1
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Luo J, Li S, Pang C, Wang M, Ma X, Zhang C. Highly selective fluorescence probe for imidacloprid measurement based on fluorescence resonance energy transfer. Microchem J 2022. [DOI: 10.1016/j.microc.2021.107172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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2
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Petrović AZ, Ćoćić DC, Bockfeld D, Živanović M, Milivojević N, Virijević K, Janković N, Scheurer A, Vraneš M, Bogojeski JV. Biological activity of bis(pyrazolylpyridine) and terpiridine Os( ii) complexes in the presence of biocompatible ionic liquids. Inorg Chem Front 2021. [DOI: 10.1039/d0qi01540g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
New bis(pyrazolylpyridine) Os(ii) complexes showing possible biological activity with diverse modes of action in the presence of biocompatible ionic liquids as non-toxic cosolvents for sparingly soluble complexes.
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Affiliation(s)
| | - Dušan C. Ćoćić
- University of Kragujevac
- Faculty of Science
- 34000 Kragujevac
- Serbia
| | - Dirk Bockfeld
- Institut für Anorganische und Analytische Chemie
- Technische Universität Braunschweig
- 38106 Braunschweig
- Germany
| | - Marko Živanović
- University of Kragujevac
- Institute for Information Technologies Kragujevac
- Department of Science
- 34000 Kragujevac
- Serbia
| | - Nevena Milivojević
- University of Kragujevac
- Institute for Information Technologies Kragujevac
- Department of Science
- 34000 Kragujevac
- Serbia
| | - Katarina Virijević
- University of Kragujevac
- Institute for Information Technologies Kragujevac
- Department of Science
- 34000 Kragujevac
- Serbia
| | - Nenad Janković
- University of Kragujevac
- Institute for Information Technologies Kragujevac
- Department of Science
- 34000 Kragujevac
- Serbia
| | - Andreas Scheurer
- Inorganic Chemistry
- Department of Chemistry and Pharmacy
- University of Erlangen-Nürnberg
- 91058 Erlangen
- Germany
| | - Milan Vraneš
- Department of Chemistry
- Biochemistry and Environmental Protection University of Novi Sad
- Faculty of Science
- 21000 Novi Sad
- Serbia
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3
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Petrović A, Živanović M, Puchta R, Ćoćić D, Scheurer A, Milivojevic N, Bogojeski J. Experimental and quantum chemical study оn the DNA/protein binding and the biological activity of a rhodium(iii) complex with 1,2,4-triazole as an inert ligand. Dalton Trans 2020; 49:9070-9085. [DOI: 10.1039/d0dt01343a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A rhodium(iii) complex with 1,2,4-triazole and a pincer type nitrogen-donor ligand was synthesized, and its interaction with biomolecules was examined.
