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Xie C, Chen Z, Chen K, Hu Y, Xu F, Pan L. Diverse Chiral Nanotubes Assembled from Identical DNA Strands. NANO LETTERS 2024; 24:8696-8701. [PMID: 38967319 DOI: 10.1021/acs.nanolett.4c02071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
DNA nanotubes with controllable geometries hold a wide range of interdisciplinary applications. When preparing DNA nanotubes of varying widths or distinct chirality, existing methods require repeatedly designing and synthesizing specific DNA sequences, which can be costly and laborious. Here, we proposed an intercalator-assisted DNA tile assembly method which enables the production of DNA nanotubes of diverse widths and chirality using identical DNA strands. Through adjusting the concentration of intercalators during assembly, the twisting direction and extent of DNA tiles could be modulated, leading to the formation of DNA nanotubes featuring controllable widths and chirality. Moreover, through introducing additional intercalators and secondary annealing, right-handed nanotubes could be reconfigured into distinct left-handed nanotubes. We expect that this method could be universally applied to modulating the self-assembly pathways of various DNA tiles and other chiral materials, advancing the landscape of DNA tile assembly.
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Affiliation(s)
- Chun Xie
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Zhekun Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Kuiting Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang 050043 Hebei, China
| | - Fei Xu
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
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2
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Kim T, Lee C, Lee JY, Kim DN. Controlling Chiroptical Responses via Chemo-Mechanical Deformation of DNA Origami Structures. ACS NANO 2024; 18:3414-3423. [PMID: 38236130 DOI: 10.1021/acsnano.3c10386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
DNA origami-based templates have been widely used to fabricate chiral plasmonic metamaterials due to their precise control of the placement of nanoparticles (NPs) in a desired configuration. However, achieving various chiroptical responses inevitably requires a change in the structure of DNA origami-based templates or binding sites on them, leading to the use of significantly different sets of DNA strands. Here, we propose an approach to controlling various chiroptical responses with a single DNA origami design using its chemo-mechanical deformation induced by DNA intercalators. The chiroptical response could be finely tuned by altering the concentration of intercalators only. The silver (Ag) enhancement was used to amplify the chiroptical signal by enlarging NPs and to maintain it by stiffening the template DNA structure. Furthermore, the sensitivity in the chiroptical signal change to the concentration of intercalators could be modulated by the type of intercalator, the mixture of two intercalators, and the stiffness of DNA origami structures. This approach would be useful in a variety of optical applications that require programmed spatial modification of chiroptical responses.
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Affiliation(s)
- Taehwi Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Do-Nyun Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
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3
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Kolbeck PJ, Tišma M, Analikwu BT, Vanderlinden W, Dekker C, Lipfert J. Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments. Nucleic Acids Res 2024; 52:59-72. [PMID: 38000393 PMCID: PMC10783501 DOI: 10.1093/nar/gkad1055] [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: 06/29/2023] [Revised: 10/02/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
DNA stores our genetic information and is ubiquitous in applications, where it interacts with binding partners ranging from small molecules to large macromolecular complexes. Binding is modulated by mechanical strains in the molecule and can change local DNA structure. Frequently, DNA occurs in closed topological forms where topology and supercoiling add a global constraint to the interplay of binding-induced deformations and strain-modulated binding. Here, we present a quantitative model with a straight-forward numerical implementation of how the global constraints introduced by DNA topology modulate binding. We focus on fluorescent intercalators, which unwind DNA and enable direct quantification via fluorescence detection. Our model correctly describes bulk experiments using plasmids with different starting topologies, different intercalators, and over a broad range of intercalator and DNA concentrations. We demonstrate and quantitatively model supercoiling-dependent binding in a single-molecule assay, where we directly observe the different intercalator densities going from supercoiled to nicked DNA. The single-molecule assay provides direct access to binding kinetics and DNA supercoil dynamics. Our model has broad implications for the detection and quantification of DNA, including the use of psoralen for UV-induced DNA crosslinking to quantify torsional tension in vivo, and for the modulation of DNA binding in cellular contexts.
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Affiliation(s)
- Pauline J Kolbeck
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Miloš Tišma
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Brian T Analikwu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Willem Vanderlinden
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Jan Lipfert
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
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4
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Mazur AK, Gladyshev E. C-DNA may facilitate homologous DNA pairing. Trends Genet 2023:S0168-9525(23)00023-9. [PMID: 36804168 DOI: 10.1016/j.tig.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/17/2023]
Abstract
Recombination-independent homologous pairing represents a prominent yet largely enigmatic feature of chromosome biology. As suggested by studies in the fungus Neurospora crassa, this process may be based on the direct pairing of homologous DNA molecules. Theoretical search for the DNA structures consistent with those genetic results has led to an all-atom model in which the B-DNA conformation of the paired double helices is strongly shifted toward C-DNA. Coincidentally, C-DNA also features a very shallow major groove that could permit initial homologous contacts without atom-atom clashes. The hereby conjectured role of C-DNA in homologous pairing should encourage the efforts to discover its biological functions and may also clarify the mechanism of recombination-independent recognition of DNA homology.
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Affiliation(s)
- Alexey K Mazur
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, Paris, France; Institut Pasteur, Université Paris Cité, Group Fungal Epigenomics, Paris, France.
| | - Eugene Gladyshev
- Institut Pasteur, Université Paris Cité, Group Fungal Epigenomics, Paris, France.
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5
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Pansare AV, Shedge AA, Sonawale MC, Pansare SV, Mahakal AD, Khairkar SR, Chhatre SY, Kulal DK, Patil VR. Deciphering the sensing of α-amyrin acetate with hs-DNA: a multipronged biological probe. RSC Adv 2022; 12:1238-1243. [PMID: 35425164 PMCID: PMC8978960 DOI: 10.1039/d1ra07195e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/15/2021] [Indexed: 11/22/2022] Open
Abstract
In this study, we focus on the biomimetic development of small molecules and their biological sensing with DNA. The binding of herring sperm deoxyribonucleic acid (hs-DNA) with naturally occurring bioactive small molecule α-amyrin acetate (α-AA), a biomimetic - isolated from the leaves of Ficus (F.) arnottiana is investigated. Collective information from various imaging, spectroscopic and biophysical experiments provides evidence that α-AA is a minor groove sensor of hs-DNA and preferentially binds to the A-T-rich regions. Interactions of different concentrations of small molecule α-AA with hsDNA were evaluated via various analytical techniques such as UV-Vis, circular dichroism (CD) and fluorescence emission spectroscopy. Fluorescence emission spectroscopy results suggest that α-AA decreases the emission level of hsDNA. DNA minor groove sensor Hoechst 33258 and intercalative sensor EB, melting transition analysis (T M) and viscosity analysis clarified that α-AA binds to hs-DNA via a groove site. Biophysical chemistry and molecular docking studies show that hydrophobic interactions play a major role in this binding. The present research deals with a natural product biosynthesis-linked chemical-biology interface sensor as a biological probe for α-AA: hs-DNA.
