1
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Kretzer B, Herényi L, Csík G, Supala E, Orosz Á, Tordai H, Kiss B, Kellermayer M. TMPyP binding evokes a complex, tunable nanomechanical response in DNA. Nucleic Acids Res 2024; 52:8399-8418. [PMID: 38943349 PMCID: PMC11317170 DOI: 10.1093/nar/gkae560] [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: 10/17/2023] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 07/01/2024] Open
Abstract
TMPyP is a porphyrin capable of DNA binding and used in photodynamic therapy and G-quadruplex stabilization. Despite its broad applications, TMPyP's effect on DNA nanomechanics is unknown. Here we investigated, by manipulating λ-phage DNA with optical tweezers combined with microfluidics in equilibrium and perturbation kinetic experiments, how TMPyP influences DNA nanomechanics across wide ranges of TMPyP concentration (5-5120 nM), mechanical force (0-100 pN), NaCl concentration (0.01-1 M) and pulling rate (0.2-20 μm/s). Complex responses were recorded, for the analysis of which we introduced a simple mathematical model. TMPyP binding, which is a highly dynamic process, leads to dsDNA lengthening and softening. dsDNA stability increased at low (<10 nM) TMPyP concentrations, then decreased progressively upon increasing TMPyP concentration. Overstretch cooperativity decreased, due most likely to mechanical roadblocks of ssDNA-bound TMPyP. TMPyP binding increased ssDNA's contour length. The addition of NaCl at high (1 M) concentration competed with the TMPyP-evoked nanomechanical changes. Because the largest amplitude of the changes is induced by the pharmacologically relevant TMPyP concentration range, this porphyrin derivative may be used to tune DNA's structure and properties, hence control the wide array of biomolecular DNA-dependent processes including replication, transcription, condensation and repair.
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Affiliation(s)
- Balázs Kretzer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Eszter Supala
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Ádám Orosz
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Hedvig Tordai
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
- HUNREN-SE Biophysical Virology Group, Tűzoltó Str. 37-47, H1094 Budapest, Hungary
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2
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Kodipaka A, Vuradi RK, Airva PK, Nambigari N, Sirasani S. Application of Novel Ruthenium (II) Polypyridyl Complexes as Robust DNA Probes, Optical Material and Antimicrobials-An Experimental and DFT Approach. J Fluoresc 2024:10.1007/s10895-024-03626-8. [PMID: 38602589 DOI: 10.1007/s10895-024-03626-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 02/19/2024] [Indexed: 04/12/2024]
Abstract
The nature of the interaction of DNA with heteroleptic Ruthenium (II) Polypyridyl complexes of the type [Ru (A)2TPIP]2+, where TPIP = 2-(1-p-tolyl-1H pyrazol-4 -yl)-1H-imidazo [4, 5-f[1. 10] phenanthroline and A = 1,10 phenanthroline (1),4,4'-dimethyl-1,10-ortho Phenanthroline (2), 2,2' - bipyridine (3) and 4, 4' dimethyl 2, 2'- bipyridine (4), has been investigated by experimentaland molecular docking approaches. The order of the DNA binding affinities of the synthesised complexes is 1 > 2 > 3 > 4. The findings imply that the unsubstituted complex has a better affinity to bind with DNA than the substituted (dmp and dmb) emphasizing the significance of the auxiliary ligand. Additionally, as the medium's ionic strength drops, the DNA/Ru ratio rises, or when water is displaced by glycerol, the intercalation of complexes into DNA increases. DFT calculations at the B3LYP/LANL2MB level was used for molecular geometry (Ground State) and electronic characteristic calculations. The HOMO-LUMO gap of the Ru [II] complex is less than the intercalator and hence kinetically labile. Among the complexes, the bpy complex has shown utmost non-linear optical properties (α = -153.9099 10-24esu and β = 3.8498 10-30esu). The docking study shows the significance of the Metal-intercalator's shorter length may increase DNA binding affinity. This study divulges that the Ruthenium (II) polypyridyl complexes bind to DNA preponderantly by intercalation supporting Viscosity studies. All the complexes have a considerable attraction for guanine. The standard disk diffusion method reveals that complexes (1, 2, 3 and 4) have good antibacterial activity.
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Affiliation(s)
- Aruna Kodipaka
- Department of Chemistry, University College of Science, Osmania University, Saifabad, Hyderabad, 500 004, Telangana, India
| | - Ravi Kumar Vuradi
- Department of Chemistry, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Praveen Kumar Airva
- Department of Biotechnology, Sri Satya Sai University of Technology & Medical Sciences, Bhopal- Indore Road, Opp. Oilfed Plant, Sehore, 466001, Madhya Pradesh, India
| | - Navaneetha Nambigari
- Department of Chemistry, University College of Science, Osmania University, Saifabad, Hyderabad, 500 004, Telangana, India.
- Department of Chemistry, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India.
| | - Satyanarayana Sirasani
- Department of Chemistry, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India.
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3
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Joshi J, McCauley MJ, Morse M, Muccio MR, Kanlong JG, Rocha MS, Rouzina I, Musier-Forsyth K, Williams MC. Mechanism of DNA Intercalation by Chloroquine Provides Insights into Toxicity. Int J Mol Sci 2024; 25:1410. [PMID: 38338688 PMCID: PMC10855526 DOI: 10.3390/ijms25031410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Chloroquine has been used as a potent antimalarial, anticancer drug, and prophylactic. While chloroquine is known to interact with DNA, the details of DNA-ligand interactions have remained unclear. Here we characterize chloroquine-double-stranded DNA binding with four complementary approaches, including optical tweezers, atomic force microscopy, duplex DNA melting measurements, and isothermal titration calorimetry. We show that chloroquine intercalates into double stranded DNA (dsDNA) with a KD ~ 200 µM, and this binding is entropically driven. We propose that chloroquine-induced dsDNA intercalation, which happens in the same concentration range as its observed toxic effects on cells, is responsible for the drug's cytotoxicity.
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Affiliation(s)
- Joha Joshi
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Micah J. McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Michael R. Muccio
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Joseph G. Kanlong
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Márcio S. Rocha
- Department of Physics, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil;
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
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4
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Meyer AC, Karbach M, Lu P, Müller G. Mechanical response to tension and torque of molecular chains via statistically interacting particles associated with extension, contraction, twist, and supercoiling. Phys Rev E 2022; 105:064502. [PMID: 35854540 DOI: 10.1103/physreve.105.064502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination of tension and torque involves, in the framework of this method of analysis, the (thermal or mechanical) activation of a specific mix of statistically interacting particles carrying quanta of extension or contraction and quanta of twist or supercoiling. The methodology, which is elucidated in applications of increasing complexity, is capable of describing the conversion between twist chirality and plectonemic chirality in quasistatic processes. The control variables are force or extension and torque or linkage (a combination of twist and writhe). The versatility of this approach is demonstrated in two applications relevant and promising for double-stranded DNA under controlled tension and torque. One application describes conformational transformations between (native) B-DNA, (underwound) S-DNA, and (overwound) P-DNA in accord with experimental data. The other application describes how the conversion between a twisted chain and a supercoiled chain accommodates variations of linkage and excess length in a buckling transition.