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Affiliation(s)
| | - Marko Živanović
- University of Kragujevac
- Institute of Information Technologies Kragujevac
- 34000 Kragujevac
- Serbia
| | - Ralph Puchta
- Inorganic Chemistry
- Department of Chemistry and Pharmacy
- University of Erlangen-Nürnberg
- 91058 Erlangen
- Germany
| | - Dušan Ćoćić
- University of Kragujevac
- Faculty of Science
- 34000 Kragujevac
- Serbia
| | - Andreas Scheurer
- Inorganic Chemistry
- Department of Chemistry and Pharmacy
- University of Erlangen-Nürnberg
- 91058 Erlangen
- Germany
| | - Nevena Milivojevic
- University of Kragujevac
- Institute of Information Technologies Kragujevac
- 34000 Kragujevac
- Serbia
| | - Jovana Bogojeski
- University of Kragujevac
- Faculty of Science
- 34000 Kragujevac
- Serbia
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4
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Mariam J, Krishnamoorthy G, Anand R. Use of 6‐Methylisoxanthopterin, a Fluorescent Guanine Analog, to Probe Fob1‐Mediated Dynamics at the Stalling Fork Barrier DNA Sequences. Chem Asian J 2019; 14:4760-4766. [DOI: 10.1002/asia.201901061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/19/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Jessy Mariam
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
| | | | - Ruchi Anand
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
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5
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Mismatch Recognition by Saccharomyces cerevisiae Msh2-Msh6: Role of Structure and Dynamics. Int J Mol Sci 2019; 20:ijms20174271. [PMID: 31480444 PMCID: PMC6747400 DOI: 10.3390/ijms20174271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 12/12/2022] Open
Abstract
The mismatch repair (MMR) pathway maintains genome integrity by correcting errors such as mismatched base pairs formed during DNA replication. In MMR, Msh2–Msh6, a heterodimeric protein, targets single base mismatches and small insertion/deletion loops for repair. By incorporating the fluorescent nucleoside base analog 6-methylisoxanthopterin (6-MI) at or adjacent to a mismatch site to probe the structural and dynamic elements of the mismatch, we address how Msh2–Msh6 recognizes these mismatches for repair within the context of matched DNA. Fluorescence quantum yield and rotational correlation time measurements indicate that local base dynamics linearly correlate with Saccharomyces cerevisiae Msh2–Msh6 binding affinity where the protein exhibits a higher affinity (KD ≤ 25 nM) for mismatches that have a significant amount of dynamic motion. Energy transfer measurements measuring global DNA bending find that mismatches that are both well and poorly recognized by Msh2–Msh6 experience the same amount of protein-induced bending. Finally, base-specific dynamics coupled with protein-induced blue shifts in peak emission strongly support the crystallographic model of directional binding, in which Phe 432 of Msh6 intercalates 3′ of the mismatch. These results imply an important role for local base dynamics in the initial recognition step of MMR.
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6
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DNA-RNA interactions are critical for chromosome condensation in Escherichia coli. Proc Natl Acad Sci U S A 2017; 114:12225-12230. [PMID: 29087325 DOI: 10.1073/pnas.1711285114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial chromosome (nucleoid) conformation dictates faithful regulation of gene transcription. The conformation is condition-dependent and is guided by several nucleoid-associated proteins (NAPs) and at least one nucleoid-associated noncoding RNA, naRNA4. Here we investigated the molecular mechanism of how naRNA4 and the major NAP, HU, acting together organize the chromosome structure by establishing multiple DNA-DNA contacts (DNA condensation). We demonstrate that naRNA4 uniquely acts by forming complexes that may not involve long stretches of DNA-RNA hybrid. Also, uncommonly, HU, a chromosome-associated protein that is essential in the DNA-RNA interactions, is not present in the final complex. Thus, HU plays a catalytic (chaperone) role in the naRNA4-mediated DNA condensation process.
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7
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Tan C, Terakawa T, Takada S. Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics. J Am Chem Soc 2016; 138:8512-22. [DOI: 10.1021/jacs.6b03729] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Cheng Tan
- Department
of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Tsuyoshi Terakawa
- Department
of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
| | - Shoji Takada
- Department
of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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8
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Qi L, Huo Y, Wang H, Zhang J, Dang FQ, Zhang ZQ. Fluorescent DNA-Protected Silver Nanoclusters for Ligand-HIV RNA Interaction Assay. Anal Chem 2015; 87:11078-83. [PMID: 26447651 DOI: 10.1021/acs.analchem.5b03166] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Studying ligand-biomacromolecule interactions provides opportunities for creating new compounds that can efficiently regulate specific biological processes. Ribonucleic acid (RNA) molecules have become attractive drug targets since the discovery of their roles in modulating gene expression, while only a limited number of studies have investigated interactions between ligands and functional RNA molecules, especially those based on nanotechnology. DNA-protected silver nanoclusters (AgNCs) were used to investigate ligand-RNA interactions for the first time in this study. The anthracycline anticancer drug mitoxantrone (MTX) was found to quench the fluorescence of AgNCs. After adding human immunodeficiency virus trans-activation responsive region (TAR) RNA or Rev-response element (RRE) RNA to AgNCs-MTX mixtures, the fluorescence of the AgNCs recovered due to interactions between MTX with RNAs. The binding constants and number of binding sites of MTX to TAR and RRE RNA were determined through theoretical calculations. MTX-RNA interactions were further confirmed in fluorescence polarization and mass spectrometry experiments. The mechanism of MTX-based fluorescence quenching of the AgNCs was also explored. This study provides a new strategy for ligand-RNA binding interaction assay.
