti-tute of Photonic Technology, Albert-Einstein-Str.9, Jena 07745, Germany
| | - Malgorzata Baranska
- Department
of Chemical Physics, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Jagiellonian
Centre for Exper-Imental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
| | - Volker Deckert
- Friedrich
Schiller University Jena, Institute of Physical Chemistry and Abbe
Center of Photonics, Helmholtzweg 4, Jena 07743, Germany
- Leibniz
Insti-tute of Photonic Technology, Albert-Einstein-Str.9, Jena 07745, Germany
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2
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Allen FI, De Teresa JM, Onoa B. Focused Helium Ion and Electron Beam-Induced Deposition of Organometallic Tips for Dynamic Atomic Force Microscopy of Biomolecules in Liquid. ACS APPLIED MATERIALS & INTERFACES 2024; 16:4439-4448. [PMID: 38244049 DOI: 10.1021/acsami.3c16407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
We demonstrate the fabrication of sharp nanopillars of high aspect ratio onto specialized atomic force microscopy (AFM) microcantilevers and their use for high-speed AFM of DNA and nucleoproteins in liquid. The fabrication technique uses localized charged-particle-induced deposition with either a focused beam of helium ions or electrons in a helium ion microscope (HIM) or scanning electron microscope (SEM). This approach enables customized growth onto delicate substrates with nanometer-scale placement precision and in situ imaging of the final tip structures using the HIM or SEM. Tip radii of <10 nm are obtained and the underlying microcantilever remains intact. Instead of the more commonly used organic precursors employed for bio-AFM applications, we use an organometallic precursor (tungsten hexacarbonyl) resulting in tungsten-containing tips. Transmission electron microscopy reveals a thin layer of carbon on the tips. The interaction of the new tips with biological specimens is therefore likely very similar to that of standard carbonaceous tips, with the added benefit of robustness. A further advantage of the organometallic tips is that compared to carbonaceous tips they better withstand UV-ozone cleaning treatments to remove residual organic contaminants between experiments, which are inevitable during the scanning of soft biomolecules in liquid. Our tips can also be grown onto the blunted tips of previously used cantilevers, thus providing a means to recycle specialized cantilevers and restore their performance to the original manufacturer specifications. Finally, a focused helium ion beam milling technique to reduce the tip radii and thus further improve lateral spatial resolution in the AFM scans is demonstrated.
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Affiliation(s)
- Frances I Allen
- Department of Materials Science and Engineering, University of California, Berkeley, California 97420, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 97420, United States
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 97420, United States
| | - José María De Teresa
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain
| | - Bibiana Onoa
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 97420, United States
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3
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Ibrahim M, Wenzel C, Lallemang M, Balzer BN, Schwierz N. Adsorbing DNA to Mica by Cations: Influence of Valency and Ion Type. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15553-15562. [PMID: 37877163 DOI: 10.1021/acs.langmuir.3c01835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Ion-mediated attraction between DNA and mica plays a crucial role in biotechnological applications and molecular imaging. Here, we combine molecular dynamics simulations and single-molecule atomic force microscopy experiments to characterize the detachment forces of single-stranded DNA at mica surfaces mediated by the metal cations Li+, Na+, K+, Cs+, Mg2+, and Ca2+. Ion-specific adsorption at the mica/water interface compensates (Li+ and Na+) or overcompensates (K+, Cs+, Mg2+, and Ca2+) the bare negative surface charge of mica. In addition, direct and water-mediated contacts are formed between the ions, the phosphate oxygens of DNA, and mica. The different contact types give rise to low- and high-force pathways and a broad distribution of detachment forces. Weakly hydrated ions, such as Cs+ and water-mediated contacts, lead to low detachment forces and high mobility of the DNA on the surface. Direct ion-DNA or ion-surface contacts lead to significantly higher forces. The comprehensive view gained from our combined approach allows us to highlight the most promising cations for imaging in physiological conditions: K+, which overcompensates the negative mica charge and induces long-ranged attractions. Mg2+ and Ca2+, which form a few specific and long-lived contacts to bind DNA with high affinity.
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Affiliation(s)
- Mohd Ibrahim
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Christiane Wenzel
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Max Lallemang
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
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4
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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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5
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Seweryn S, Skirlińska-Nosek K, Sofińska K, Szajna K, Kobierski J, Awsiuk K, Szymoński M, Lipiec E. Optimization of tip-enhanced Raman spectroscopy for probing the chemical structure of DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121595. [PMID: 35843060 DOI: 10.1016/j.saa.2022.121595] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/09/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Tip-enhanced Raman (TER) spectroscopy combines the nanometric spatial resolution of atomic force microscopy (AFM) and the chemical sensitivity of Raman spectroscopy. Thus, it provides a unique possibility to obtain spectroscopic information on individual, nanometre-size molecules. The enhancement of Raman scattering cross-section requires modification of the AFM tip apex with a plasmonic nanostructure. Despite numerous advances of TERS research, attaining good reproducibility and stable enhancement is still challenging mainly due to the lack of optimized probes and sample preparation procedures. Moreover, current nanospectroscopic standard samples - carbon nanotubes (CNTs) have relatively simple chemical structure, and therefore, they are far from real-life analytes, especially biological samples. In this work we focus on the optimization of TERS technique for efficient DNA measurements, including: a preparation of atomically-flat gold substrates, fixative free deposition of DNA and optimization of TERS probe preparation. Here we demonstrate a comprehensive comparison of the efficacy of several types of TERS probes. Applying the systematic approach, we obtained reliable and reproducible TER spectra of DNA. Thus, we provide preparation procedures of a new standard TERS sample, TERS substrates and TERS probes. Our research provides a solid foundation for further research on DNA and its interaction with other biomolecules upon biologically significant processes such as DNA damage and repair.