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Affiliation(s)
- Aaron C Meyer
- Department of Physics, University of Rhode Island, Kingston Rhode Island 02881, USA
| | - Michael Karbach
- Fachgruppe Physik, Bergische Universität Wuppertal, D-42097 Wuppertal, Germany
| | - Ping Lu
- Department of Physics, Stetson University, DeLand, Florida 32723, USA
| | - Gerhard Müller
- Department of Physics, University of Rhode Island, Kingston Rhode Island 02881, USA
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5
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Costa EA, Gonçalves AP, Batista JAD, Bazoni RF, Santos AA, Rocha MS. New Insights into the Mechanism of Action of the Drug Chloroquine: Direct Interaction with DNA and Cytotoxicity. J Phys Chem B 2022; 126:3512-3521. [PMID: 35533378 DOI: 10.1021/acs.jpcb.2c01119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chloroquine (CLQ) and hydroxychloroquine (HCLQ) are compounds largely employed in the treatment of various human diseases for decades. Nevertheless, a number of intrinsic details concerning their mechanisms of action, especially at the molecular level, are still unknown or have presented controversial results in the literature. Using optical tweezers, here, we investigate at the single-molecule level the molecular mechanism of action of the drug CLQ in its intrinsic interaction with the double-stranded (ds)DNA molecule, one of its targets inside cells, determining the binding modes and the physicochemical (binding) parameters of the interaction. In particular, we show that the ionic strength of the surrounding medium strongly influences such interaction, changing even the main binding mode. In addition, the cytotoxicity of CLQ against three different cell lines was also investigated here, allowing one to evaluate and compare the effect of the drug on the cell viability. In particular, we show that CLQ is highly cytotoxic at a very low (a few micromolar) concentration range for all cell lines tested. These results were rigorously compared to the equivalent ones obtained for the closely related compound hydroxychloroquine (HCLQ), allowing a critical comparison between the action of these drugs at the molecular and cellular levels.
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Affiliation(s)
- Ethe A Costa
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Amanda P Gonçalves
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Josiane A D Batista
- Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais 36.036-900, Brazil
| | - Raniella F Bazoni
- Departamento de Ciências Naturais, Universidade Federal do Espírito Santo, São Mateus, Espírito Santo 29.932-900, Brazil
| | - Anésia A Santos
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
| | - Márcio S Rocha
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil
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6
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Gien H, Morse M, McCauley MJ, Kitzrow JP, Musier-Forsyth K, Gorelick RJ, Rouzina I, Williams MC. HIV-1 Nucleocapsid Protein Binds Double-Stranded DNA in Multiple Modes to Regulate Compaction and Capsid Uncoating. Viruses 2022; 14:235. [PMID: 35215829 PMCID: PMC8879225 DOI: 10.3390/v14020235] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/07/2023] Open
Abstract
The HIV-1 nucleocapsid protein (NC) is a multi-functional protein necessary for viral replication. Recent studies have demonstrated reverse transcription occurs inside the fully intact viral capsid and that the timing of reverse transcription and uncoating are correlated. How a nearly 10 kbp viral DNA genome is stably contained within a narrow capsid with diameter similar to the persistence length of double-stranded (ds) DNA, and the role of NC in this process, are not well understood. In this study, we use optical tweezers, fluorescence imaging, and atomic force microscopy to observe NC binding a single long DNA substrate in multiple modes. We find that NC binds and saturates the DNA substrate in a non-specific binding mode that triggers uniform DNA self-attraction, condensing the DNA into a tight globule at a constant force up to 10 pN. When NC is removed from solution, the globule dissipates over time, but specifically-bound NC maintains long-range DNA looping that is less compact but highly stable. Both binding modes are additionally observed using AFM imaging. These results suggest multiple binding modes of NC compact DNA into a conformation compatible with reverse transcription, regulating the genomic pressure on the capsid and preventing premature uncoating.
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Affiliation(s)
- Helena Gien
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| | - Micah J. McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
| | - Jonathan P. Kitzrow
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (J.P.K.); (K.M.-F.); (I.R.)
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (J.P.K.); (K.M.-F.); (I.R.)
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA;
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (J.P.K.); (K.M.-F.); (I.R.)
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (H.G.); (M.M.); (M.J.M.)
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7
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Moura TA, Junior RLR, Rocha MS. Caffeine modulates the intercalation of drugs on DNA: A study at the single molecule level. Biophys Chem 2021; 277:106653. [PMID: 34217911 DOI: 10.1016/j.bpc.2021.106653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/15/2021] [Accepted: 06/24/2021] [Indexed: 11/20/2022]
Abstract
We use optical tweezers to characterize the ability of Caffeine (Caf) to modulate the intercalation of drugs into the DNA double-helix at the single molecule level. When previously bound to the double-helix, Caf hinders ethidium bromide (EtBr) intercalation, decreasing its effective equilibrium binding constant with DNA. The dominant mechanism of such singular ability is a direct binding of Caf to the intercalating drugs in solution, which decreases the effective concentration of such compounds available to interact with DNA. When EtBr intercalation into the DNA double-helix occurs firstly, on the other hand, the measured cooperativity between Caf molecules interacting with DNA can be modulated, a feature also correlated to the Caf-EtBr interaction in solution. The results achieved here unveil many peculiarities about the details of such interactions at the molecular level and provide new insights on the use of Caf in therapeutic applications.
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Affiliation(s)
- T A Moura
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - R L R Junior
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M S Rocha
- Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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8
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Kolbeck PJ, Vanderlinden W, Gemmecker G, Gebhardt C, Lehmann M, Lak A, Nicolaus T, Cordes T, Lipfert J. Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold. Nucleic Acids Res 2021; 49:5143-5158. [PMID: 33905507 PMCID: PMC8136779 DOI: 10.1093/nar/gkab265] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/29/2021] [Accepted: 04/05/2021] [Indexed: 01/08/2023] Open
Abstract
SYBR Gold is a commonly used and particularly bright fluorescent DNA stain, however, its chemical structure is unknown and its binding mode to DNA remains controversial. Here, we solve the structure of SYBR Gold by NMR and mass spectrometry to be [2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium] and determine its extinction coefficient. We quantitate SYBR Gold binding to DNA using two complementary approaches. First, we use single-molecule magnetic tweezers (MT) to determine the effects of SYBR Gold binding on DNA length and twist. The MT assay reveals systematic lengthening and unwinding of DNA by 19.1° ± 0.7° per molecule upon binding, consistent with intercalation, similar to the related dye SYBR Green I. We complement the MT data with spectroscopic characterization of SYBR Gold. The data are well described by a global binding model for dye concentrations ≤2.5 μM, with parameters that quantitatively agree with the MT results. The fluorescence increases linearly with the number of intercalated SYBR Gold molecules up to dye concentrations of ∼2.5 μM, where quenching and inner filter effects become relevant. In summary, we provide a mechanistic understanding of DNA-SYBR Gold interactions and present practical guidelines for optimal DNA detection and quantitative DNA sensing applications using SYBR Gold.
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Affiliation(s)
- Pauline J Kolbeck
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Willem Vanderlinden
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Gerd Gemmecker
- Bavarian NMR Center (BNMRZ), Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Martin Lehmann
- Plant Molecular Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Aidin Lak
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Thomas Nicolaus
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Jan Lipfert
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
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9
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Tibbs J, Tabei SMA, Kidd TE, Peters JP. Effects of Intercalating Molecules on the Polymer Properties of DNA. J Phys Chem B 2020; 124:8572-8582. [PMID: 32941733 DOI: 10.1021/acs.jpcb.0c06867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atomic force microscopy (AFM) enables determination of physical properties from single DNA molecules. Insertion of aromatic molecules into the structure of DNA results in morphological changes. However, the accompanying changes to elastic properties due to this insertion are not fully understood. AFM was used to examine the morphological effects of intercalator binding and report changes in the elastic properties of intrinsically straight DNA molecules. The persistence length and polymer extension were characterized in the presence of three intercalating molecules: ethidium bromide and the less well studied chloroquine and acridine. It was found that all three intercalators significantly increased the bending persistence length. In addition, an analysis of the normal bending modes of the static molecules corroborated these results. This approach of measuring binding effects of intercalators on DNA physical properties using a model system of intrinsically straight DNA is applicable to other DNA binding ligands and other modes of DNA interaction.