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Affiliation(s)
- Amol V Pansare
- Composite Group, Swiss Federal Laboratories for Materials Science and Technology-Empa 8600 Dübendorf Switzerland
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
| | - Amol A Shedge
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
| | | | - Shubham V Pansare
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
| | - Akshay D Mahakal
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
| | - Shyam R Khairkar
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
| | - Shraddha Y Chhatre
- National Chemical Laboratory (NCL) Dr. Homi Bhabha Road Pune 411008 India
| | - Dnyaneshwar K Kulal
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
| | - Vishwanath R Patil
- Department of Chemistry, University of Mumbai Santacruz (E) Mumbai 400098 India
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6
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Kim YJ, Park J, Lee JY, Kim DN. Programming ultrasensitive threshold response through chemomechanical instability. Nat Commun 2021; 12:5177. [PMID: 34462430 PMCID: PMC8405678 DOI: 10.1038/s41467-021-25406-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 08/03/2021] [Indexed: 11/09/2022] Open
Abstract
The ultrasensitive threshold response is ubiquitous in biochemical systems. In contrast, achieving ultrasensitivity in synthetic molecular structures in a controllable way is challenging. Here, we propose a chemomechanical approach inspired by Michell's instability to realize it. A sudden reconfiguration of topologically constrained rings results when the torsional stress inside reaches a critical value. We use DNA origami to construct molecular rings and then DNA intercalators to induce torsional stress. Michell's instability is achieved successfully when the critical concentration of intercalators is applied. Both the critical point and sensitivity of this ultrasensitive threshold reconfiguration can be controlled by rationally designing the cross-sectional shape and mechanical properties of DNA rings.
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Affiliation(s)
- Young-Joo Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea
| | - Junho Park
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Jae Young Lee
- Department of Mechanical Engineering, Seoul National University, Seoul, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul, Korea. .,Department of Mechanical Engineering, Seoul National University, Seoul, Korea. .,Institute of Engineering Research, Seoul National University, Seoul, Korea.
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7
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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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8
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Galindo-Murillo R, Cheatham TE. Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations. Nucleic Acids Res 2021; 49:3735-3747. [PMID: 33764383 PMCID: PMC8053101 DOI: 10.1093/nar/gkab143] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/03/2021] [Accepted: 03/16/2021] [Indexed: 01/27/2023] Open
Abstract
Visualization of double stranded DNA in gels with the binding of the fluorescent dye ethidium bromide has been a basic experimental technique in any molecular biology laboratory for >40 years. The interaction between ethidium and double stranded DNA has been observed to be an intercalation between base pairs with strong experimental evidence. This presents a unique opportunity for computational chemistry and biomolecular simulation techniques to benchmark and assess their models in order to see if the theory can reproduce experiments and ultimately provide new insights. We present molecular dynamics simulations of the interaction of ethidium with two different double stranded DNA models. The first model system is the classic sequence d(CGCGAATTCGCG)2 also known as the Drew–Dickerson dodecamer. We found that the ethidium ligand binds mainly stacked on, or intercalated between, the terminal base pairs of the DNA with little to no interaction with the inner base pairs. As the intercalation at the terminal CpG steps is relatively rapid, the resultant DNA unwinding, rigidification, and increased stability of the internal base pair steps inhibits further intercalation. In order to reduce these interactions and to provide a larger groove space, a second 18-mer DNA duplex system with the sequence d(GCATGAACGAACGAACGC) was tested. We computed molecular dynamics simulations for 20 independent replicas with this sequence, each with ∼27 μs of sampling time. Results show several spontaneous intercalation and base-pair eversion events that are consistent with experimental observations. The present work suggests that extended MD simulations with modern DNA force fields and optimized simulation codes are allowing the ability to reproduce unbiased intercalation events that we were not able to previously reach due to limits in computing power and the lack of extensively tested force fields and analysis tools.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, UT 84112, USA
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, UT 84112, USA
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Walter JC, Lepage T, Dorignac J, Geniet F, Parmeggiani A, Palmeri J, Bouet JY, Junier I. Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex. PLoS Comput Biol 2021; 17:e1008869. [PMID: 33861734 PMCID: PMC8092679 DOI: 10.1371/journal.pcbi.1008869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/03/2021] [Accepted: 03/11/2021] [Indexed: 11/18/2022] Open
Abstract
ParABS, the most widespread bacterial DNA segregation system, is composed of a centromeric sequence, parS, and two proteins, the ParA ATPase and the ParB DNA binding proteins. Hundreds of ParB proteins assemble dynamically to form nucleoprotein parS-anchored complexes that serve as substrates for ParA molecules to catalyze positioning and segregation events. The exact nature of this ParBS complex has remained elusive, what we address here by revisiting the Stochastic Binding model (SBM) introduced to explain the non-specific binding profile of ParB in the vicinity of parS. In the SBM, DNA loops stochastically bring loci inside a sharp cluster of ParB. However, previous SBM versions did not include the negative supercoiling of bacterial DNA, leading to use unphysically small DNA persistences to explain the ParB binding profiles. In addition, recent super-resolution microscopy experiments have revealed a ParB cluster that is significantly smaller than previous estimations and suggest that it results from a liquid-liquid like phase separation. Here, by simulating the folding of long (≥ 30 kb) supercoiled DNA molecules calibrated with realistic DNA parameters and by considering different possibilities for the physics of the ParB cluster assembly, we show that the SBM can quantitatively explain the ChIP-seq ParB binding profiles without any fitting parameter, aside from the supercoiling density of DNA, which, remarkably, is in accord with independent measurements. We also predict that ParB assembly results from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., ParB clusters behave like liquid-like protein condensates with unconventional “leaky” boundaries. In bacteria, faithful genome inheritance requires the two replicated DNA molecules to be segregated at the opposite halves of the cell. ParABS, the most widespread bacterial DNA segregation system, is composed of a centromere sequence, parS, and two proteins, the ParA ATPase and the ParB DNA binding protein. Hundreds of ParB assemble dynamically to form clusters around parS, which then serve as substrates for ParA molecules to catalyze the positioning and segregation events. The nature of these clusters and their interaction with DNA have remained elusive. Here, we propose a realistic minimal model that captures quantitatively the peculiar DNA binding profile of ParB in the vicinity of parS in Escherichia coli. From the viewpoint of DNA, the only fitting parameter is the in vivo supercoiling density resulting from the removal of DNA helices by toposiomerases, which is in accord with previous independent estimations. From the viewpoint of ParB clusters, we predict that they behave like liquid-like protein condensates with unconventional boundaries. Namely, we predict boundaries to be leaky (i.e. not sharp) as a result of the non-equilibrium protein production, diffusion and dilution. Altogether, our work provides novel insights into bacterial DNA organization and intracellular liquid-liquid phase separation.