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Affiliation(s)
- Sara Seweryn
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | | | - Kamila Sofińska
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Konrad Szajna
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Jan Kobierski
- Department of Pharmaceutical Biophysics, Faculty of Pharmacy, Jagiellonian University Medical College, 31-007 Kraków, Poland
| | - Kamil Awsiuk
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Marek Szymoński
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Ewelina Lipiec
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland.
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6
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Capocefalo A, Bizien T, Sennato S, Ghofraniha N, Bordi F, Brasili F. Responsivity of Fractal Nanoparticle Assemblies to Multiple Stimuli: Structural Insights on the Modulation of the Optical Properties. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:1529. [PMID: 35564238 PMCID: PMC9099587 DOI: 10.3390/nano12091529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/23/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022]
Abstract
Multi-responsive nanomaterials based on the self-limited assembly of plasmonic nanoparticles are of great interest due to their widespread employment in sensing applications. We present a thorough investigation of a hybrid nanomaterial based on the protein-mediated aggregation of gold nanoparticles at varying protein concentration, pH and temperature. By combining Small Angle X-ray Scattering with extinction spectroscopy, we are able to frame the morphological features of the formed fractal aggregates in a theoretical model based on patchy interactions. Based on this, we established the main factors that determine the assembly process and their strong correlation with the optical properties of the assemblies. Moreover, the calibration curves that we obtained for each parameter investigated based on the extinction spectra point out to the notable flexibility of this nanomaterial, enabling the selection of different working ranges with high sensitivity. Our study opens for the rational tuning of the morphology and the optical properties of plasmonic assemblies to design colorimetric sensors with improved performances.
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Affiliation(s)
- Angela Capocefalo
- Institute for Complex Systems (ISC-CNR), National Research Council, 00185 Rome, Italy; (S.S.); (N.G.); (F.B.)
- Department of Physics, Sapienza University of Rome, 00185 Rome, Italy
| | - Thomas Bizien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48, CEDEX, 91192 Gif-sur-Yvette, France;
| | - Simona Sennato
- Institute for Complex Systems (ISC-CNR), National Research Council, 00185 Rome, Italy; (S.S.); (N.G.); (F.B.)
| | - Neda Ghofraniha
- Institute for Complex Systems (ISC-CNR), National Research Council, 00185 Rome, Italy; (S.S.); (N.G.); (F.B.)
| | - Federico Bordi
- Institute for Complex Systems (ISC-CNR), National Research Council, 00185 Rome, Italy; (S.S.); (N.G.); (F.B.)
- Department of Physics, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Brasili
- Institute for Complex Systems (ISC-CNR), National Research Council, 00185 Rome, Italy; (S.S.); (N.G.); (F.B.)
- Department of Physics, Sapienza University of Rome, 00185 Rome, Italy
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7
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Chardon F, Japaridze A, Witt H, Velikovsky L, Chakraborty C, Wilhelm T, Dumont M, Yang W, Kikuti C, Gangnard S, Mace AS, Wuite G, Dekker C, Fachinetti D. CENP-B-mediated DNA loops regulate activity and stability of human centromeres. Mol Cell 2022; 82:1751-1767.e8. [PMID: 35320753 DOI: 10.1016/j.molcel.2022.02.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/25/2022]
Abstract
Chromosome inheritance depends on centromeres, epigenetically specified regions of chromosomes. While conventional human centromeres are known to be built of long tandem DNA repeats, much of their architecture remains unknown. Using single-molecule techniques such as AFM, nanopores, and optical tweezers, we find that human centromeric DNA exhibits complex DNA folds such as local hairpins. Upon binding to a specific sequence within centromeric regions, the DNA-binding protein CENP-B compacts centromeres by forming pronounced DNA loops between the repeats, which favor inter-chromosomal centromere compaction and clustering. This DNA-loop-mediated organization of centromeric chromatin participates in maintaining centromere position and integrity upon microtubule pulling during mitosis. Our findings emphasize the importance of DNA topology in centromeric regulation and stability.
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Affiliation(s)
- Florian Chardon
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Hannes Witt
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Leonid Velikovsky
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Camellia Chakraborty
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Therese Wilhelm
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Marie Dumont
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Wayne Yang
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Carlos Kikuti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Stephane Gangnard
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Anne-Sophie Mace
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Gijs Wuite
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France.