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Affiliation(s)
| | | | | | - Justin P Peters
- Department of Chemistry and Biochemistry, University of Northern Iowa 1227 West 27th Street Cedar Falls, Iowa 50614-0423, United States
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10
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Meyer AC, Öz Y, Gundlach N, Karbach M, Lu P, Müller G. Molecular chains under tension: Thermal and mechanical activation of statistically interacting extension and contraction particles. Phys Rev E 2020; 101:022504. [PMID: 32168618 DOI: 10.1103/physreve.101.022504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/23/2020] [Indexed: 11/07/2022]
Abstract
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds between monomers or of entire groups of monomers to tension is governed by the activation of statistically interacting particles representing quanta of extension or contraction. This method of analysis is capable of describing thermal unbending of the freely jointed or wormlike chain kind, linear or nonlinear contour elasticity, and structural transformations including effects of cooperativity. The versatility of this approach is demonstrated in an application to double-stranded DNA undergoing torsionally unconstrained stretching across three regimes of mechanical response including an overstretching transition. The three-regime force-extension characteristic, derived from a single free-energy expression, accurately matches empirical evidence.
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Affiliation(s)
- Aaron C Meyer
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Yahya Öz
- Fachgruppe Physik, Bergische Universität Wuppertal, D-42097 Wuppertal, Germany
| | - Norman Gundlach
- Fachgruppe Physik, Bergische Universität Wuppertal, D-42097 Wuppertal, Germany
| | - Michael Karbach
- Fachgruppe Physik, Bergische Universität Wuppertal, D-42097 Wuppertal, Germany
| | - Ping Lu
- Department of Applied Science and Mathematics, Bluefield State College, Bluefield, West Virginia 24701, USA
| | - Gerhard Müller
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
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11
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Sahoo AK, Bagchi B, Maiti PK. Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes. J Chem Phys 2019; 151:164902. [PMID: 31675856 DOI: 10.1063/1.5117163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA that lead to the stability of the intercalated drug is lacking. Of particular interest are the modifications of the mechanical properties of dsDNA observed in experiments. The latter could affect many biological functions, such as DNA transcription and replication. Here, we probe, via all-atom molecular dynamics (MD) simulations, the change in the mechanical properties of intercalated drug-DNA complexes for two intercalators, daunomycin and ethidium. We find that, upon drug intercalation, the stretch modulus of DNA increases significantly, whereas its persistence length and bending modulus decrease. Steered MD simulations reveal that it requires higher forces to stretch the intercalated dsDNA complexes than the normal dsDNA. Adopting various pulling protocols to study force-induced DNA melting, we find that the dissociation of dsDNA becomes difficult in the presence of intercalators. The results obtained here provide a plausible mechanism of function of the anticancer drugs, i.e., via altering the mechanical properties of DNA. We also discuss long-time consequences of using these drugs, which require further in vivo investigations.
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Affiliation(s)
- Anil Kumar Sahoo
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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12
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Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA. Biophys J 2019; 116:1394-1405. [PMID: 30954211 DOI: 10.1016/j.bpj.2019.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/12/2019] [Indexed: 01/17/2023] Open
Abstract
DNA intercalators bind nucleic acids by stacking between adjacent basepairs. This causes a considerable elongation of the DNA backbone as well as untwisting of the double helix. In the past few years, single-molecule mechanical experiments have become a common tool to characterize these deformations and to quantify important parameters of the intercalation process. Parameter extraction typically relies on the neighbor-exclusion model, in which a bound intercalator prevents intercalation into adjacent sites. Here, we challenge the neighbor-exclusion model by carefully quantifying and modeling the force-extension and twisting behavior of single ethidium-complexed DNA molecules. We show that only an anticooperative ethidium binding that allows for a disfavored but nonetheless possible intercalation into nearest-neighbor sites can consistently describe the mechanical behavior of intercalator-bound DNA. At high ethidium concentrations and elevated mechanical stress, this causes an almost complete occupation of nearest-neighbor sites and almost a doubling of the DNA contour length. We furthermore show that intercalation into nearest-neighbor sites needs to be considered when estimating intercalator parameters from zero-stress elongation and twisting data. We think that the proposed anticooperative binding mechanism may also be applicable to other intercalating molecules.
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13
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van Mameren J, Vermeulen K, Wuite GJL, Peterman EJG. A polarized view on DNA under tension. J Chem Phys 2018; 148:123306. [PMID: 29604805 DOI: 10.1063/1.5004019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the past decades, sensitive fluorescence microscopy techniques have contributed significantly to our understanding of the dynamics of DNA. The specific labeling of DNA using intercalating dyes has allowed for quantitative measurement of the thermal fluctuations the polymers undergo. On the other hand, recent advances in single-molecule manipulation techniques have unraveled the mechanical and elastic properties of this intricate polymer. Here, we have combined these two approaches to study the conformational dynamics of DNA under a wide range of tensions. Using polarized fluorescence microscopy in conjunction with optical-tweezers-based manipulation of YOYO-intercalated DNA, we controllably align the YOYO dyes using DNA tension, enabling us to disentangle the rapid dynamics of the dyes from that of the DNA itself. With unprecedented control of the DNA alignment, we resolve an inconsistency in reports about the tilted orientation of intercalated dyes. We find that intercalated dyes are on average oriented perpendicular to the long axis of the DNA, yet undergo fast dynamics on the time scale of absorption and fluorescence emission. In the overstretching transition of double-stranded DNA, we do not observe changes in orientation or orientational dynamics of the dyes. Only beyond the overstretching transition, a considerable depolarization is observed, presumably caused by an average tilting of the DNA base pairs. Our combined approach thus contributes to the elucidation of unique features of the molecular dynamics of DNA.
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Affiliation(s)
- Joost van Mameren
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, Amsterdam, The Netherlands
| | - Karen Vermeulen
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB, Vrije Universiteit, Amsterdam, The Netherlands
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14
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Benedito M, Giordano S. Thermodynamics of small systems with conformational transitions: The case of two-state freely jointed chains with extensible units. J Chem Phys 2018; 149:054901. [DOI: 10.1063/1.5026386] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Manon Benedito
- Institute of Electronics, Microelectronics and Nanotechnology, UMR 8520, University Lille, CNRS, Centrale Lille, ISEN, University Valenciennes, LIA LICS/LEMAC, F-59000 Lille, France
| | - Stefano Giordano
- Institute of Electronics, Microelectronics and Nanotechnology, UMR 8520, University Lille, CNRS, Centrale Lille, ISEN, University Valenciennes, LIA LICS/LEMAC, F-59000 Lille, France
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15
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Naufer MN, Furano AV, Williams MC. Protein-nucleic acid interactions of LINE-1 ORF1p. Semin Cell Dev Biol 2018; 86:140-149. [PMID: 29596909 PMCID: PMC6428221 DOI: 10.1016/j.semcdb.2018.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/19/2018] [Accepted: 03/23/2018] [Indexed: 11/03/2022]
Abstract
Long interspersed nuclear element 1 (LINE-1 or L1) is the dominant retrotransposon in mammalian genomes. L1 encodes two proteins ORF1p and ORF2p that are required for retrotransposition. ORF2p functions as the replicase. ORF1p is a coiled coil-mediated trimeric, high affinity RNA binding protein that packages its full- length coding transcript into an ORF2p-containing ribonucleoprotein (RNP) complex, the retrotransposition intermediate. ORF1p also is a nucleic acid chaperone that presumably facilitates the proposed nucleic acid remodeling steps involved in retrotransposition. Although detailed mechanistic understanding of ORF1p function in this process is lacking, recent studies showed that the rate at which ORF1p can form stable nucleic acid-bound oligomers in vitro is positively correlated with formation of an active L1 RNP as assayed in vivo using a cell culture-based retrotransposition assay. This rate was sensitive to minor amino acid changes in the coiled coil domain, which had no effect on nucleic acid chaperone activity. Additional studies linking the complex nucleic acid binding properties to the conformational changes of the protein are needed to understand how ORF1p facilitates retrotransposition.
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Affiliation(s)
- M Nabuan Naufer
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - Anthony V Furano
- The Laboratory of Molecular and Cellular Biology, NIDDK, NIH, Bethesda, MD 20892, USA
| | - Mark C Williams
- Northeastern University, Department of Physics, Boston, MA 02115, USA.