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Affiliation(s)
- Liang Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Yuan Huo
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Huan Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Jing Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Fu-Quan Dang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Zhi-Qi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
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9
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Zhen SJ, Yu Y, Li CM, Huang CZ. Graphene oxide amplified fluorescence anisotropy for label-free detection of potassium ion. Analyst 2015; 140:353-7. [DOI: 10.1039/c4an01433b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A label-free fluorescence anisotropy method for the sensitive detection of potassium ion, by using graphene oxide as enhancer, was established.
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Affiliation(s)
- Shu Jun Zhen
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- P.R. China
| | - Yan Yu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Pharmaceutical Sciences
- Southwest University
- P.R. China
| | - Chun Mei Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Pharmaceutical Sciences
- Southwest University
- P.R. China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- P.R. China
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10
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Kundukad B, Cong P, van der Maarel JRC, Doyle PS. Time-dependent bending rigidity and helical twist of DNA by rearrangement of bound HU protein. Nucleic Acids Res 2013; 41:8280-8. [PMID: 23828037 PMCID: PMC3783175 DOI: 10.1093/nar/gkt593] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
HU is a protein that plays a role in various bacterial processes including compaction, transcription and replication of the genome. Here, we use atomic force microscopy to study the effect of HU on the stiffness and supercoiling of double-stranded DNA. First, we measured the persistence length, height profile, contour length and bending angle distribution of the DNA-HU complex after different incubation times of HU with linear DNA. We found that the persistence and contour length depend on the incubation time. At high concentrations of HU, DNA molecules first become stiff with a larger value of the persistence length. The persistence length then decreases over time and the molecules regain the flexibility of bare DNA after ∼2 h. Concurrently, the contour length shows a slight increase. Second, we measured the change in topology of closed circular relaxed DNA following binding of HU. Here, we observed that HU induces supercoiling over a similar time span as the measured change in persistence length. Our observations can be rationalized in terms of the formation of a nucleoprotein filament followed by a structural rearrangement of the bound HU on DNA. The rearrangement results in a change in topology, an increase in bending flexibility and an increase in contour length through a decrease in helical pitch of the duplex.
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Affiliation(s)
- Binu Kundukad
- BioSystems and Micromechanics (BioSym) IRG, Singapore MIT Alliance for Research and Technology (SMART), Singapore 138602, Singapore-Massachusetts Institute of Technology Alliance, National University of Singapore, Singapore 117576, Department of Physics, National University of Singapore, Singapore 117542 and Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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11
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Medalion S, Rabin Y. On binding of DNA-bending proteins to DNA minicircles. J Chem Phys 2012; 136:025102. [PMID: 22260615 DOI: 10.1063/1.3674978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a theoretical study of binding of DNA-bending proteins to circular DNA, using computer simulations of the wormlike chain model of DNA. We find that the binding affinity is affected by the bending elasticity and the conformational entropy of the polymer and that while protein adsorption is identical on open and closed long DNA molecules, there is significant enhancement of binding on DNA minicircles, compared to their linear counterparts. We also find that the ratio of the radii of gyration of open and closed chains depends on protein concentration for short DNA molecules. Experimental tests of our predictions are proposed.
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Affiliation(s)
- Shlomi Medalion
- Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel.