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8
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Cialla-May D, Krafft C, Rösch P, Deckert-Gaudig T, Frosch T, Jahn IJ, Pahlow S, Stiebing C, Meyer-Zedler T, Bocklitz T, Schie I, Deckert V, Popp J. Raman Spectroscopy and Imaging in Bioanalytics. Anal Chem 2021; 94:86-119. [PMID: 34920669 DOI: 10.1021/acs.analchem.1c03235] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Dana Cialla-May
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Christoph Krafft
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Tanja Deckert-Gaudig
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Torsten Frosch
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Izabella J Jahn
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Susanne Pahlow
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Clara Stiebing
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Tobias Meyer-Zedler
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Thomas Bocklitz
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Iwan Schie
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany.,Ernst-Abbe-Hochschule Jena, University of Applied Sciences, Department of Biomedical Engineering and Biotechnology, Carl-Zeiss-Promenade 2, 07745 Jena, Germany
| | - Volker Deckert
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Jürgen Popp
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance - Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany.,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
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9
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Revealing DNA Structure at Liquid/Solid Interfaces by AFM-Based High-Resolution Imaging and Molecular Spectroscopy. Molecules 2021; 26:molecules26216476. [PMID: 34770895 PMCID: PMC8587808 DOI: 10.3390/molecules26216476] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
DNA covers the genetic information in all living organisms. Numerous intrinsic and extrinsic factors may influence the local structure of the DNA molecule or compromise its integrity. Detailed understanding of structural modifications of DNA resulting from interactions with other molecules and surrounding environment is of central importance for the future development of medicine and pharmacology. In this paper, we review the recent achievements in research on DNA structure at nanoscale. In particular, we focused on the molecular structure of DNA revealed by high-resolution AFM (Atomic Force Microscopy) imaging at liquid/solid interfaces. Such detailed structural studies were driven by the technical developments made in SPM (Scanning Probe Microscopy) techniques. Therefore, we describe here the working principles of AFM modes allowing high-resolution visualization of DNA structure under native (liquid) environment. While AFM provides well-resolved structure of molecules at nanoscale, it does not reveal the chemical structure and composition of studied samples. The simultaneous information combining the structural and chemical details of studied analyte allows achieve a comprehensive picture of investigated phenomenon. Therefore, we also summarize recent molecular spectroscopy studies, including Tip-Enhanced Raman Spectroscopy (TERS), on the DNA structure and its structural rearrangements.
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10
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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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11
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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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12
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Brasili F, Capocefalo A, Palmieri D, Capitani F, Chiessi E, Paradossi G, Bordi F, Domenici F. Assembling patchy plasmonic nanoparticles with aggregation-dependent antibacterial activity. J Colloid Interface Sci 2020; 580:419-428. [DOI: 10.1016/j.jcis.2020.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023]
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13
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Structural and DNA binding properties of mycobacterial integration host factor mIHF. J Struct Biol 2020; 209:107434. [PMID: 31846718 DOI: 10.1016/j.jsb.2019.107434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/06/2019] [Accepted: 12/11/2019] [Indexed: 01/08/2023]
Abstract
In bacteria, nucleoid associated proteins (NAPs) take part in active chromosome organization by supercoil management, three-dimensional DNA looping and direct transcriptional control. Mycobacterial integration host factor (mIHF, rv1388) is a NAP restricted to Actinobacteria and essential for survival of the human pathogen Mycobacterium tuberculosis. We show in vitro that DNA binding by mIHF strongly stabilizes the protein and increases its melting temperature. The structure obtained by Nuclear Magnetic Resonance (NMR) spectroscopy characterizes mIHF as a globular protein with a protruding alpha helix and a disordered N-terminus, similar to Streptomyces coelicolor IHF (sIHF). NMR revealed no residues of high flexibility, suggesting that mIHF is a rigid protein overall that does not undergo structural rearrangements. We show that mIHF only binds to double stranded DNA in solution, through two DNA binding sites (DBSs) similar to those identified in the X-ray structure of sIHF. According to Atomic Force Microscopy, mIHF is able to introduce left-handed loops of ca. 100 nm size (~300 bp) in supercoiled cosmids, thereby unwinding and relaxing the DNA.
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14
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Caprara D, Ripanti F, Capocefalo A, Sarra A, Brasili F, Petrillo C, Fasolato C, Postorino P. DNA-functionalized gold nanoparticle assemblies for Surface Enhanced Raman Scattering. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2019.124399] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Heenan PR, Perkins TT. Imaging DNA Equilibrated onto Mica in Liquid Using Biochemically Relevant Deposition Conditions. ACS NANO 2019; 13:4220-4229. [PMID: 30938988 DOI: 10.1021/acsnano.8b09234] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
For over 25 years, imaging of DNA by atomic force microscopy has been intensely pursued. Ideally, such images are then used to probe the physical properties of DNA and characterize protein-DNA interactions. The atomic flatness of mica makes it the preferred substrate for high signal-to-noise ratio (SNR) imaging, but the negative charge of mica and DNA hinders deposition. Traditional methods for imaging DNA and protein-DNA complexes in liquid have drawbacks: DNA conformations with an anomalous persistence length ( p), low SNR, and/or ionic deposition conditions detrimental to preserving protein-DNA interactions. Here, we developed a process to bind DNA to mica in a buffer containing both MgCl2 and KCl that resulted in high SNR images of equilibrated DNA in liquid. Achieving an equilibrated 2D configuration ( i. e., p = 50 nm) not only implied a minimally perturbative binding process but also improved data quality and quantity because the DNA's configuration was more extended. In comparison to a purely NiCl2-based protocol, we showed that an 8-fold larger fraction (90%) of 680-nm-long DNA molecules could be quantified. High-resolution images of select equilibrated molecules revealed the right-handed structure of DNA with a helical pitch of 3.5 nm. Deposition and imaging of DNA was achieved over a wide range of monovalent and divalent ionic conditions, including a buffer containing 50 mM KCl and 3 mM MgCl2. Finally, we imaged two protein-DNA complexes using this protocol: a restriction enzyme bound to DNA and a small three-nucleosome array. We expect such deposition of protein-DNA complexes at biochemically relevant ionic conditions will facilitate biophysical insights derived from imaging diverse protein-DNA complexes.