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16
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Abstract
The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely used in biophysical/chemical assays and drug treatments. We present single-molecule experiments and a three-state statistical mechanical model that provide a quantitative understanding of the interplay between B-DNA, overstretched DNA and intercalated DNA. The predictions of this model include a hitherto unconfirmed hyperstretched state, twice the length of B-DNA. Our force-fluorescence experiments confirm this hyperstretched state and reveal its sequence dependence. These results pin down the physical principles that govern DNA mechanics under the influence of tension and biochemical reactions. A predictive understanding of the possibilities and limitations of DNA extension can guide refined exploitation of DNA in, e.g., programmable soft materials and DNA origami applications. The mechanics and structural transitions of DNA are important to many essential processes inside living cells. Here the authors combine theory and single-molecule experiments to show that intercalator binding stabilises a new structural state of DNA: hyperstretched DNA.
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17
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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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18
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Vlijm R, Kim SH, De Zwart PL, Dalal Y, Dekker C. The supercoiling state of DNA determines the handedness of both H3 and CENP-A nucleosomes. NANOSCALE 2017; 9:1862-1870. [PMID: 28094382 PMCID: PMC7959483 DOI: 10.1039/c6nr06245h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nucleosomes form the unit structure of the genome in eukaryotes, thereby constituting a fundamental tenet of chromatin biology. In canonical nucleosomes, DNA wraps around the histone octamer in a left-handed toroidal ramp. Here, in single-molecule magnetic tweezers studies of chaperone-assisted nucleosome assembly, we show that the handedness of the DNA wrapping around the nucleosome core is intrinsically ambidextrous, and depends on the pre-assembly supercoiling state of the DNA, i.e., it is not uniquely determined by the octameric histone core. Nucleosomes assembled onto negatively supercoiled DNA are found to exhibit a left-handed conformation, whereas assembly onto positively supercoiled DNA results in right-handed nucleosomes. This intrinsic flexibility to adopt both chiralities is observed both for canonical H3 nucleosomes, and for centromere-specific variant CENP-A nucleosomes. These data support recent advances suggesting an intrinsic adaptability of the nucleosome, and provide insights into how nucleosomes might rapidly re-assemble after cellular processes that generate positive supercoiling in vivo.
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Affiliation(s)
- R Vlijm
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - S H Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - P L De Zwart
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
| | - Y Dalal
- Chromatin Structure and Epigenetic Mechanisms Unit, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - C Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2628CJ, The Netherlands
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19
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DNA intercalation optimized by two-step molecular lock mechanism. Sci Rep 2016; 6:37993. [PMID: 27917863 PMCID: PMC5137138 DOI: 10.1038/srep37993] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/03/2016] [Indexed: 11/25/2022] Open
Abstract
The diverse properties of DNA intercalators, varying in affinity and kinetics over several orders of magnitude, provide a wide range of applications for DNA-ligand assemblies. Unconventional intercalation mechanisms may exhibit high affinity and slow kinetics, properties desired for potential therapeutics. We used single-molecule force spectroscopy to probe the free energy landscape for an unconventional intercalator that binds DNA through a novel two-step mechanism in which the intermediate and final states bind DNA through the same mono-intercalating moiety. During this process, DNA undergoes significant structural rearrangements, first lengthening before relaxing to a shorter DNA-ligand complex in the intermediate state to form a molecular lock. To reach the final bound state, the molecular length must increase again as the ligand threads between disrupted DNA base pairs. This unusual binding mechanism results in an unprecedented optimized combination of high DNA binding affinity and slow kinetics, suggesting a new paradigm for rational design of DNA intercalators.
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20
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Almaqwashi AA, Paramanathan T, Rouzina I, Williams MC. Mechanisms of small molecule-DNA interactions probed by single-molecule force spectroscopy. Nucleic Acids Res 2016; 44:3971-88. [PMID: 27085806 PMCID: PMC4872107 DOI: 10.1093/nar/gkw237] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/24/2016] [Indexed: 12/31/2022] Open
Abstract
There is a wide range of applications for non-covalent DNA binding ligands, and optimization of such interactions requires detailed understanding of the binding mechanisms. One important class of these ligands is that of intercalators, which bind DNA by inserting aromatic moieties between adjacent DNA base pairs. Characterizing the dynamic and equilibrium aspects of DNA-intercalator complex assembly may allow optimization of DNA binding for specific functions. Single-molecule force spectroscopy studies have recently revealed new details about the molecular mechanisms governing DNA intercalation. These studies can provide the binding kinetics and affinity as well as determining the magnitude of the double helix structural deformations during the dynamic assembly of DNA–ligand complexes. These results may in turn guide the rational design of intercalators synthesized for DNA-targeted drugs, optical probes, or integrated biological self-assembly processes. Herein, we survey the progress in experimental methods as well as the corresponding analysis framework for understanding single molecule DNA binding mechanisms. We discuss briefly minor and major groove binding ligands, and then focus on intercalators, which have been probed extensively with these methods. Conventional mono-intercalators and bis-intercalators are discussed, followed by unconventional DNA intercalation. We then consider the prospects for using these methods in optimizing conventional and unconventional DNA-intercalating small molecules.
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Affiliation(s)
- Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | | | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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21
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Bahira M, McCauley MJ, Almaqwashi AA, Lincoln P, Westerlund F, Rouzina I, Williams MC. A ruthenium dimer complex with a flexible linker slowly threads between DNA bases in two distinct steps. Nucleic Acids Res 2015; 43:8856-67. [PMID: 26365236 PMCID: PMC4605314 DOI: 10.1093/nar/gkv864] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/15/2015] [Indexed: 01/06/2023] Open
Abstract
Several multi-component DNA intercalating small molecules have been designed around ruthenium-based intercalating monomers to optimize DNA binding properties for therapeutic use. Here we probe the DNA binding ligand [μ-C4(cpdppz)2(phen)4Ru2]4+, which consists of two Ru(phen)2dppz2+ moieties joined by a flexible linker. To quantify ligand binding, double-stranded DNA is stretched with optical tweezers and exposed to ligand under constant applied force. In contrast to other bis-intercalators, we find that ligand association is described by a two-step process, which consists of fast bimolecular intercalation of the first dppz moiety followed by ∼10-fold slower intercalation of the second dppz moiety. The second step is rate-limited by the requirement for a DNA-ligand conformational change that allows the flexible linker to pass through the DNA duplex. Based on our measured force-dependent binding rates and ligand-induced DNA elongation measurements, we are able to map out the energy landscape and structural dynamics for both ligand binding steps. In addition, we find that at zero force the overall binding process involves fast association (∼10 s), slow dissociation (∼300 s), and very high affinity (Kd ∼10 nM). The methodology developed in this work will be useful for studying the mechanism of DNA binding by other multi-step intercalating ligands and proteins.
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Affiliation(s)
- Meriem Bahira
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Micah J McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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22
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Biebricher AS, Heller I, Roijmans RFH, Hoekstra TP, Peterman EJG, Wuite GJL. The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics. Nat Commun 2015; 6:7304. [PMID: 26084388 PMCID: PMC4557362 DOI: 10.1038/ncomms8304] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 04/27/2015] [Indexed: 11/09/2022] Open
Abstract
DNA intercalators are widely used as fluorescent probes to visualize DNA and DNA transactions in vivo and in vitro. It is well known that they perturb DNA structure and stability, which can in turn influence DNA-processing by proteins. Here we elucidate this perturbation by combining single-dye fluorescence microscopy with force spectroscopy and measuring the kinetics of DNA intercalation by the mono- and bis-intercalating cyanine dyes SYTOX Orange, SYTOX Green, SYBR Gold, YO-PRO-1, YOYO-1 and POPO-3. We show that their DNA-binding affinity is mainly governed by a strongly tension-dependent dissociation rate. These rates can be tuned over a range of seven orders of magnitude by changing DNA tension, intercalating species and ionic strength. We show that optimizing these rates minimizes the impact of intercalators on strand separation and enzymatic activity. These new insights provide handles for the improved use of intercalators as DNA probes with minimal perturbation and maximal efficacy. DNA intercalators, a type of fluorescent probes widely used to visualize DNA, can perturb DNA structure and stability. Here, the authors show how DNA-binding affinity can be tuned using DNA tension, ionic strength and dye species, and how this can be used to minimize DNA structural perturbations.