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Affiliation(s)
- Jean-Charles Walter
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
- * E-mail: (J-CW); (IJ)
| | | | - Jérôme Dorignac
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Frédéric Geniet
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | - Andrea Parmeggiani
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
- LPHI, Univ. Montpellier, CNRS, Montpellier, France
| | - John Palmeri
- Laboratoire Charles Coulomb (L2C), Univ. Montpellier, CNRS, Montpellier, France
| | | | - Ivan Junier
- CNRS, Univ. Grenoble Alpes, TIMC, Grenoble, France
- * E-mail: (J-CW); (IJ)
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10
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Yuan JM, Wei K, Zhang GH, Chen NY, Wei XW, Pan CX, Mo DL, Su GF. Cryptolepine and aromathecin based mimics as potent G-quadruplex-binding, DNA-cleavage and anticancer agents: Design, synthesis and DNA targeting-induced apoptosis. Eur J Med Chem 2019; 169:144-158. [DOI: 10.1016/j.ejmech.2019.02.072] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 01/05/2023]
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11
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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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12
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Kriegel F, Matek C, Dršata T, Kulenkampff K, Tschirpke S, Zacharias M, Lankaš F, Lipfert J. The temperature dependence of the helical twist of DNA. Nucleic Acids Res 2018; 46:7998-8009. [PMID: 30053087 PMCID: PMC6125625 DOI: 10.1093/nar/gky599] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 06/08/2018] [Accepted: 07/20/2018] [Indexed: 01/11/2023] Open
Abstract
DNA is the carrier of all cellular genetic information and increasingly used in nanotechnology. Quantitative understanding and optimization of its functions requires precise experimental characterization and accurate modeling of DNA properties. A defining feature of DNA is its helicity. DNA unwinds with increasing temperature, even for temperatures well below the melting temperature. However, accurate quantitation of DNA unwinding under external forces and a microscopic understanding of the corresponding structural changes are currently lacking. Here we combine single-molecule magnetic tweezers measurements with atomistic molecular dynamics and coarse-grained simulations to obtain a comprehensive view of the temperature dependence of DNA twist. Experimentally, we find that DNA twist changes by ΔTw(T) = (-11.0 ± 1.2)°/(°C·kbp), independent of applied force, in the range of forces where torque-induced melting is negligible. Our atomistic simulations predict ΔTw(T) = (-11.1 ± 0.3)°/(°C·kbp), in quantitative agreement with experiments, and suggest that the untwisting of DNA with temperature is predominantly due to changes in DNA structure for defined backbone substates, while the effects of changes in substate populations are minor. Coarse-grained simulations using the oxDNA framework yield a value of ΔTw(T) = (-6.4 ± 0.2)°/(°C·kbp) in semi-quantitative agreement with experiments.
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Affiliation(s)
- Franziska Kriegel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Christian Matek
- Technical University of Munich and Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Tomáš Dršata
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Klara Kulenkampff
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Sophie Tschirpke
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Martin Zacharias
- Physics-Department T38, Technical University of Munich, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Filip Lankaš
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
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13
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Reymer A, Zakrzewska K, Lavery R. Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism. Nucleic Acids Res 2018; 46:1684-1694. [PMID: 29267977 PMCID: PMC5829783 DOI: 10.1093/nar/gkx1270] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/07/2017] [Accepted: 12/09/2017] [Indexed: 01/31/2023] Open
Abstract
Torsional restraints on DNA change in time and space during the life of the cell and are an integral part of processes such as gene expression, DNA repair and packaging. The mechanical behavior of DNA under torsional stress has been studied on a mesoscopic scale, but little is known concerning its response at the level of individual base pairs and the effects of base pair composition. To answer this question, we have developed a geometrical restraint that can accurately control the total twist of a DNA segment during all-atom molecular dynamics simulations. By applying this restraint to four different DNA oligomers, we are able to show that DNA responds to both under- and overtwisting in a very heterogeneous manner. Certain base pair steps, in specific sequence environments, are able to absorb most of the torsional stress, leaving other steps close to their relaxed conformation. This heterogeneity also affects the local torsional modulus of DNA. These findings suggest that modifying torsional stress on DNA could act as a modulator for protein binding via the heterogeneous changes in local DNA structure.
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Affiliation(s)
- Anna Reymer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg 40530, Sweden
- Institut de Biologie et Chimie des Protéines, Université de Lyon I/CNRS UMR 5086, Lyon 69367, France
| | - Krystyna Zakrzewska
- Institut de Biologie et Chimie des Protéines, Université de Lyon I/CNRS UMR 5086, Lyon 69367, France
| | - Richard Lavery
- Institut de Biologie et Chimie des Protéines, Université de Lyon I/CNRS UMR 5086, Lyon 69367, France
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14
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Slator C, Molphy Z, McKee V, Kellett A. Triggering autophagic cell death with a di-manganese(II) developmental therapeutic. Redox Biol 2017; 12:150-161. [PMID: 28236767 PMCID: PMC5328722 DOI: 10.1016/j.redox.2017.01.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/07/2017] [Accepted: 01/11/2017] [Indexed: 12/16/2022] Open
Abstract
There is an unmet need for novel metal-based chemotherapeutics with alternative modes of action compared to clinical agents such as cisplatin and metallo-bleomycin. Recent attention in this field has focused on designing intracellular ROS-mediators as powerful cytotoxins of human cancers and identifying potentially unique toxic mechanisms underpinning their utility. Herein, we report the developmental di-manganese(II) therapeutic [Mn2(μ-oda)(phen)4(H2O)2][Mn2(μ-oda)(phen)4(oda)2]·4H2O (Mn-Oda) induces autophagy-promoted apoptosis in human ovarian cancer cells (SKOV3). The complex was initially identified to intercalate DNA by topoisomerase I unwinding and circular dichroism spectroscopy. Intracellular DNA damage, detected by γH2AX and the COMET assay, however, is not linked to direct Mn-Oda free radical generation, but is instead mediated through the promotion of intracellular reactive oxygen species (ROS) leading to autophagic vacuole formation and downstream nuclear degradation. To elucidate the cytotoxic profile of Mn-Oda, a wide range of biomarkers specific to apoptosis and autophagy including caspase release, mitochondrial membrane integrity, fluorogenic probe localisation, and cell cycle analysis were employed. Through these techniques, the activity of Mn-Oda was compared directly to i.) the pro-apoptotic clinical anticancer drug doxorubicin, ii.) the multimodal histone deacetylase inhibitor suberoyanilide hydroxamic acid, and iii.) the autophagy inducer rapamycin. In conjunction with ROS-specific trapping agents and established inhibitors of autophagy, we have identified autophagy-induction linked to mitochondrial superoxide production, with confocal image analysis of SKOV3 cells further supporting autophagosome formation.
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Affiliation(s)
- Creina Slator
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
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15
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Peng CK, Zeng T, Xu XJ, Chang YQ, Hou W, Lu K, Lin H, Sun PH, Lin J, Chen WM. Novel 4-(4-substituted amidobenzyl)furan-2(5H)-one derivatives as topoisomerase I inhibitors. Eur J Med Chem 2017; 127:187-199. [DOI: 10.1016/j.ejmech.2016.12.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/13/2016] [Accepted: 12/17/2016] [Indexed: 11/29/2022]
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16
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Novel securinine derivatives as topoisomerase I based antitumor agents. Eur J Med Chem 2016; 122:149-163. [DOI: 10.1016/j.ejmech.2016.06.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 06/06/2016] [Accepted: 06/13/2016] [Indexed: 11/19/2022]
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17
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Krueger E, Shim J, Fathizadeh A, Chang AN, Subei B, Yocham KM, Davis PH, Graugnard E, Khalili-Araghi F, Bashir R, Estrada D, Fologea D. Modeling and Analysis of Intercalant Effects on Circular DNA Conformation. ACS NANO 2016; 10:8910-7. [PMID: 27559753 PMCID: PMC5111899 DOI: 10.1021/acsnano.6b04876] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The large-scale conformation of DNA molecules plays a critical role in many basic elements of cellular functionality and viability. By targeting the structural properties of DNA, many cancer drugs, such as anthracyclines, effectively inhibit tumor growth but can also produce dangerous side effects. To enhance the development of innovative medications, rapid screening of structural changes to DNA can provide important insight into their mechanism of interaction. In this study, we report changes to circular DNA conformation from intercalation with ethidium bromide using all-atom molecular dynamics simulations and characterized experimentally by translocation through a silicon nitride solid-state nanopore. Our measurements reveal three distinct current blockade levels and a 6-fold increase in translocation times for ethidium bromide-treated circular DNA as compared to untreated circular DNA. We attribute these increases to changes in the supercoiled configuration hypothesized to be branched or looped structures formed in the circular DNA molecule. Further evidence of the conformational changes is demonstrated by qualitative atomic force microscopy analysis. These results expand the current methodology for predicting and characterizing DNA tertiary structure and advance nanopore technology as a platform for deciphering structural changes of other important biomolecules.