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Affiliation(s)
- Patrick R Heenan
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
- Department of Physics , University of Colorado , Boulder , Colorado 80309 , United States
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado , Boulder , Colorado 80309 , United States
- Department of Molecular, Cellular, and Developmental Biology , University of Colorado , Boulder , Colorado 80309 , United States
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16
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Kim E, Agarwal S, Kim N, Hage FS, Leonardo V, Gelmi A, Stevens MM. Bioinspired Fabrication of DNA-Inorganic Hybrid Composites Using Synthetic DNA. ACS NANO 2019; 13:2888-2900. [PMID: 30741535 PMCID: PMC6439439 DOI: 10.1021/acsnano.8b06492] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 02/06/2019] [Indexed: 05/19/2023]
Abstract
Nucleic acid nanostructures have attracted significant interest as potential therapeutic and diagnostic platforms due to their intrinsic biocompatibility and biodegradability, structural and functional diversity, and compatibility with various chemistries for modification and stabilization. Among the fabrication approaches for such structures, the rolling circle techniques have emerged as particularly promising, producing morphologically round, flower-shaped nucleic acid particles: typically hybrid composites of long nucleic acid strands and inorganic magnesium pyrophosphate (Mg2PPi). These constructs are known to form via anisotropic nucleic acid-driven crystallization in a sequence-independent manner, rendering monodisperse and densely packed RNA or DNA-inorganic composites. However, it still remains to fully explore how flexible polymer-like RNA or DNA strands (acting as biomolecular additives) mediate the crystallization process of Mg2PPi and affect the structure and properties of the product crystals. To address this, we closely examined nanoscale details to mesoscopic features of Mg2PPi/DNA hybrid composites fabricated by two approaches, namely rolling circle amplification (RCA)-based in situ synthesis and long synthetic DNA-mediated crystallization. Similar to the DNA constructs fabricated by RCA, the rapid crystallization of Mg2PPi was retarded on a short-range order when we precipitated the crystals in the presence of presynthesized long DNA, which resulted in effective incorporation of biomolecular additives such as DNA and enzymes. These findings further provide a more feasible way to encapsulate bioactive enzymes within DNA constructs compared to in situ RCA-mediated synthesis, i.e., by not only protecting them from possible denaturation under the reaction conditions but also preventing nonselective association of proteins arising from the RCA reaction mixtures.
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Affiliation(s)
- Eunjung Kim
- Department
of Materials, Department of Bioengineering and Institute for Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Shweta Agarwal
- Department
of Materials, Department of Bioengineering and Institute for Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Nayoung Kim
- Department
of Materials, Department of Bioengineering and Institute for Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Fredrik Sydow Hage
- SuperSTEM
Laboratory, SciTech Daresbury Campus, Daresbury WA4 4AD, United Kingdom
| | - Vincent Leonardo
- Department
of Materials, Department of Bioengineering and Institute for Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Amy Gelmi
- Department
of Materials, Department of Bioengineering and Institute for Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Molly M. Stevens
- Department
of Materials, Department of Bioengineering and Institute for Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
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17
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Atomic force microscopy study of EDTA induced desorption of metal ions immobilized DNA from mica surface. Ultramicroscopy 2019; 199:7-15. [PMID: 30711717 DOI: 10.1016/j.ultramic.2019.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/26/2019] [Indexed: 01/25/2023]
Abstract
Adsorption of DNA molecules onto substrate, such as mica, is well documented. However, desorption of the immobilized DNA molecules from substrate, which is also an important aspect of DNA behavior on substrate, has not been paid much attention. Here, DNA molecules were first immobilized on mica surface by using divalent metal ions as the bridge agents. Desorption of the immobilized DNA from mica surface was realized via ethylenediamine tetraacetic acid disodium salt (EDTA) treatment. EDTA is a chelating agent; it can remove the bridging metal ions between DNA and mica, which leads to the release of DNA molecules from mica substrate. The divalent metal ions assisted DNA adsorption onto mica surface and the EDTA induced DNA desorption from mica surface were followed by atomic force microscopy (AFM). Randomly dispersed DNA strands and DNA networks are two distinct adsorption morphologies of DNA on mica surface and their desorption processes from mica surface induced by EDTA are also different. Other factors that influence the EDTA-induced DNA desorption, such as type of bridging metal ion and DNA molecule length, have also been systematically studied. Moreover, EDTA treatment has no effect on the integrity of DNA molecule. The EDTA induced desorption of metal ions immobilized DNA from mica surface is simple and effective, which has potential applications in DNA separation and purification, DNA biophysics, and DNA-based nanotechnology.
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18
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Kobierski J, Lipiec E. DNA structure change induced by guanosine radicals – A theoretical and spectroscopic study of proton radiation damage. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.10.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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19
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Lipiec E, Perez‐Guaita D, Kaderli J, Wood BR, Zenobi R. Direct Nanospectroscopic Verification of the Amyloid Aggregation Pathway. Angew Chem Int Ed Engl 2018; 57:8519-8524. [DOI: 10.1002/anie.201803234] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/22/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Ewelina Lipiec
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences 31-342 Krakow Poland
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - David Perez‐Guaita
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Janina Kaderli
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
| | - Bayden R. Wood
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
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20
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Lipiec E, Perez‐Guaita D, Kaderli J, Wood BR, Zenobi R. Direct Nanospectroscopic Verification of the Amyloid Aggregation Pathway. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ewelina Lipiec
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences 31-342 Krakow Poland
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - David Perez‐Guaita
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Janina Kaderli
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
| | - Bayden R. Wood
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
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21
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Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States. Sci Rep 2018; 8:6163. [PMID: 29670174 PMCID: PMC5906655 DOI: 10.1038/s41598-018-24499-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/04/2018] [Indexed: 01/03/2023] Open
Abstract
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated and the supercoiling degree of defined genome regions may change according to physiological and environmental conditions. Elucidation of structural properties of DNA molecules with different topology may thus help to better understand genome functions. Whereas a number of structural studies have been published on highly negatively supercoiled DNA molecules, only preliminary observations of highly positively supercoiled are available, and a description of DNA structural properties over the full range of supercoiling degree is lacking. Atomic Force Microscopy (AFM) is a powerful tool to study DNA structure at single molecule level. We here report a comprehensive analysis by AFM of DNA plasmid molecules with defined supercoiling degree, covering the full spectrum of biologically relevant topologies, under different observation conditions. Our data, supported by statistical and biochemical analyses, revealed striking differences in the behavior of positive and negative plasmid molecules.