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Affiliation(s)
- Andreas S Biebricher
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands
| | - Iddo Heller
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands
| | - Roel F H Roijmans
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands
| | - Tjalle P Hoekstra
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands
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23
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Wang X, Gao L, Liang B, Li X, Guo X. Revealing the direct effect of individual intercalations on DNA conductance toward single-molecule electrical biodetection. J Mater Chem B 2015; 3:5150-5154. [DOI: 10.1039/c5tb00666j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of individual intercalations on DNA conductance is revealed electrically at the single-molecule level by using DNA-functionalized molecular junctions.
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Affiliation(s)
- Xiaolong Wang
- Center for Nanochemistry
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- College of Chemistry and Molecular Engineering
- Peking University
| | - Li Gao
- Center for Nanochemistry
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- College of Chemistry and Molecular Engineering
- Peking University
| | - Bo Liang
- Adesso Advanced Materials Wuxi Co., Ltd
- Huihong Industrial Park
- Wuxi
- P. R. China
| | - Xin Li
- Adesso Advanced Materials Wuxi Co., Ltd
- Huihong Industrial Park
- Wuxi
- P. R. China
| | - Xuefeng Guo
- Center for Nanochemistry
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- College of Chemistry and Molecular Engineering
- Peking University
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24
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Griffis JW, Safranovitch MM, Vyas SP, Gerrin S, Protozanova E, Malkin G, Meltzer RH. Single molecule DNA intercalation in continuous homogenous elongational flow. LAB ON A CHIP 2014; 14:3881-3893. [PMID: 25133764 DOI: 10.1039/c4lc00781f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Sequence-nonspecific staining of DNA with intercalating fluorophores is required for fluorescence-based length estimation of elongated DNA in optical mapping techniques. However, the observed length of a DNA molecule is affected by the relative concentrations of DNA and dye. In some applications, predetermination of DNA concentration may not be possible. Here we present a microfluidic approach in which individual DNA molecules are entrained by converging laminar sheath flows containing the intercalating dye PO-PRO-1. This provides uniform staining regardless of DNA concentration, and uniform elastic stretching of DNA in continuous elongational flow. On-chip intercalation provides a unique process for concentration-independent staining of long DNA fragments for the optical mapping method Genome Sequence Scanning (GSS), and normalizes intramolecular elasticity across a broad range of molecule lengths. These advances permit accurate mapping of observed molecules to sequence derived templates, thus improving detection of complex bacterial mixtures using GSS.
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25
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Almaqwashi AA, Paramanathan T, Lincoln P, Rouzina I, Westerlund F, Williams MC. Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex. Nucleic Acids Res 2014; 42:11634-41. [PMID: 25245944 PMCID: PMC4191423 DOI: 10.1093/nar/gku859] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ‐bidppz‐(phen)4Ru2]4+ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Δ,Δ-P intercalation Kd is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Δ-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Δ,Δ-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes.
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Affiliation(s)
- Ali A Almaqwashi
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Thayaparan Paramanathan
- Department of Physics, Northeastern University, Boston, MA 02115, USA Department of Physics, Bridgewater State University, Bridgewater, MA 02324, USA
| | - Per Lincoln
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Fredrik Westerlund
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg SE-41296, Sweden
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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26
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Murugesapillai D, McCauley MJ, Huo R, Nelson Holte MH, Stepanyants A, Maher LJ, Israeloff NE, Williams MC. DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin. Nucleic Acids Res 2014; 42:8996-9004. [PMID: 25063301 PMCID: PMC4132745 DOI: 10.1093/nar/gku635] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The regulation of chromatin structure in eukaryotic cells involves abundant architectural factors such as high mobility group B (HMGB) proteins. It is not understood how these factors control the interplay between genome accessibility and compaction. In vivo, HMO1 binds the promoter and coding regions of most ribosomal RNA genes, facilitating transcription and possibly stabilizing chromatin in the absence of histones. To understand how HMO1 performs these functions, we combine single molecule stretching and atomic force microscopy (AFM). By stretching HMO1-bound DNA, we demonstrate a hierarchical organization of interactions, in which HMO1 initially compacts DNA on a timescale of seconds, followed by bridge formation and stabilization of DNA loops on a timescale of minutes. AFM experiments demonstrate DNA bridging between strands as well as looping by HMO1. Our results support a model in which HMO1 maintains the stability of nucleosome-free chromatin regions by forming complex and dynamic DNA structures mediated by protein–protein interactions.
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Affiliation(s)
| | - Micah J McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ran Huo
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Molly H Nelson Holte
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Armen Stepanyants
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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27
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Wang W, Naiyer N, Mitra M, Li J, Williams MC, Rouzina I, Gorelick RJ, Wu Z, Musier-Forsyth K. Distinct nucleic acid interaction properties of HIV-1 nucleocapsid protein precursor NCp15 explain reduced viral infectivity. Nucleic Acids Res 2014; 42:7145-59. [PMID: 24813443 PMCID: PMC4066767 DOI: 10.1093/nar/gku335] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
During human immunodeficiency virus type 1 (HIV-1) maturation, three different forms of nucleocapsid (NC) protein—NCp15 (p9 + p6), NCp9 (p7 + SP2) and NCp7—appear successively. A mutant virus expressing NCp15 shows greatly reduced infectivity. Mature NCp7 is a chaperone protein that facilitates remodeling of nucleic acids (NAs) during reverse transcription. To understand the strict requirement for NCp15 processing, we compared the chaperone function of the three forms of NC. NCp15 anneals tRNA to the primer-binding site at a similar rate as NCp7, whereas NCp9 is the most efficient annealing protein. Assays to measure NA destabilization show a similar trend. Dynamic light scattering studies reveal that NCp15 forms much smaller aggregates relative to those formed by NCp7 and NCp9. Nuclear magnetic resonance studies suggest that the acidic p6 domain of HIV-1 NCp15 folds back and interacts with the basic zinc fingers. Neutralizing the acidic residues in p6 improves the annealing and aggregation activity of NCp15 to the level of NCp9 and increases the protein–NA aggregate size. Slower NCp15 dissociation kinetics is observed by single-molecule DNA stretching, consistent with the formation of electrostatic inter-protein contacts, which likely contribute to the distinct aggregate morphology, irregular HIV-1 core formation and non-infectious virus.
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Affiliation(s)
- Wei Wang
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Nada Naiyer
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mithun Mitra
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Jialin Li
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ioulia Rouzina
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Zhengrong Wu
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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28
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Joshi H, Sengupta A, Gavvala K, Hazra P. Unraveling the mode of binding of the anticancer drug topotecan with dsDNA. RSC Adv 2014. [DOI: 10.1039/c3ra42462f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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29
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Wu H, Mitra M, Naufer MN, McCauley MJ, Gorelick RJ, Rouzina I, Musier-Forsyth K, Williams MC. Differential contribution of basic residues to HIV-1 nucleocapsid protein's nucleic acid chaperone function and retroviral replication. Nucleic Acids Res 2013; 42:2525-37. [PMID: 24293648 PMCID: PMC3936775 DOI: 10.1093/nar/gkt1227] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) protein contains 15 basic residues located throughout its 55-amino acid sequence, as well as one aromatic residue in each of its two CCHC-type zinc finger motifs. NC facilitates nucleic acid (NA) rearrangements via its chaperone activity, but the structural basis for this activity and its consequences in vivo are not completely understood. Here, we investigate the role played by basic residues in the N-terminal domain, the N-terminal zinc finger and the linker region between the two zinc fingers. We use in vitro ensemble and single-molecule DNA stretching experiments to measure the characteristics of wild-type and mutant HIV-1 NC proteins, and correlate these results with cell-based HIV-1 replication assays. All of the cationic residue mutations lead to NA interaction defects, as well as reduced HIV-1 infectivity, and these effects are most pronounced on neutralizing all five N-terminal cationic residues. HIV-1 infectivity in cells is correlated most strongly with NC’s NA annealing capabilities as well as its ability to intercalate the DNA duplex. Although NC’s aromatic residues participate directly in DNA intercalation, our findings suggest that specific basic residues enhance these interactions, resulting in optimal NA chaperone activity.