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Affiliation(s)
- Eric Krueger
- Department of Physics, Boise State University, Boise, ID, United States
- Department of Materials Science and Engineering, Boise State University, Boise, ID, United States
| | - Jiwook Shim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Arman Fathizadeh
- Department of Physics, University of Illinois at Chicago, Chicago, IL, United States
| | - A. Nicole Chang
- Department of Materials Science and Engineering, Boise State University, Boise, ID, United States
| | - Basheer Subei
- Department of Physics, University of Illinois at Chicago, Chicago, IL, United States
| | - Katie M. Yocham
- Department of Materials Science and Engineering, Boise State University, Boise, ID, United States
| | - Paul H. Davis
- Department of Materials Science and Engineering, Boise State University, Boise, ID, United States
| | - Elton Graugnard
- Department of Materials Science and Engineering, Boise State University, Boise, ID, United States
| | | | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - David Estrada
- Department of Materials Science and Engineering, Boise State University, Boise, ID, United States
| | - Daniel Fologea
- Department of Physics, Boise State University, Boise, ID, United States
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18
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Lee S, Oh Y, Lee J, Choe S, Lim S, Lee HS, Jo K, Schwartz DC. DNA binding fluorescent proteins for the direct visualization of large DNA molecules. Nucleic Acids Res 2016; 44:e6. [PMID: 26264666 PMCID: PMC4705684 DOI: 10.1093/nar/gkv834] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/03/2015] [Accepted: 08/06/2015] [Indexed: 12/14/2022] Open
Abstract
Fluorescent proteins that also bind DNA molecules are useful reagents for a broad range of biological applications because they can be optically localized and tracked within cells, or provide versatile labels for in vitro experiments. We report a novel design for a fluorescent, DNA-binding protein (FP-DBP) that completely 'paints' entire DNA molecules, whereby sequence-independent DNA binding is accomplished by linking a fluorescent protein to two small peptides (KWKWKKA) using lysine for binding to the DNA phosphates, and tryptophan for intercalating between DNA bases. Importantly, this ubiquitous binding motif enables fluorescent proteins (Kd = 14.7 μM) to confluently stain DNA molecules and such binding is reversible via pH shifts. These proteins offer useful robust advantages for single DNA molecule studies: lack of fluorophore mediated photocleavage and staining that does not perturb polymer contour lengths. Accordingly, we demonstrate confluent staining of naked DNA molecules presented within microfluidic devices, or localized within live bacterial cells.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Yeeun Oh
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Jungyoon Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Sojeong Choe
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Korea
| | - Hyun Soo Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53705, USA
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19
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Smith RJ, Beck RW, Prevette LE. Impact of molecular weight and degree of conjugation on the thermodynamics of DNA complexation and stability of polyethylenimine-graft-poly(ethylene glycol) copolymers. Biophys Chem 2015; 203-204:12-21. [DOI: 10.1016/j.bpc.2015.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 12/13/2022]
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20
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Banerjee A, Majumder P, Sanyal S, Singh J, Jana K, Das C, Dasgupta D. The DNA intercalators ethidium bromide and propidium iodide also bind to core histones. FEBS Open Bio 2014; 4:251-9. [PMID: 24649406 PMCID: PMC3958746 DOI: 10.1016/j.fob.2014.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 02/11/2014] [Accepted: 02/11/2014] [Indexed: 01/17/2023] Open
Abstract
Eukaryotic DNA is compacted in the form of chromatin, in a complex with histones and other non-histone proteins. The intimate association of DNA and histones in chromatin raises the possibility that DNA-interactive small molecules may bind to chromatin-associated proteins such as histones. Employing biophysical and biochemical techniques we have characterized the interaction of a classical intercalator, ethidium bromide (EB) and its structural analogue propidium iodide (PI) with hierarchical genomic components: long chromatin, chromatosome, core octamer and chromosomal DNA. Our studies show that EB and PI affect both chromatin structure and function, inducing chromatin compaction and disruption of the integrity of the chromatosome. Calorimetric studies and fluorescence measurements of the ligands demonstrated and characterized the association of these ligands with core histones and the intact octamer in absence of DNA. The ligands affect acetylation of histone H3 at lysine 9 and acetylation of histone H4 at lysine 5 and lysine 8 ex vivo. PI alters the post-translational modifications to a greater extent than EB. This is the first report showing the dual binding (chromosomal DNA and core histones) property of a classical intercalator, EB, and its longer analogue, PI, in the context of chromatin.
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Affiliation(s)
- Amrita Banerjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Parijat Majumder
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Sulagna Sanyal
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Jasdeep Singh
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Kuladip Jana
- Division of Molecular Medicine, Centre for Translational Animal Research, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, West Bengal, India
| | - Chandrima Das
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Dipak Dasgupta
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
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21
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Greschner AA, Bujold KE, Sleiman HF. Intercalators as Molecular Chaperones in DNA Self-Assembly. J Am Chem Soc 2013; 135:11283-8. [PMID: 23829631 DOI: 10.1021/ja404402b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea A. Greschner
- Department of Chemistry
and Center for Self-Assembled
Chemical Structures (CSACS), McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Katherine E. Bujold
- Department of Chemistry
and Center for Self-Assembled
Chemical Structures (CSACS), McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
| | - Hanadi F. Sleiman
- Department of Chemistry
and Center for Self-Assembled
Chemical Structures (CSACS), McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada
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22
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Xu X, Zhi X, Leng F. Determining DNA supercoiling enthalpy by isothermal titration calorimetry. Biochimie 2012; 94:2665-72. [PMID: 22940593 DOI: 10.1016/j.biochi.2012.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/03/2012] [Indexed: 11/16/2022]
Abstract
DNA supercoiling plays a critical role in certain essential DNA transactions, such as DNA replication, recombination, and transcription. For this reason, exploring energetics of DNA supercoiling is fundamentally important for understanding its biological functions. In this paper, using a unique property of DNA intercalators, such as ethidium bromide and daunorubicin, which bind to supercoiled, nicked, and relaxed DNA templates with different DNA-binding enthalpies, we determined DNA supercoiling enthalpy of plasmid pXXZ6, a 4.5 kb plasmid to be about 11.5 kcal/mol per linking number change. This determination allowed us to partition the DNA supercoiling free energy into enthalpic and entropic contributions where the unfavorable DNA supercoiling free energy exclusively originated from the large positive supercoiling enthalpy and was compensated by a large, favorable entropy term (TΔS).