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22
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Deckert-Gaudig T, Taguchi A, Kawata S, Deckert V. Tip-enhanced Raman spectroscopy - from early developments to recent advances. Chem Soc Rev 2018. [PMID: 28640306 DOI: 10.1039/c7cs00209b] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An analytical technique operating at the nanoscale must be flexible regarding variable experimental conditions while ideally also being highly specific, extremely sensitive, and spatially confined. In this respect, tip-enhanced Raman scattering (TERS) has been demonstrated to be ideally suited to, e.g., elucidating chemical reaction mechanisms, determining the distribution of components and identifying and localizing specific molecular structures at the nanometre scale. TERS combines the specificity of Raman spectroscopy with the high spatial resolution of scanning probe microscopies by utilizing plasmonic nanostructures to confine the incident electromagnetic field and increase it by many orders of magnitude. Consequently, molecular structure information in the optical near field that is inaccessible to other optical microscopy methods can be obtained. In this general review, the development of this still-young technique, from early experiments to recent achievements concerning inorganic, organic, and biological materials, is addressed. Accordingly, the technical developments necessary for stable and reliable AFM- and STM-based TERS experiments, together with the specific properties of the instruments under different conditions, are reviewed. The review also highlights selected experiments illustrating the capabilities of this emerging technique, the number of users of which has steadily increased since its inception in 2000. Finally, an assessment of the frontiers and new concepts of TERS, which aim towards rendering it a general and widely applicable technique that combines the highest possible lateral resolution and extreme sensitivity, is provided.
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Affiliation(s)
- Lifu Xiao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Zachary D Schultz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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24
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Meroni A, Lazzaro F, Muzi-Falconi M, Podestà A. Characterization of Structural and Configurational Properties of DNA by Atomic Force Microscopy. Methods Mol Biol 2018; 1672:557-573. [PMID: 29043648 DOI: 10.1007/978-1-4939-7306-4_37] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We describe a method to extract quantitative information on DNA structural and configurational properties from high-resolution topographic maps recorded by atomic force microscopy (AFM). DNA molecules are deposited on mica surfaces from an aqueous solution, carefully dehydrated, and imaged in air in Tapping Mode. Upon extraction of the spatial coordinates of the DNA backbones from AFM images, several parameters characterizing DNA structure and configuration can be calculated. Here, we explain how to obtain the distribution of contour lengths, end-to-end distances, and gyration radii. This modular protocol can be also used to characterize other statistical parameters from AFM topographies.
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Affiliation(s)
- Alice Meroni
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133, Milano, Italy
| | - Federico Lazzaro
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133, Milano, Italy
| | - Marco Muzi-Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133, Milano, Italy
| | - Alessandro Podestà
- Dipartimento di Fisica and C.I.Ma.I.Na, Università degli Studi di Milano, via Celoria 16, 20133, Milano, Italy.
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25
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Bonhommeau S, Lecomte S. Tip-Enhanced Raman Spectroscopy: A Tool for Nanoscale Chemical and Structural Characterization of Biomolecules. Chemphyschem 2017; 19:8-18. [DOI: 10.1002/cphc.201701067] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/04/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Sébastien Bonhommeau
- University of Bordeaux; Institut des Sciences Moléculaires; CNRS UMR 5255; 351 cours de la Libération 33405 Talence cedex France
| | - Sophie Lecomte
- University of Bordeaux; Institut de Chimie et Biologie des Membranes et des Nano-objets; CNRS UMR 5248; Allée Geoffroy Saint Hilaire 33600 Pessac France
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26
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Meroni A, Mentegari E, Crespan E, Muzi-Falconi M, Lazzaro F, Podestà A. The Incorporation of Ribonucleotides Induces Structural and Conformational Changes in DNA. Biophys J 2017; 113:1373-1382. [PMID: 28978432 PMCID: PMC5627062 DOI: 10.1016/j.bpj.2017.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/20/2017] [Accepted: 07/25/2017] [Indexed: 02/04/2023] Open
Abstract
Ribonucleotide incorporation is the most common error occurring during DNA replication. Cells have hence developed mechanisms to remove ribonucleotides from the genome and restore its integrity. Indeed, the persistence of ribonucleotides into DNA leads to severe consequences, such as genome instability and replication stress. Thus, it becomes important to understand the effects of ribonucleotides incorporation, starting from their impact on DNA structure and conformation. Here we present a systematic study of the effects of ribonucleotide incorporation into DNA molecules. We have developed, to our knowledge, a new method to efficiently synthesize long DNA molecules (hundreds of basepairs) containing ribonucleotides, which is based on a modified protocol for the polymerase chain reaction. By means of atomic force microscopy, we could therefore investigate the changes, upon ribonucleotide incorporation, of the structural and conformational properties of numerous DNA populations at the single-molecule level. Specifically, we characterized the scaling of the contour length with the number of basepairs and the scaling of the end-to-end distance with the curvilinear distance, the bending angle distribution, and the persistence length. Our results revealed that ribonucleotides affect DNA structure and conformation on scales that go well beyond the typical dimension of the single ribonucleotide. In particular, the presence of ribonucleotides induces a systematic shortening of the molecules, together with a decrease of the persistence length. Such structural changes are also likely to occur in vivo, where they could directly affect the downstream DNA transactions, as well as interfere with protein binding and recognition.