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Affiliation(s)
- Hao Wu
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA, AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA and Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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30
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Chung JW, Shin D, Kwak JM, Seog J. Direct force measurement of single DNA-peptide interactions using atomic force microscopy. J Mol Recognit 2013; 26:268-75. [PMID: 23595808 DOI: 10.1002/jmr.2269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/24/2013] [Accepted: 02/01/2013] [Indexed: 11/10/2022]
Abstract
The selective interactions between DNA and miniature (39 residues) engineered peptide were directly measured at the single-molecule level by using atomic force microscopy. This peptide (p007) contains an α-helical recognition site similar to leucine zipper GCN4 and specifically recognizes the ATGAC sequence in the DNA with nanomolar affinity. The average rupture force was 42.1 pN, which is similar to the unbinding forces of the digoxigenin-antidigoxigenin complex, one of the strongest interactions in biological systems. The single linear fit of the rupture forces versus the logarithm of pulling rates showed a single energy barrier with a transition state located at 0.74 nm from the bound state. The smaller koff compared with that of other similar systems was presumably due to the increased stability of the helical structure by putative folding residues in p007. This strong sequence-specific DNA-peptide interaction has a potential to be utilized to prepare well-defined mechanically stable DNA-protein hybrid nanostructures.
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Affiliation(s)
- Ji W Chung
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
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31
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Chaurasiya KR, Ruslie C, Silva MC, Voortman L, Nevin P, Lone S, Beuning PJ, Williams MC. Polymerase manager protein UmuD directly regulates Escherichia coli DNA polymerase III α binding to ssDNA. Nucleic Acids Res 2013; 41:8959-68. [PMID: 23901012 PMCID: PMC3799427 DOI: 10.1093/nar/gkt648] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Replication by Escherichia coli DNA polymerase III is disrupted on encountering DNA damage. Consequently, specialized Y-family DNA polymerases are used to bypass DNA damage. The protein UmuD is extensively involved in modulating cellular responses to DNA damage and may play a role in DNA polymerase exchange for damage tolerance. In the absence of DNA, UmuD interacts with the α subunit of DNA polymerase III at two distinct binding sites, one of which is adjacent to the single-stranded DNA-binding site of α. Here, we use single molecule DNA stretching experiments to demonstrate that UmuD specifically inhibits binding of α to ssDNA. We predict using molecular modeling that UmuD residues D91 and G92 are involved in this interaction and demonstrate that mutation of these residues disrupts the interaction. Our results suggest that competition between UmuD and ssDNA for α binding is a new mechanism for polymerase exchange.
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Affiliation(s)
- Kathy R. Chaurasiya
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Clarissa Ruslie
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Michelle C. Silva
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Lukas Voortman
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Philip Nevin
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Samer Lone
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
| | - Penny J. Beuning
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
- *To whom correspondence should be addressed. Tel: +1 617 373 7323; Fax: +1 617 373 2943;
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Department of Chemical Sciences, Bridgewater State University, Bridgewater, MA 02325, USA
- *To whom correspondence should be addressed. Tel: +1 617 373 7323; Fax: +1 617 373 2943;
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32
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Paik DH, Perkins TT. Dynamics and Multiple Stable Binding Modes of DNA Intercalators Revealed by Single-Molecule Force Spectroscopy. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201105540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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33
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Paramanathan T, Vladescu I, McCauley MJ, Rouzina I, Williams MC. Force spectroscopy reveals the DNA structural dynamics that govern the slow binding of Actinomycin D. Nucleic Acids Res 2012; 40:4925-32. [PMID: 22328730 PMCID: PMC3367174 DOI: 10.1093/nar/gks069] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Actinomycin D (ActD) is a small molecule with strong antibiotic and anticancer activity. However, its biologically relevant DNA-binding mechanism has never been resolved, with some studies suggesting that the primary binding mode is intercalation, and others suggesting that single-stranded DNA binding is most important. To resolve this controversy, we develop a method to quantify ActD’s equilibrium and kinetic DNA-binding properties as a function of stretching force applied to a single DNA molecule. We find that destabilization of double stranded DNA (dsDNA) by force exponentially facilitates the extremely slow ActD-dsDNA on and off rates, with a much stronger effect on association, resulting in overall enhancement of equilibrium ActD binding. While we find the preferred ActD–DNA-binding mode to be to two DNA strands, major duplex deformations appear to be a pre-requisite for ActD binding. These results provide quantitative support for a model in which the biologically active mode of ActD binding is to pre-melted dsDNA, as found in transcription bubbles. DNA in transcriptionally hyperactive cancer cells will therefore likely efficiently and rapidly bind low ActD concentrations (∼10 nM), essentially locking ActD within dsDNA due to its slow dissociation, blocking RNA synthesis and leading to cell death.
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34
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Liu D, Vanasse J, Müller G, Karbach M. Generalized Pauli principle for particles with distinguishable traits. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:011144. [PMID: 22400549 DOI: 10.1103/physreve.85.011144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Indexed: 05/31/2023]
Abstract
The s=3/2 Ising spin chain with uniform nearest-neighbor coupling, quadratic single-site potential, and magnetic field is shown to be equivalent to a system of 17 species of particles with internal structure. The same set of particles (with different energies) is shown to generate the spectrum of the s=1/2 Ising chain with dimerized nearest-neighbor coupling. The particles are free of interaction energies even at high densities. The mutual exclusion statistics of particles from all species is determined by their internal structure and encoded in a generalized Pauli principle. The exact statistical mechanical analysis can be performed for thermodynamically open or closed systems and with arbitrary energies assigned to all particle species. Special circumstances make it possible to merge two or more species into a single species. All traits that distinguish the original species become ignorable. The particles from the merged species are effectively indistinguishable and obey modified exclusion statistics. Different mergers may yield the same end product, implying that the inverse process (splitting any species into subspecies) is not unique. In a macroscopic system of two merged species at thermal equilibrium, the concentrations of the original species satisfy a functional relation governed by their mutual statistical interaction. That relation is derivable from an extremum principle. In the Ising context the system is open and the particle energies depend on the Hamiltonian parameters. Simple models of polymerization and solitonic paramagnetism each represent a closed system of two species that can transform into each other. Here they represent distinguishable traits with different energies of the same physical particle.
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Affiliation(s)
- Dan Liu
- Department of Physics, University of Rhode Island, Kingston, Rhode Island 02881, USA
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35
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Paik DH, Perkins TT. Dynamics and multiple stable binding modes of DNA intercalators revealed by single-molecule force spectroscopy. Angew Chem Int Ed Engl 2011; 51:1811-5. [PMID: 22162006 DOI: 10.1002/anie.201105540] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Indexed: 11/06/2022]
Affiliation(s)
- D Hern Paik
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309-0440, USA
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36
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Balaeff A, Craig SL, Beratan DN. B-DNA to zip-DNA: simulating a DNA transition to a novel structure with enhanced charge-transport characteristics. J Phys Chem A 2011; 115:9377-91. [PMID: 21598926 PMCID: PMC3615717 DOI: 10.1021/jp110871g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The forced extension of a DNA segment is studied in a series of steered molecular dynamics simulations, employing a broad range of pulling forces. Throughout the entire force range, the formation of a zipper-like (zip-) DNA structure is observed. In that structure, first predicted by Lohikoski et al., the bases of the DNA strands interdigitate with each other and form a single-base aromatic stack. Similar motifs, albeit only a few base pairs in extent, have been observed in experimental crystal structures. Analysis of the dynamics of structural changes in pulled DNA shows that S-form DNA, thought to be adopted by DNA under applied force, serves as an intermediate between B-DNA and zip-DNA. Therefore, the phase transition plateau observed in force-extension curves of DNA is suggested to reflect the B-DNA to zip-DNA structural transition. Electronic structure analysis of purine bases in zip-DNA indicates a several-fold to order of magnitude increase in the π-π electronic coupling among nearest-neighbor nucleobases, compared to B-DNA. We further observe that zip-DNA does not require base pair complementarity between DNA strands, and we predict that the increased electronic coupling in zip-DNA will result in a much higher rate of charge transfer through an all-purine zip-DNA compared to B-DNA of equal length.