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Affiliation(s)
- Xiaozhou Xu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA
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23
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Instability of Escherichia coli R-factors in Salmonella enterica serovar Typhi involves formation of recombinant composite plasmid structures. Plasmid 2012; 68:125-32. [PMID: 22579995 DOI: 10.1016/j.plasmid.2012.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 04/10/2012] [Accepted: 04/30/2012] [Indexed: 11/23/2022]
Abstract
In spite of a well-documented ability of Samonella enterica Typhi strains to receive R factors from Escherichia coli and other enterobacteria, epidemiological data show that Typhi is a rather poor host of antibiotic-resistance genes and in fact, of plasmids, suggesting that most of the plasmids naturally acquired by Typhi strains become unstable and eventually segregate. We have previously reported evidence that each of three plasmids conjugatively transferred to S. enterica Typhi experienced deletion-mediated loss of a resistance determinant before plasmid segregation occurred. We now report that in Typhi strains containing these unstable plasmids a superhelical DNA species of lower mobility is detected, probably representing plasmid dimer structures. Plasmid deletion is a RecA-dependent process since it is not detected in derivatives of a recA1 S. enterica Typhi strain containing the corresponding plasmids, and in such strains we were unable to detect either the low-mobility species. We propose that the deletable segments contain key information for plasmid stability in S. enterica Typhi, possibly a multimer resolution system.
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24
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The importance of being supercoiled: how DNA mechanics regulate dynamic processes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:632-8. [PMID: 22233557 DOI: 10.1016/j.bbagrm.2011.12.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 12/13/2011] [Accepted: 12/14/2011] [Indexed: 12/22/2022]
Abstract
Through dynamic changes in structure resulting from DNA-protein interactions and constraints given by the structural features of the double helix, chromatin accommodates and regulates different DNA-dependent processes. All DNA transactions (such as transcription, DNA replication and chromosomal segregation) are necessarily linked to strong changes in the topological state of the double helix known as torsional stress or supercoiling. As virtually all DNA transactions are in turn affected by the torsional state of DNA, these changes have the potential to serve as regulatory signals detected by protein partners. This two-way relationship indicates that DNA dynamics may contribute to the regulation of many events occurring during cell life. In this review we will focus on the role of DNA supercoiling in the cellular processes, with particular emphasis on transcription. Besides giving an overview on the multiplicity of factors involved in the generation and dissipation of DNA torsional stress, we will discuss recent studies which give new insight into the way cells use DNA dynamics to perform functions otherwise not achievable. This article is part of a Special Issue entitled: Chromatin in time and space.
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25
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Yata PK, Shilpa M, Nagababu P, Reddy MR, Kotha LR, Gabra NM, Satyanarayana S. Study of DNA Light Switch Ru(II) Complexes : Synthesis, Characterization, Photocleavage and Antimicrobial Activity. J Fluoresc 2011; 22:835-47. [DOI: 10.1007/s10895-011-1018-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 11/21/2011] [Indexed: 11/29/2022]
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26
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The torsional state of DNA within the chromosome. Chromosoma 2011; 120:323-34. [PMID: 21567156 DOI: 10.1007/s00412-011-0324-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 05/02/2011] [Accepted: 05/03/2011] [Indexed: 12/14/2022]
Abstract
Virtually all processes of the genome biology affect or are affected by the torsional state of DNA. Torsional energy associated with an altered twist facilitates or hinders the melting of the double helix, its molecular interactions, and its spatial folding in the form of supercoils. Yet, understanding how the torsional state of DNA is modulated remains a challenging task due to the multiplicity of cellular factors involved in the generation, transmission, and dissipation of DNA twisting forces. Here, an overview of the implication of DNA topoisomerases, DNA revolving motors, and other DNA interactions that determine local levels of torsional stress in bacterial and eukaryotic chromosomes is provided. Particular emphasis is made on the experimental approaches being developed to assess the torsional state of intracellular DNA and its organization into topological domains.
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27
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Medalion S, Kessler DA, Rabin Y. Effect of spontaneous twist on DNA minicircles. Biophys J 2010; 99:2987-94. [PMID: 21044596 PMCID: PMC2966040 DOI: 10.1016/j.bpj.2010.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/01/2010] [Accepted: 08/05/2010] [Indexed: 10/18/2022] Open
Abstract
Monte Carlo simulations are used to study the effect of spontaneous (intrinsic) twist on the conformation of topologically equilibrated minicircles of dsDNA. The twist, writhe, and radius of gyration distributions and their moments are calculated for different spontaneous twist angles and DNA lengths. The average writhe and twist deviate in an oscillatory fashion (with the period of the double helix) from their spontaneous values, as one spans the range between two neighboring integer values of intrinsic twist. Such deviations vanish in the limit of long DNA plasmids.
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Affiliation(s)
- Shlomi Medalion
- Department of Physics, Bar-Ilan University, Ramat-Gan, Israel.
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28
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Nagababu P, Shilpa M, Latha JNL, Bhatnagar I, Srinivas PNBS, Kumar YP, Reddy KL, Satyanarayana S. Synthesis, characterization, DNA binding properties, fluorescence studies and toxic activity of cobalt(III) and ruthenium(II) polypyridyl complexes. J Fluoresc 2010; 21:563-72. [PMID: 20931268 DOI: 10.1007/s10895-010-0743-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 09/29/2010] [Indexed: 11/29/2022]
Abstract
The new ligand 4-(isopropylbenzaldehyde)imidazo[4,5-f ][1,10]phenanthroline (ippip) and its complexes [Ru(phen)(2)(ippip)](2+)(1),[Co(phen)(2)(ippip)](3+)(2),[Ru(bpy)(2)(ippip)](2+)(3),[Co(bpy)(2)(ippip)](3+)(4)(bpy=2,2-bipyridine) and (phen=1,10-phenanthroline) were synthesized and characterized by ES(+)-MS, (1)H and (13)C NMR. The DNA binding properties of the four complexes were investigated by different spectrophotometric methods and viscosity measurements. The results suggest that complexes bind to calf thymus DNA (CT-DNA) through intercalation. When irradiated at 365 nm, the complexes promote the photocleavage of pBR322 DNA, and complex 1 cleaves DNA more effectively than 2, 3, 4 complexes under comparable experimental conditions. Furthermore, photocleavage studies reveal that singlet oxygen ((1)O(2)) plays a significant role in the photocleavage.
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Affiliation(s)
- Penumaka Nagababu
- Department of Chemistry, Osmania University, Hyderabad, Andhra Pradesh, India PIN-500 007
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29
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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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30
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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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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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32
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Vetcher AA, McEwen AE, Abujarour R, Hanke A, Levene SD. Gel mobilities of linking-number topoisomers and their dependence on DNA helical repeat and elasticity. Biophys Chem 2010; 148:104-11. [PMID: 20346570 PMCID: PMC2867096 DOI: 10.1016/j.bpc.2010.02.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 02/25/2010] [Accepted: 02/26/2010] [Indexed: 11/15/2022]
Abstract
Agarose-gel electrophoresis has been used for more than thirty years to characterize the linking-number (Lk) distribution of closed-circular DNA molecules. Although the physical basis of this technique remains poorly understood, the gel-electrophoretic behavior of covalently closed DNAs has been used to determine the local unwinding of DNA by proteins and small-molecule ligands, characterize supercoiling-dependent conformational transitions in duplex DNA, and to measure helical-repeat changes due to shifts in temperature and ionic strength. Those results have been analyzed by assuming that the absolute mobility of a particular topoisomer is mainly a function of the integral number of superhelical turns, and thus a slowly varying function of plasmid molecular weight. In examining the mobilities of Lk topoisomers for a series of plasmids that differ incrementally in size over more than one helical turn, we found that the size-dependent agarose-gel mobility of individual topoisomers with identical values of Lk (but different values of the excess linking number, DeltaLk) vary dramatically over a duplex turn. Our results suggest that a simple semi-empirical relationship holds between the electrophoretic mobility of linking-number topoisomers and their average writhe in solution.