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Affiliation(s)
- Alice Meroni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Elisa Mentegari
- DNA Enzymology and Molecular Virology, Institute of Molecular Genetics IGM-CNR, Pavia, Italy
| | - Emmanuele Crespan
- DNA Enzymology and Molecular Virology, Institute of Molecular Genetics IGM-CNR, Pavia, Italy
| | - Marco Muzi-Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
| | - Federico Lazzaro
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Alessandro Podestà
- Dipartimento di Fisica and C.I.Ma.I.Na, Università degli Studi di Milano, Milano, Italy.
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27
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Murugesapillai D, Bouaziz S, Maher LJ, Israeloff NE, Cameron CE, Williams MC. Accurate nanoscale flexibility measurement of DNA and DNA-protein complexes by atomic force microscopy in liquid. NANOSCALE 2017; 9:11327-11337. [PMID: 28762410 PMCID: PMC5597049 DOI: 10.1039/c7nr04231k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The elasticity of double-stranded DNA (dsDNA), as described by its persistence length, is critical for many biological processes, including genomic regulation. A persistence length value can be obtained using atomic force microscopy (AFM) imaging. However, most AFM studies have been done by depositing the sample on a surface using adhesive ligands and fitting the contour to a two-dimensional (2D) wormlike chain (WLC) model. This often results in a persistence length measurement that is different from the value determined using bulk and single molecule methods. We describe a method for obtaining accurate three-dimensional (3D) persistence length measurements for DNA and DNA-protein complexes by using a previously developed liquid AFM imaging method and then applying the 3D WLC model. To demonstrate the method, we image in both air and liquid several different dsDNA constructs and DNA-protein complexes that both increase (HIV-1 Vpr) and decrease (yeast HMO1) dsDNA persistence length. Fitting the liquid AFM-imaging contour to the 3D WLC model results in a value in agreement with measurements obtained in optical tweezers experiments. Because AFM also allows characterization of local DNA properties, the ability to correctly measure global flexibility will strongly increase the impact of measurements that use AFM imaging.
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Affiliation(s)
| | - Serge Bouaziz
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 75006 Paris, France
| | - L James Maher
- Mayo Clinic College of Medicine and Science, Department of Biochemistry and Molecular Biology, Rochester, MN 55905, USA
| | | | - Craig E Cameron
- The Pennsylvania State University, Department of Biochemistry and Molecular Biology, University Park, PA 16802, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA, USA.
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28
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Japaridze A, Orlandini E, Smith KB, Gmür L, Valle F, Micheletti C, Dietler G. Spatial confinement induces hairpins in nicked circular DNA. Nucleic Acids Res 2017; 45:4905-4914. [PMID: 28201616 PMCID: PMC5605231 DOI: 10.1093/nar/gkx098] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/25/2017] [Accepted: 02/06/2017] [Indexed: 01/05/2023] Open
Abstract
In living cells, DNA is highly confined in space with the help of condensing agents, DNA binding proteins and high levels of supercoiling. Due to challenges associated with experimentally studying DNA under confinement, little is known about the impact of spatial confinement on the local structure of the DNA. Here, we have used well characterized slits of different sizes to collect high resolution atomic force microscopy images of confined circular DNA with the aim of assessing the impact of the spatial confinement on global and local conformational properties of DNA. Our findings, supported by numerical simulations, indicate that confinement imposes a large mechanical stress on the DNA as evidenced by a pronounced anisotropy and tangent-tangent correlation function with respect to non-constrained DNA. For the strongest confinement we observed nanometer sized hairpins and interwound structures associated with the nicked sites in the DNA sequence. Based on these findings, we propose that spatial DNA confinement in vivo can promote the formation of localized defects at mechanically weak sites that could be co-opted for biological regulatory functions.
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Affiliation(s)
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Universita di Padova, Via Marzolo 8, 35131 Padova, Italy
| | | | - Lucas Gmür
- Laboratory of Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
| | - Francesco Valle
- Consiglio Nazionale delle Ricerche (CNR), Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Via P.Gobetti 101, Bologna 40129, Italy
| | - Cristian Micheletti
- SISSA - Scuola Internazionale Superiore di Studi Avanzati and CNR-IOM Democritos, Via Bonomea 265, 34136 Trieste, Italy
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
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29
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Japaridze A, Renevey S, Sobetzko P, Stoliar L, Nasser W, Dietler G, Muskhelishvili G. Spatial organization of DNA sequences directs the assembly of bacterial chromatin by a nucleoid-associated protein. J Biol Chem 2017; 292:7607-7618. [PMID: 28316324 PMCID: PMC5418058 DOI: 10.1074/jbc.m117.780239] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/11/2017] [Indexed: 11/28/2022] Open
Abstract
Structural differentiation of bacterial chromatin depends on cooperative binding of abundant nucleoid-associated proteins at numerous genomic DNA sites and stabilization of distinct long-range nucleoprotein structures. Histone-like nucleoid-structuring protein (H-NS) is an abundant DNA-bridging, nucleoid-associated protein that binds to an AT-rich conserved DNA sequence motif and regulates both the shape and the genetic expression of the bacterial chromosome. Although there is ample evidence that the mode of H-NS binding depends on environmental conditions, the role of the spatial organization of H-NS-binding sequences in the assembly of long-range nucleoprotein structures remains unknown. In this study, by using high-resolution atomic force microscopy combined with biochemical assays, we explored the formation of H-NS nucleoprotein complexes on circular DNA molecules having different arrangements of identical sequences containing high-affinity H-NS-binding sites. We provide the first experimental evidence that variable sequence arrangements result in various three-dimensional nucleoprotein structures that differ in their shape and the capacity to constrain supercoils and compact the DNA. We believe that the DNA sequence-directed versatile assembly of periodic higher-order structures reveals a general organizational principle that can be exploited for knowledge-based design of long-range nucleoprotein complexes and purposeful manipulation of the bacterial chromatin architecture.