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Affiliation(s)
- Alexander Balaeff
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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37
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Celedon A, Wirtz D, Sun S. Torsional mechanics of DNA are regulated by small-molecule intercalation. J Phys Chem B 2010; 114:16929-35. [PMID: 21090816 DOI: 10.1021/jp107541q] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Whether the bend and twist mechanics of DNA molecules are coupled is unclear. Here, we report the direct measurement of the resistive torque of single DNA molecules to study the effect of ethidium bromide (EtBr) intercalation and pulling force on DNA twist mechanics. DNA molecules were overwound and unwound using recently developed magnetic tweezers where the molecular resistive torque was obtained from Brownian angular fluctuations. The effect of EtBr intercalation on the twist stiffness was found to be significantly different from the effect on the bend persistence length. The twist stiffness of DNA was dramatically reduced at low intercalator concentration (<10 nM); however, it did not decrease further when the intercalator concentration was increased by 3 orders of magnitude. We also determined the dependence of EtBr intercalation on the torque applied to DNA. We propose a model for the elasticity of DNA base pairs with intercalated EtBr molecules to explain the abrupt decrease of twist stiffness at low EtBr concentration. These results indicate that the bend and twist stiffnesses of DNA are independent and can be differently affected by small-molecule binding.
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Affiliation(s)
- Alfredo Celedon
- Johns Hopkins Physical Science Oncology Center, The Johns Hopkins University, Baltimore, Maryland 21218, USA.
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38
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Wu H, Rouzina I, Williams MC. Single-molecule stretching studies of RNA chaperones. RNA Biol 2010; 7:712-23. [PMID: 21045548 PMCID: PMC3073330 DOI: 10.4161/rna.7.6.13776] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 01/25/2023] Open
Abstract
RNA chaperone proteins play significant roles in diverse biological contexts. The most widely studied RNA chaperones are the retroviral nucleocapsid proteins (NC), also referred to as nucleic acid (NA) chaperones. Surprisingly, the biophysical properties of the NC proteins vary significantly for different viruses, and it appears that HIV-1 NC has optimal NA chaperone activity. In this review we discuss the physical nature of the NA chaperone activity of NC. We conclude that the optimal NA chaperone must saturate NA binding, leading to strong NA aggregation and slight destabilization of all NA duplexes. Finally, rapid kinetics of the chaperone protein interaction with NA is another primary component of its NA chaperone activity. We discuss these characteristics of HIV-1 NC and compare them with those of other NA binding proteins and ligands that exhibit only some characteristics of NA chaperone activity, as studied by single molecule DNA stretching.
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Affiliation(s)
- Hao Wu
- Department of Physics, Northeastern University, Boston, MA, USA
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39
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Atomic force microscopy study of DNA conformation in the presence of drugs. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 40:59-68. [PMID: 20882274 DOI: 10.1007/s00249-010-0627-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 08/27/2010] [Accepted: 09/03/2010] [Indexed: 10/19/2022]
Abstract
Binding of ligands to DNA gives rise to several relevant biological and biomedical effects. Here, through the use of atomic force microscopy (AFM), we studied the consequences of drug binding on the morphology of single DNA molecules. In particular, we quantitatively analyzed the effects of three different DNA-binding molecules (doxorubicin, ethidium bromide, and netropsin) that exert various pharmacologic and therapeutic effects. The results of this study show the consequences of intercalation and groove molecular binding on DNA conformation. These single-molecule measurements demonstrate morphological features that reflect the specific modes of drug-DNA interaction. This experimental approach may have implications in the design of therapeutically effective agents.
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40
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Metzler R. Wonderful world of single biopolymer thermodynamics. Comment on "Biophysical characterization of DNA binding from single molecule force measurements" by K.R. Chaurasiya et al. Phys Life Rev 2010; 7:355-7; discussion 358-61. [PMID: 20667796 DOI: 10.1016/j.plrev.2010.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 07/20/2010] [Indexed: 11/19/2022]
Affiliation(s)
- Ralf Metzler
- Physics Department, Technical University of Munich, 85747 Garching, Germany.
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41
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Lipfert J, Klijnhout S, Dekker NH. Torsional sensing of small-molecule binding using magnetic tweezers. Nucleic Acids Res 2010; 38:7122-32. [PMID: 20624816 PMCID: PMC2978369 DOI: 10.1093/nar/gkq598] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
DNA-binding small molecules are widespread in the cell and heavily used in biological applications. Here, we use magnetic tweezers, which control the force and torque applied to single DNAs, to study three small molecules: ethidium bromide (EtBr), a well-known intercalator; netropsin, a minor-groove binding anti-microbial drug; and topotecan, a clinically used anti-tumor drug. In the low-force limit in which biologically relevant torques can be accessed (<10 pN), we show that ethidium intercalation lengthens DNA ∼1.5-fold and decreases the persistence length, from which we extract binding constants. Using our control of supercoiling, we measure the decrease in DNA twist per intercalation to be 27.3 ± 1° and demonstrate that ethidium binding delays the accumulation of torsional stress in DNA, likely via direct reduction of the torsional modulus and torque-dependent binding. Furthermore, we observe that EtBr stabilizes the DNA duplex in regimes where bare DNA undergoes structural transitions. In contrast, minor groove binding by netropsin affects neither the contour nor persistence length significantly, yet increases the twist per base of DNA. Finally, we show that topotecan binding has consequences similar to those of EtBr, providing evidence for an intercalative binding mode. These insights into the torsional consequences of ligand binding can help elucidate the effects of small-molecule drugs in the cellular environment.
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Affiliation(s)
- Jan Lipfert
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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42
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Salerno D, Brogioli D, Cassina V, Turchi D, Beretta GL, Seruggia D, Ziano R, Zunino F, Mantegazza F. Magnetic tweezers measurements of the nanomechanical properties of DNA in the presence of drugs. Nucleic Acids Res 2010; 38:7089-99. [PMID: 20601682 PMCID: PMC2978368 DOI: 10.1093/nar/gkq597] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Herein, we study the nanomechanical characteristics of single DNA molecules in the presence of DNA binders, including intercalating agents (ethidium bromide and doxorubicin), a minor groove binder (netropsin) and a typical alkylating damaging agent (cisplatin). We have used magnetic tweezers manipulation techniques, which allow us to measure the contour and persistence lengths together with the bending and torsional properties of DNA. For each drug, the specific variations of the nanomechanical properties induced in the DNA have been compared. We observed that the presence of drugs causes a specific variation in the DNA extension, a shift in the natural twist and a modification of bending dependence on the imposed twist. By introducing a naive model, we have justified an anomalous correlation of torsion data observed in the presence of intercalators. Finally, a data analysis criterion for discriminating between different molecular interactions among DNA and drugs has been suggested.
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Affiliation(s)
- Domenico Salerno
- Dipartimento di Medicina Sperimentale, Universita' di Milano-Bicocca, via Cadore 48, Monza (MI) 20052, Italy.
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43
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Chaurasiya KR, Paramanathan T, McCauley MJ, Williams MC. Biophysical characterization of DNA binding from single molecule force measurements. Phys Life Rev 2010; 7:299-341. [PMID: 20576476 DOI: 10.1016/j.plrev.2010.06.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/19/2010] [Accepted: 05/20/2010] [Indexed: 11/25/2022]
Abstract
Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.