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Affiliation(s)
- Alexandre A. Vetcher
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 USA
| | - Abbye E. McEwen
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 USA
| | - Ramzey Abujarour
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 USA
| | - Andreas Hanke
- Department of Physics and Astronomy, University of Texas at Brownsville, Brownsville, TX 78520 USA
| | - Stephen D. Levene
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083 USA
- Department of Physics, University of Texas at Dallas, Richardson, TX 75083 USA
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Abstract
I was born in China and would have remained there but for the tumultuous events that led many of my generation to the United States for graduate studies. Norman Davidson introduced me to DNA when I became a postdoctoral fellow in his group at the California Institute of Technology in 1964, and a fortuitous conversation there ignited my interest in DNA ring formation, which later led me to study different topological forms of DNA rings-catenanes, knots, and supercoils. In 1968, a chance observation led me to identify a new enzyme capable of converting one DNA ring form to another, an enzyme now known as a DNA topoisomerase. My interest in DNA rings and DNA topoisomerases continued throughout my years at the University of California, Berkeley, and Harvard. The fascinating ability of the topoisomerases in passing DNA strands or double helices through one another and their importance in cellular processes have kept me and many others excited in their studies.
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Affiliation(s)
- James C Wang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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Krasinska L, Fisher D. Replication initiation complex formation in the absence of nuclear function in Xenopus. Nucleic Acids Res 2009; 37:2238-48. [PMID: 19237397 PMCID: PMC2673427 DOI: 10.1093/nar/gkp081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In this article, we study how intercalation-induced changes in chromatin and DNA topology affect chromosomal DNA replication using Xenopus egg extracts. Unexpectedly, intercalation by ethidium or doxorubicin prevents formation of a functional nucleus: although nucleosome formation occurs, DNA decondensation is arrested, membranous vesicles accumulate around DNA but do not fuse to form a nuclear membrane, active transport is abolished and lamins are found on chromatin, but do not assemble into a lamina. DNA replication is inhibited at the stage of initiation complex activation, as shown by molecular combing of DNA and by the absence of checkpoint activation. Replication of single-stranded DNA is not prevented. Surprisingly, in spite of the absence of nuclear function, DNA-replication proteins of pre-replication and initiation complexes are loaded onto chromatin. This is a general phenomenon as initiation complexes could also be seen without ethidium in membrane-depleted extracts which do not form nuclei. These results suggest that DNA or chromatin topology is required for generation of a functional nucleus, and activation, but not formation, of initiation complexes.
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Affiliation(s)
- Liliana Krasinska
- CNRS, UMR 5535-Institut de Génétique Moléculaire de Montpellier (IGMM), 34293 Montpellier cedex 5, France
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35
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Sone H, Fugetsu B, Tanaka S. Development of DNA/Polyurethane Composite Foam for Adsorption of Chemical Hazards. BUNSEKI KAGAKU 2009. [DOI: 10.2116/bunsekikagaku.58.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Hiroaki Sone
- Graduate School of Environmental Science, Hokkaido University
| | - Bunshi Fugetsu
- Graduate School of Environmental Science, Hokkaido University
| | - Shunitz Tanaka
- Graduate School of Environmental Science, Hokkaido University
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36
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Abstract
The electrophoretic velocity of a duplex DNA ring is mainly determined by its overall shape. Consequently, DNA topoisomers of opposite supercoiling handedness can have identical gel velocity, and topoisomers highly supercoiled cannot be separated beyond some point. These problems are overcome by two-dimensional agarose gel electrophoresis, which involves two successive electrophoresis steps in one gel slab. The first and second electrophoresis steps are conducted in orthogonal directions with different concentrations of DNA intercalating agents. These compounds alter the overall shape of the DNA and, thereby, change the relative mobility of individual DNA topoisomers.
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37
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Mukherjee A, Sokunbi AO, Grove A. DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima. Nucleic Acids Res 2008; 36:3956-68. [PMID: 18515342 PMCID: PMC2475624 DOI: 10.1093/nar/gkn348] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In mesophilic prokaryotes, the DNA-binding protein HU participates in nucleoid organization as well as in regulation of DNA-dependent processes. Little is known about nucleoid organization in thermophilic eubacteria. We show here that HU from the hyperthermophilic eubacterium Thermotoga maritima HU bends DNA and constrains negative DNA supercoils in the presence of topoisomerase I. However, while binding to a single site occludes approximately 35 bp, association of T. maritima HU with DNA of sufficient length to accommodate multiple protomers results in an apparent shorter occluded site size. Such complexes consist of ordered arrays of protomers, as revealed by the periodicity of DNase I cleavage. Association of TmHU with plasmid DNA yields a complex that is remarkably resistant to DNase I-mediated degradation. TmHU is the only member of this protein family capable of occluding a 35 bp nonspecific site in duplex DNA; we propose that this property allows TmHU to form exceedingly stable associations in which DNA flanking the kinks is sandwiched between adjacent proteins. We suggest that T. maritima HU serves an architectural function when associating with a single 35 bp site, but generates a very stable and compact aggregate at higher protein concentrations that organizes and protects the genomic DNA.
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Affiliation(s)
- Anirban Mukherjee
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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38
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Jaldappagari S, Motohashi N, Gangeenahalli MP, Naismith JH. Bioactive Mechanism of Interaction Between Anthocyanins and Macromolecules Like DNA and Proteins. TOPICS IN HETEROCYCLIC CHEMISTRY 2008. [DOI: 10.1007/7081_2008_124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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39
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Bera R, Sahoo BK, Ghosh KS, Dasgupta S. Studies on the interaction of isoxazolcurcumin with calf thymus DNA. Int J Biol Macromol 2008; 42:14-21. [DOI: 10.1016/j.ijbiomac.2007.08.010] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Revised: 08/15/2007] [Accepted: 08/29/2007] [Indexed: 10/22/2022]
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40
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Strekowski L, Wilson B. Noncovalent interactions with DNA: an overview. Mutat Res 2007; 623:3-13. [PMID: 17445837 DOI: 10.1016/j.mrfmmm.2007.03.008] [Citation(s) in RCA: 303] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 03/14/2007] [Accepted: 03/15/2007] [Indexed: 05/15/2023]
Abstract
Over the last four decades, intense research has focused on the effects of small organic compounds that noncovalently bind to nucleic acids. These interactions have been shown to disrupt replication and/or transcription culminating in cellular death. Accordingly, DNA binding compounds have potential applications as anti-cancer and anti-viral agents. This report provides an overview of the different DNA-binding modes with an emphasis on DNA groove specificity for the groove-binding and intercalation modes. While most DNA-interacting agents selectively bind to DNA by either groove binding or intercalation, some compounds can exhibit both binding modes. The binding mode with the most favorable free energy for complex formation depends on the DNA sequence and structural features of the bound ligand.
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Affiliation(s)
- Lucjan Strekowski
- Department of Chemistry, Georgia State University, Atlanta, GA 30302-4098, United States.