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Affiliation(s)
- Aleksandre Japaridze
- From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland
| | - Sylvain Renevey
- From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland
| | | | | | - William Nasser
- UMR5240 CNRS/INSA/UCB, Université de Lyon, F-69003 INSA Lyon, Villeurbanne F-69621, France, and
| | - Giovanni Dietler
- From the Laboratory of Physics of Living Matter, EPFL (École Polytechnique Fédérale de Lausanne), CE 3 316 Lausanne, Switzerland,
| | - Georgi Muskhelishvili
- Jacobs University, D-28759 Bremen, Germany, .,Agricultural University of Georgia, 240 David Aghmashenebeli Alley, 0159 Tbilisi, Republik of Georgia
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30
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Japaridze A, Muskhelishvili G, Benedetti F, Gavriilidou AFM, Zenobi R, De Los Rios P, Longo G, Dietler G. Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization. NANO LETTERS 2017; 17:1938-1948. [PMID: 28191853 DOI: 10.1021/acs.nanolett.6b05294] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bacterial chromosome has a compact structure that dynamically changes its shape in response to bacterial growth rate and growth phase. Determining how chromatin remains accessible to DNA binding proteins, and transcription machinery is crucial to understand the link between genetic regulation, DNA structure, and topology. Here, we study very large supercoiled dsDNA using high-resolution characterization, theoretical modeling, and molecular dynamics calculations. We unveil a new type of highly ordered DNA organization forming in the presence of attractive DNA-DNA interactions, which we call hyperplectonemes. We demonstrate that their formation depends on DNA size, supercoiling, and bacterial physiology. We compare structural, nanomechanic, and dynamic properties of hyperplectonemes bound by three highly abundant nucleoid-associated proteins (FIS, H-NS, and HU). In all these cases, the negative supercoiling of DNA determines molecular dynamics, modulating their 3D shape. Overall, our findings provide a mechanistic insight into the critical role of DNA topology in genetic regulation.
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Affiliation(s)
- Aleksandre Japaridze
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Georgi Muskhelishvili
- Jacobs University , D-28759 Bremen, Germany
- Agricultural University of Georgia , 0159 Tbilisi, Georgia
| | - Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne , 1015 Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland
| | - Agni F M Gavriilidou
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Paolo De Los Rios
- Vital-IT, SIB Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland
- Laboratoire de Biophysique Statistique, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Giovanni Longo
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche , Rome, Italy
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
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31
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Pongor CI, Bianco P, Ferenczy G, Kellermayer R, Kellermayer M. Optical Trapping Nanometry of Hypermethylated CPG-Island DNA. Biophys J 2017; 112:512-522. [PMID: 28109529 PMCID: PMC5300791 DOI: 10.1016/j.bpj.2016.12.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 12/21/2016] [Accepted: 12/21/2016] [Indexed: 12/31/2022] Open
Abstract
Cytosine methylation is a key mechanism of epigenetic regulation. CpG-dense loci, called "CpG islands", play a particularly important role in modulating gene expression. Methylation has long been suspected to alter the physical properties of DNA, but the full spectrum of the evoked changes is unknown. Here we measured the methylation-induced nanomechanical changes in a DNA molecule with the sequence of a CpG island. For the molecule under tension, contour length, bending rigidity and intrinsic stiffness decreased in hypermethylated dsDNA, pointing at structural compaction which may facilitate DNA packaging in vivo. Intriguingly, increased forces were required to convert hypermethylated dsDNA into an extended S-form configuration. The reduction of force hysteresis during mechanical relaxation indicated that methylation generates a barrier against strand unpeeling and melting-bubble formation. The high structural stability is likely to have significant consequences on the recognition, replication, transcription, and reparation of hypermethylated genetic regions.
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Affiliation(s)
- Csaba I Pongor
- Biophysics and Radiation Biolology, Semmelweis University, Budapest, Hungary
| | - Pasquale Bianco
- Biophysics and Radiation Biolology, Semmelweis University, Budapest, Hungary; Physiolab, Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
| | - György Ferenczy
- Biophysics and Radiation Biolology, Semmelweis University, Budapest, Hungary; Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Richárd Kellermayer
- Department of Pediatrics, Section of Pediatric Gastroenterology, Baylor College of Medicine, Houston, Texas
| | - Miklós Kellermayer
- Biophysics and Radiation Biolology, Semmelweis University, Budapest, Hungary; MTA-SE Molecular Biophysics Research Group, Semmelweis University, Budapest, Hungary.
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32
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Salari H, Eslami-Mossallam B, Ranjbar HF, Ejtehadi MR. Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy. Phys Rev E 2017; 94:062407. [PMID: 28085439 DOI: 10.1103/physreve.94.062407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Indexed: 11/07/2022]
Abstract
Using analytical approach and Monte Carlo (MC) simulations, we study the elastic behavior of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We show that, due to the bending anisotropy, the persistence length of dsDNA in 2D conformations is always greater than three-dimensional (3D) conformations. This result is in consistence with the measured values for DNA persistence length in 2D and 3D in equal biological conditions. We also show that in two dimensions, an anisotropic, intrinsically twisted polymer exhibits an implicit twist-bend coupling, which leads to the transient curvature increasing with a half helical turn periodicity along the bent polymer.