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Affiliation(s)
- Kathy R Chaurasiya
- Department of Physics, Northeastern University, 111 Dana Research Center, Boston, MA 02115, USA
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44
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45
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Kleimann C, Sischka A, Spiering A, Tönsing K, Sewald N, Diederichsen U, Anselmetti D. Binding kinetics of bisintercalator Triostin a with optical tweezers force mechanics. Biophys J 2009; 97:2780-4. [PMID: 19917232 PMCID: PMC2776255 DOI: 10.1016/j.bpj.2009.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 08/28/2009] [Accepted: 09/01/2009] [Indexed: 10/20/2022] Open
Abstract
The binding kinetics of the intercalative binding of Triostin A to lambda-DNA was investigated by measuring the force extension response of the DNA-ligand complexes with an optical tweezers system. These force response curves, containing the information about different binding properties, were analyzed based on a recent method (put forth by another research group) for monointercalators that was extended to bisintercalators. Our binding analysis reveals an exponential dependence of the association constant on the applied external force as well as a decreasing binding site size. In general, our results are in agreement with those for the monointercalator ethidium. However, to explain the high-force binding site size, a new model for bisintercalation of Triostin A at high forces is proposed.
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Affiliation(s)
- Christoph Kleimann
- Department of Physics, Experimental Biophysics and Applied Nanoscience, Bielefeld University, Bielefeld, Germany
| | - Andy Sischka
- Department of Physics, Experimental Biophysics and Applied Nanoscience, Bielefeld University, Bielefeld, Germany
| | - Andre Spiering
- Department of Physics, Experimental Biophysics and Applied Nanoscience, Bielefeld University, Bielefeld, Germany
| | - Katja Tönsing
- Department of Physics, Experimental Biophysics and Applied Nanoscience, Bielefeld University, Bielefeld, Germany
| | - Norbert Sewald
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, Bielefeld, Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry, Göttingen University, Göttingen, Germany
| | - Dario Anselmetti
- Department of Physics, Experimental Biophysics and Applied Nanoscience, Bielefeld University, Bielefeld, Germany
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Murade CU, Subramaniam V, Otto C, Bennink ML. Interaction of oxazole yellow dyes with DNA studied with hybrid optical tweezers and fluorescence microscopy. Biophys J 2009; 97:835-43. [PMID: 19651041 DOI: 10.1016/j.bpj.2009.05.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 04/18/2009] [Accepted: 05/07/2009] [Indexed: 10/20/2022] Open
Abstract
We have integrated single molecule fluorescence microscopy imaging into an optical tweezers set-up and studied the force extension behavior of individual DNA molecules in the presence of various YOYO-1 and YO-PRO-1 concentrations. The fluorescence modality was used to record fluorescent images during the stretching and relaxation cycle. Force extension curves recorded in the presence of either dye did not show the overstretching transition that is characteristic for bare DNA. Using the modified wormlike chain model to curve-fit the force extension data revealed a contour length increase of 6% and 30%, respectively, in the presence of YO-PRO-1 and YOYO-1 at 100 nM. The fluorescence images recorded simultaneously showed that the number of bound dye molecules increased as the DNA molecule was stretched and decreased again as the force on the complex was lowered. The binding constants and binding site sizes for YO-PRO-1 and YOYO-1 were determined as a function of the force. The rate of YO-PRO-1 binding and unbinding was found to be 2 orders of magnitude larger than that for YOYO-1. A kinetic model is proposed to explain this observation.
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Affiliation(s)
- C U Murade
- Department of Biophysical Engineering and MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente, 7500 AE Enschede, The Netherlands
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Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging. Proc Natl Acad Sci U S A 2009; 106:18231-6. [PMID: 19841258 DOI: 10.1073/pnas.0904322106] [Citation(s) in RCA: 196] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-molecule manipulation studies have revealed that double-stranded DNA undergoes a structural transition when subjected to tension. At forces that depend on the attachment geometry of the DNA (65 pN or 110 pN), it elongates approximately 1.7-fold and its elastic properties change dramatically. The nature of this overstretched DNA has been under debate. In one model, the DNA cooperatively unwinds, while base pairing remains intact. In a competing model, the hydrogen bonds between base pairs break and two single DNA strands are formed, comparable to thermal DNA melting. Here, we resolve the structural basis of DNA overstretching using a combination of fluorescence microscopy, optical tweezers, and microfluidics. In DNA molecules undergoing the transition, we visualize double- and single-stranded segments using specific fluorescent labels. Our data directly demonstrate that overstretching comprises a gradual conversion from double-stranded to single-stranded DNA, irrespective of the attachment geometry. We found that these conversions favorably initiate from nicks or free DNA ends. These discontinuities in the phosphodiester backbone serve as energetically favorable nucleation points for melting. When both DNA strands are intact and no nicks or free ends are present, the overstretching force increases from 65 to 110 pN and melting initiates throughout the molecule, comparable to thermal melting. These results provide unique insights in the thermodynamics of DNA and DNA-protein interactions.
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Shokri L, Rouzina I, Williams MC. Interaction of bacteriophage T4 and T7 single-stranded DNA-binding proteins with DNA. Phys Biol 2009; 6:025002. [PMID: 19571366 DOI: 10.1088/1478-3975/6/2/025002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bacteriophages T4 and T7 are well-studied model replication systems, which have allowed researchers to determine the roles of many proteins central to DNA replication, recombination and repair. Here we summarize and discuss the results from two recently developed single-molecule methods to determine the salt-dependent DNA-binding kinetics and thermodynamics of the single-stranded DNA (ssDNA)-binding proteins (SSBs) from these systems. We use these methods to characterize both the equilibrium double-stranded DNA (dsDNA) and ssDNA binding of the SSBs T4 gene 32 protein (gp32) and T7 gene 2.5 protein (gp2.5). Despite the overall two-orders-of-magnitude weaker binding of gp2.5 to both forms of DNA, we find that both proteins exhibit four-orders-of-magnitude preferential binding to ssDNA relative to dsDNA. This strong preferential ssDNA binding as well as the weak dsDNA binding is essential for the ability of both proteins to search dsDNA in one dimension to find available ssDNA-binding sites at the replication fork.
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Affiliation(s)
- Leila Shokri
- Department of Physics, Northeastern University, 111 Dana Research Center, Boston, MA 02115, USA
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49
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McCauley MJ, Williams MC. Optical tweezers experiments resolve distinct modes of DNA-protein binding. Biopolymers 2009; 91:265-82. [PMID: 19173290 DOI: 10.1002/bip.21123] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Optical tweezers are ideally suited to perform force microscopy experiments that isolate a single biomolecule, which then provides multiple binding sites for ligands. The captured complex may be subjected to a spectrum of forces, inhibiting or facilitating ligand activity. In the following experiments, we utilize optical tweezers to characterize and quantify DNA binding of various ligands. High mobility group type B (HMGB) proteins, which bind to double-stranded DNA, are shown to serve the dual purpose of stabilizing and enhancing the flexibility of double stranded DNA. Unusual intercalating ligands are observed to thread into and lengthen the double-stranded structure. Proteins binding to both double- and single-stranded DNA, such as the alpha polymerase subunit of E. coli Pol III, are characterized, and the subdomains containing the distinct sites responsible for binding are isolated. Finally, DNA binding of bacteriophage T4 and T7 single-stranded DNA (ssDNA) binding proteins is measured for a range of salt concentrations, illustrating a binding model for proteins that slide along double-stranded DNA, ultimately binding tightly to ssDNA. These recently developed methods quantify both the binding activity of the ligand as well as the mode of binding.
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Affiliation(s)
- Micah J McCauley
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 111 Dana Research Center, Boston, MA 02115, USA
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Rocha MS. Modeling the entropic structural transition of DNA complexes formed with intercalating drugs. Phys Biol 2009; 6:036013. [DOI: 10.1088/1478-3975/6/3/036013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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