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41
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Hayashi M, Harada Y. Direct observation of the reversible unwinding of a single DNA molecule caused by the intercalation of ethidium bromide. Nucleic Acids Res 2007; 35:e125. [PMID: 17905818 PMCID: PMC2095801 DOI: 10.1093/nar/gkm529] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Ethidium bromide (EtBr) is the conventional intercalator for visualizing DNA. Previous studies suggested that EtBr lengthens and unwinds double-stranded DNA (dsDNA). However, no one has observed the unwinding of a single dsDNA molecule during intercalation. We developed a simple method to observe the twisting motions of a single dsDNA molecule under an optical microscope. A short dsDNA was attached to a glass surface of a flow chamber at one end and to a doublet bead as a rotation marker at the other end. After the addition and removal of EtBr, the bead revolved in opposite directions that corresponded to the unwinding and rewinding of a dsDNA, respectively. The amount of intercalating EtBr was estimated from the revolutions of the bead. EtBr occupied 57% of base pairs on a single dsDNA at 1 mM of EtBr, indicating that EtBr molecules could bind at contiguous sites to each other. The isotherm of intercalation showed that negative cooperativity existed between adjoining EtBr molecules. The association constant of EtBr and dsDNA (1.9 (±0.1) × 105 M−1) was consistent with that of previous results. Our system is useful to investigate the twisting of a single dsDNA interacting with various chemicals and biomolecules.
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Affiliation(s)
- Masahito Hayashi
- The Tokyo Metropolitan Institute of Medical Science, Bunkyo-ku, Tokyo, Japan.
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42
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Bugs MR, Cornélio ML. Analysis of the Ethidium Bromide Bound to DNA by Photoacoustic and FTIR Spectroscopy¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2001)0740512aotebb2.0.co2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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43
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Wamberg MC, Hassan AA, Bond AD, Pedersen EB. Intercalating nucleic acids (INAs) containing insertions of 6H-indolo[2,3-b]quinoxaline. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.09.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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44
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Dawid A, Guillemot F, Brème C, Croquette V, Heslot F. Mechanically controlled DNA extrusion from a palindromic sequence by single molecule micromanipulation. PHYSICAL REVIEW LETTERS 2006; 96:188102. [PMID: 16712400 DOI: 10.1103/physrevlett.96.188102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Indexed: 05/09/2023]
Abstract
A magnetic tweezers setup is used to control both the stretching force and the relative linking number DeltaLk of a palindromic DNA molecule. We show here, in absence of divalent ions, that twisting negatively the molecule while stretching it at approximately 1 pN induces the formation of a cruciform DNA structure. Furthermore, once the cruciform DNA structure is formed, the extrusion of several kilo-base pairs of palindromic DNA sequence is directly and reversibly controlled by varying DeltaLk. Indeed the branch point behaves as a nanomechanical gear that links rotation with translation, a feature related to the helicity of DNA. We obtain experimentally a very good linear relationship between the extension of the molecule and DeltaLk. We use then this experiment to obtain a precise measurement of the pitch of B-DNA in solution: 3.61 +/- 0.03 nm/turn.
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Affiliation(s)
- Alexandre Dawid
- Laboratoire Pierre Aigrain, Unité Mixte de Recherche 8551, Ecole Normale Supérieure, 24 Rue Lhomond, 75005 Paris, France
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45
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Fogg JM, Kolmakova N, Rees I, Magonov S, Hansma H, Perona JJ, Zechiedrich EL. Exploring writhe in supercoiled minicircle DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2006; 18:S145-S159. [PMID: 19337583 PMCID: PMC2662687 DOI: 10.1088/0953-8984/18/14/s01] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Using λ-Int recombination in E. coli, we have generated milligram quantities of supercoiled minicircle DNA. Intramolecular Int recombination was efficient down to lengths ~254 bp. When nicked and religated in the presence of ethidium bromide, 339 bp minicircles adopted at least seven unique topoisomers that presumably correspond to ΔLk ranging from 0 to -6, which we purified individually. We used these minicircles, with unique ΔLk, to address the partition into twist and writhe as a function of ΔLk. Gel electrophoresis and atomic force microscopy revealed progressively higher writhe conformations in the presence of 10 mM CaCl(2) or MgCl(2). From simplistic calculations of the bending and twisting energies, we predict the elastic free energy of supercoiling for these minicircles to be lower than if the supercoiling was partitioned mainly into twist. The predicted writhe corresponds closely with that which we observed experimentally in the presence of divalent metal ions. However, in the absence of divalent metal ions only limited writhe was observed, demonstrating the importance of electrostatic effects on DNA structure, when the screening of charges on the DNA is weak. This study represents a unique insight into the supercoiling of minicircle DNA, with implications for DNA structure in general.
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Affiliation(s)
- Jonathan M Fogg
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
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46
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Ghosh T, Maiya BG, Samanta A, Shukla AD, Jose DA, Kumar DK, Das A. Mixed-ligand complexes of ruthenium(II) containing new photoactive or electroactive ligands: synthesis, spectral characterization and DNA interactions. J Biol Inorg Chem 2005; 10:496-508. [PMID: 15981005 DOI: 10.1007/s00775-005-0660-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2005] [Accepted: 05/11/2005] [Indexed: 11/25/2022]
Abstract
Mixed-ligand ruthenium(II) complexes of three photoactive ligands, viz., (E)-1-[2-(4-methyl-2-pyridyl)-4-pyridyl]-2-(1-naphthyl)-1-ethene (mppne), (E)-1-(9-anthryl)-2-[2-(4-methyl-2-pyridyl)-4-pyridyl]-1-ethene (mppae) and (E)-1-[2-(4-methyl-2-pyridyl)-4-pyridyl]-2-(1-pyrenyl)-1-ethene (mpppe), in which a 2,2'-bipyridyl unit is linked via an ethylinic linkage to either a naphthalene, an anthracene or a pyrene chromophore and three electroactive ligands, viz., 4-(4-pyridyl)-1,2-benzenediol (catpy), 5,6-dihydroxy-1,10-phenanthroline (catphen) and 1,2-benzenediol (cat), were synthesized in good to moderate yields. Complexes [Ru(bpy)(2)(mppne)](2+) (bpy is 2, 2'-bipyridyl), [Ru(bpy)(2)(mppae)](2+), [Ru(bpy)(2)(mpppe)](2+), [Ru(bpy)(2)(sq-py)](+), [Ru(bpy)(2)(sq-phen)](+) and [Ru(phen)(2)(bsq)](+) (phen is 1,10-phenanthroline) were fully characterized by elemental analysis, IR, (1)H NMR, fast-atom bombardment or electron-impact mass, UV-vis and cyclic voltammetric methods. In the latter three complexes, the ligands catpy, catphen and cat are actually bound to the metal center as the corresponding semiquinone species, viz., 4-(4-pyridyl)-1,2-benzenedioleto(+I) (sq-py), 1,10-phenanthroline-5,6-dioleto(+I) (sq-phen) and 1,2-benzenedioleto(+I) (bsq), thus making the overall charge of the complexes formally equal to + 1 in each case. These three complexes are electron paramagnetic resonance active and exhibit an intense absorption band between 941 and 958 nm owing to metal-to-ligand charge transfer (MLCT, d (Ru)-->pi*(sq)) transitions. The other three ruthenium(II) complexes containing three photoactive ligands, mppne, mppae and mpppe, exhibit MLCT (d (Ru)-->pi*(bpy) ) bands in the 454-461-nm region and are diamagnetic. These can be characterized by the (1)H NMR method. [Ru(bpy)(2)(mppne)](2+), [Ru(bpy)(2)(mppae)](2+) and [Ru(bpy)(2)(mpppe)](2+) exhibit redox waves corresponding to the Ru(III)/Ru(II) couple along with the expected ligand (bpy and substituted bpy) based ones in their cyclic and differential pulse voltammograms (CH(3)CN, 0.1 M tetrabutylammonium hexafluorophosphate)-corresponding voltammograms of [Ru(bpy)(2)(sq-py)](+), [Ru(bpy)(2)(sq-phen)](+) and [Ru(phen)(2)(bsq)](+) are mainly characterized by waves corresponding to the quinone/semiquinone (q/sq) and semiquinone/1,2-diol (sq/cat) redox processes. The results of absorption and fluorescence titration as well as thermal denaturation studies reveal that [Ru(bpy)(2)(mppne)](2+) and [Ru(bpy)(2)(mppae)](2+) are moderate-to-strong binders of calf thymus DNA with binding constants ranging from 10(5) to 10(6) M(-1). Under the identical conditions of drug and light dose, the DNA (supercoiled pBR 322) photocleavage activities of these two complexes follow the order:[Ru(bpy)(2)(mppne)](2+)>[Ru(bpy)(2)(mppae)](2+), although the emission quantum yields follow the reverse order. The other ruthenium(II) complexes containing the semiquinone-based ligands are found to be nonluminescent and inefficient photocleavage agents of DNA. However, experiments shows that [Ru(bpy)(2)(sq)](+)-based complexes oxidize the sugar unit and could be used as mild oxidants for the sugar moiety of DNA. Possible explanations for these observations are presented.