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Affiliation(s)
- H Salari
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
| | - B Eslami-Mossallam
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, the Netherlands
| | - H F Ranjbar
- Institute of Complex Systems (ICS-2), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - M R Ejtehadi
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran and School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
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33
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Amidani D, Tramonti A, Canosa AV, Campanini B, Maggi S, Milano T, di Salvo ML, Pascarella S, Contestabile R, Bettati S, Rivetti C. Study of DNA binding and bending by Bacillus subtilis GabR, a PLP-dependent transcription factor. Biochim Biophys Acta Gen Subj 2016; 1861:3474-3489. [PMID: 27640111 DOI: 10.1016/j.bbagen.2016.09.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/02/2016] [Accepted: 09/11/2016] [Indexed: 12/23/2022]
Abstract
BACKGROUND GabR is a transcriptional regulator belonging to the MocR/GabR family, characterized by a N-terminal wHTH DNA-binding domain and a C-terminal effector binding and/or oligomerization domain, structurally homologous to aminotransferases (ATs). In the presence of γ-aminobutyrate (GABA) and pyridoxal 5'-phosphate (PLP), GabR activates the transcription of gabT and gabD genes involved in GABA metabolism. METHODS Here we report a biochemical and atomic force microscopy characterization of Bacillus subtilis GabR in complex with DNA. Complexes were assembled in vitro to study their stoichiometry, stability and conformation. RESULTS The fractional occupancy of the GabR cognate site suggests that GabR binds as a dimer with Kd of 10nM. Upon binding GabR bends the DNA by 80° as measured by anomalous electrophoretic mobility. With GABA we observed a decrease in affinity and conformational rearrangements compatible with a less compact nucleo-protein complex but no changes of the DNA bending angle. By employing promoter and GabR mutants we found that basic residues of the positively charged groove on the surface of the AT domain affect DNA affinity. CONCLUSIONS The present data extend current understanding of the GabR-DNA interaction and the effect of GABA and PLP. A model for the GabR-DNA complex, corroborated by a docking simulation, is proposed. GENERAL SIGNIFICANCE Characterization of the GabR DNA binding mode highlights the key role of DNA bending and interactions with bases outside the canonical direct repeats, and might be of general relevance for the action mechanism of MocR transcription factors.
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Affiliation(s)
- Davide Amidani
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parma, Italy
| | - Angela Tramonti
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy; Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | | | | | - Stefano Maggi
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parma, Italy
| | - Teresa Milano
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Martino L di Salvo
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Stefano Pascarella
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Roberto Contestabile
- Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli', Sapienza Università di Roma, Italy
| | - Stefano Bettati
- Dipartimento di Neuroscienze, Università di Parma, Parma, Italy; National Institute of Biostructures and Biosystems, Rome, Italy
| | - Claudio Rivetti
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parma, Italy.
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34
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Lipiec E, Japaridze A, Szczerbiński J, Dietler G, Zenobi R. Preparation of Well-Defined DNA Samples for Reproducible Nanospectroscopic Measurements. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:4821-4829. [PMID: 27434680 DOI: 10.1002/smll.201601711] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/15/2016] [Indexed: 06/06/2023]
Abstract
Due to its well-defined topology and chemical structure, DNA could become a biological standard sample in the field of nanospectroscopy. Tip-enhanced Raman spectroscopy (TERS) provides new insights into individual DNA molecules immobilized on flat mica crystals. The high sensitivity of TERS is used to assess the chemical changes that appear in DNA upon different surface immobilization protocols.
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Affiliation(s)
- Ewelina Lipiec
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, 31-342, Krakow, Poland
| | - Aleksandre Japaridze
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Jacek Szczerbiński
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland.
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35
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Vobornik D, Zou S, Lopinski GP. Analysis Method for Quantifying the Morphology of Nanotube Networks. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8735-8742. [PMID: 27506472 DOI: 10.1021/acs.langmuir.6b02475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
While atomic force microscopy (AFM) is a powerful technique for imaging assemblies and networks of nanoscale materials, approaches for quantitative assessment of the morphology of these materials are lacking. Here we present a volume-based approach for analyzing AFM images of assemblies of nano-objects that enables the extraction of relevant parameters describing their morphology. Random networks of single-walled carbon nanotubes (SWCNTs) deposited via solution-phase processing are used as an example to develop the method and demonstrate its utility. AFM imaging shows that the morphology of these networks depends on details of processing and is influenced by choice of substrate, substrate cleaning method, and postdeposition rinsing protocols. A method is outlined to analyze these images and extract relevant parameters describing the network morphology such as the density of SWCNTs and the degree to which tubes are bundled. Because this volume-based approach depends on accurate measurements of the height of individual tubes and their networks, a procedure for obtaining reliable height measurements is also discussed. Obtaining quantitative parameters that describe the network morphology allows going beyond qualitative descriptions of images and will facilitate optimizing network preparation methods based on measurable criteria and correlating performance with morphology.
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Affiliation(s)
- Dusan Vobornik
- Measurement Science and Standards, National Research Council Canada , 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
| | - Shan Zou
- Measurement Science and Standards, National Research Council Canada , 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
| | - Gregory P Lopinski
- Measurement Science and Standards, National Research Council Canada , 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
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