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Affiliation(s)
- Tamal Ghosh
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
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47
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Pastré D, Piétrement O, Zozime A, Le Cam E. Study of the DNA/ethidium bromide interactions on mica surface by atomic force microscope: influence of the surface friction. Biopolymers 2005; 77:53-62. [PMID: 15578645 DOI: 10.1002/bip.20185] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The influence of mica surface on DNA/ethidium bromide interactions is investigated by atomic force microscopy (AFM). We describe the diffusion mechanism of a DNA molecule on a mica surface by using a simple analytical model. It appears that the DNA diffusion on a mica surface is limited by the surface friction due to the counterion correlations between the divalent counterions condensed on both mica and DNA surfaces. We also study the structural changes of linear DNA adsorbed on mica upon ethidium bromide binding by AFM. It turns out that linear DNA molecules adsorbed on a mica surface are unable to relieve the topological constraint upon ethidium bromide binding. In particular, strongly adsorbed molecules tend to be highly entangled, while loosely bound DNA molecules appear more extended with very few crossovers. Adsorbed DNA molecules cannot move freely on the surface because of the surface friction. Therefore, the topological constraint increases due to the ethidium bromide binding. Moreover, we show that ethidium bromide has a lower affinity for strongly bound molecules due to the topological constraint induced by the surface friction.
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Affiliation(s)
- David Pastré
- Laboratoire d'étude des Milieux Nanométriques, Université d'Evry-Val-d'essonne Rue du Père Jarlan, 91025 Evry Cedex, France.
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48
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Braña MF, Casarrubios L, Domínguez G, Fernández C, Pérez JM, Quiroga AG, Navarro-Ranninger C, de Pascual-Teresa B. Synthesis, cytotoxic activities and proposed mode of binding of a series of bis([(9-oxo-9,10-dihydroacridine-4-carbonyl)amino]alkyl) alkylamines. Eur J Med Chem 2002; 37:301-13. [PMID: 11960665 DOI: 10.1016/s0223-5234(02)01348-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A series of bis([(9-oxo-9,10-dihydroacridine-4-carbonyl)amino]alkyl) alkylamines have been prepared and their antiproliferative properties have been tested against HT-29 cell lines. Compounds 6b and 6d showed an interesting cytotoxic profile and were subjected to further cytotoxic evaluation, DNA binding properties and molecular modelling studies. The evaluation of the cytotoxic activity of compounds 6b and 6d against pairs of cisplatin-sensitive and -resistant ovarian tumour cells shows that both compounds may be endowed with interesting antitumour properties because they are able to circumvent cisplatin resistance in A2780cisR, CH1cisR and Pam 212-ras tumour cells. On the other hand, DNA binding data indicate that compounds 6b and 6d are able to intercalate stronger than acridine within the double helix. Both compounds displace ethidium bromide with an efficiency ten times higher than acridine from several linear double-stranded DNAs and induce 43 degrees unwinding in supercoiled pBR322 DNA while acridine unwinds pBR322 DNA by only 24 degrees. Altogether these data indicate that the significant conformational changes induced by compounds 6b and 6d in the double helix are due to a bis-intercalative DNA binding mode. We propose that binding to DNA through bisintercalation might be at least in part responsible for the remarkable cytotoxic properties of these acridine derivatives. The complex of 6b with d(GCGCGC)(2) in the four possible orientations that the ligand can adopt when binding to the DNA hexamer have been modelled and subjected to molecular dynamics simulations with the aim of evaluating the binding preferences of this bisintercalating agent into the DNA molecule. The predictions suggest that 6b binds to d(GCGCGC)(2) with a parallel orientation of the chromophores relative to each other and with a preference for binding through the minor groove of the hexamer. The possible relevance of these findings to the process of bisintercalation and the antitumour profile of these compounds is discussed in this paper.
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Affiliation(s)
- Miguel F Braña
- Departamento de Química Orgánica y Farmacéutica, Facultad de Ciencias Experimentales y de la Salud, Universidad San Pablo CEU, Boadilla del Monte, E-28668 Madrid, Spain.
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49
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Chacón-García L, Martínez R. Synthesis and in vitro cytotoxic activity of pyrrolo[2,3-e]indole derivatives and a dihydro benzoindole analogue. Eur J Med Chem 2002; 37:261-6. [PMID: 11900870 DOI: 10.1016/s0223-5234(01)01328-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of pyrrolo[2,3-e]indole derivatives with the structural characteristics of DNA bis- and mono-intercalators are described. A dihydro benzoindol analogue was also synthesised to elucidate the major structural requirements for cytotoxic activity. A biological evaluation of the test compounds was carried out in six different tumoral cell lines. The factors that affect the cytotoxic activity appear to be the substituents on the phenyl group, the presence of an amide group capable of strong interactions such as hydrogen bonding and solubility.
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Affiliation(s)
- Luis Chacón-García
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacán 04510, Mexico, D.F
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50
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Lobo BA, Rogers SA, Choosakoonkriang S, Smith JG, Koe G, Middaugh CR. Differential scanning calorimetric studies of the thermal stability of plasmid DNA complexed with cationic lipids and polymers. J Pharm Sci 2002; 91:454-66. [PMID: 11835205 DOI: 10.1002/jps.10025] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The thermal stabilities of supercoiled (SC) and linear/open circular (LIN/OC) forms of plasmid DNA when complexed with cationic lipids or cationic polymers used for cellular transfection were assessed using differential scanning calorimetry. Differences in the stability of SC DNA produced by the cationic lipids DOTAP (1,2-dioleoyltrimethyl ammoniumpropane chloride), DSTAP (1,2-distearyltrimethyl ammoniumpropane chloride), and DDAB (dimethyldioctadecylammonium bromide) upon complexation suggest possible effects of headgroup structure on the stability of SC DNA and minimal effects of lipid acyl chain saturation/unsaturation. Complexation of DNA with the cationic polymers polyethylenimine (PEI) or poly-L-lysine (PLL) (but not poly-L-arginine) resulted in a decreased stability of SC DNA when the DNA was in charge excess, although all polymers stabilized SC DNA when the polymer was in charge excess. The effects of these cationic polymers on the stability of SC DNA can be explained by changes produced in the tertiary structure of SC DNA upon binding and may reflect the importance of the topological constraint of supercoiling upon the stability of the resulting complexes.
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Affiliation(s)
- Brian A Lobo
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, USA
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