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12
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Prieto AI, Kahramanoglou C, Ali RM, Fraser GM, Seshasayee ASN, Luscombe NM. Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. Nucleic Acids Res 2012; 40:3524-37. [PMID: 22180530 PMCID: PMC3333857 DOI: 10.1093/nar/gkr1236] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 11/24/2011] [Accepted: 11/28/2011] [Indexed: 11/18/2022] Open
Abstract
IHF and HU are two heterodimeric nucleoid-associated proteins (NAP) that belong to the same protein family but interact differently with the DNA. IHF is a sequence-specific DNA-binding protein that bends the DNA by over 160°. HU is the most conserved NAP, which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. Despite their importance, the in vivo interactions of the two proteins to the DNA remain to be described at a high resolution and on a genome-wide scale. Further, the effects of these proteins on gene expression on a global scale remain contentious. Finally, the contrast between the functions of the homo- and heterodimeric forms of proteins deserves the attention of further study. Here we present a genome-scale study of HU- and IHF binding to the Escherichia coli K12 chromosome using ChIP-seq. We also perform microarray analysis of gene expression in single- and double-deletion mutants of each protein to identify their regulons. The sequence-specific binding profile of IHF encompasses ∼30% of all operons, though the expression of <10% of these is affected by its deletion suggesting combinatorial control or a molecular backup. The binding profile for HU is reflective of relatively non-specific binding to the chromosome, however, with a preference for A/T-rich DNA. The HU regulon comprises highly conserved genes including those that are essential and possibly supercoiling sensitive. Finally, by performing ChIP-seq experiments, where possible, of each subunit of IHF and HU in the absence of the other subunit, we define genome-wide maps of DNA binding of the proteins in their hetero- and homodimeric forms.
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Affiliation(s)
- Ana I. Prieto
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, MRC-National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK, Centre for Biotechnology, Anna University, Chennai 600 035, National Centre for Biological Sciences, GKVK, Bellary Road, Bangalore 560 065, India and Okinawa Institute of Science and Technology, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Christina Kahramanoglou
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, MRC-National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK, Centre for Biotechnology, Anna University, Chennai 600 035, National Centre for Biological Sciences, GKVK, Bellary Road, Bangalore 560 065, India and Okinawa Institute of Science and Technology, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Ruhi M. Ali
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, MRC-National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK, Centre for Biotechnology, Anna University, Chennai 600 035, National Centre for Biological Sciences, GKVK, Bellary Road, Bangalore 560 065, India and Okinawa Institute of Science and Technology, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Gillian M. Fraser
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, MRC-National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK, Centre for Biotechnology, Anna University, Chennai 600 035, National Centre for Biological Sciences, GKVK, Bellary Road, Bangalore 560 065, India and Okinawa Institute of Science and Technology, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Aswin S. N. Seshasayee
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, MRC-National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK, Centre for Biotechnology, Anna University, Chennai 600 035, National Centre for Biological Sciences, GKVK, Bellary Road, Bangalore 560 065, India and Okinawa Institute of Science and Technology, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Nicholas M. Luscombe
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, MRC-National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK, Centre for Biotechnology, Anna University, Chennai 600 035, National Centre for Biological Sciences, GKVK, Bellary Road, Bangalore 560 065, India and Okinawa Institute of Science and Technology, Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
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13
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SCHNURR BERNHARD, VORGIAS CONSTANTINOS, STAVANS JOEL. COMPACTION AND SUPERCOILING OF SINGLE, LONG DNA MOLECULES BY HU PROTEIN. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048006000021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The bacterial cell contains the highly conserved protein HU in abundance. To characterize its architectural role, we studied the elastic behavior of single, supercoilable DNA molecules (tens of kilobases long) in solution with HU from B. stearothermophilus (BstHU) by a micromanipulation assay. We point out quantitative yet notable differences to the behavior of HU from E. coli (EcoHU) observed by others. Our main contribution here, however, is to characterize the interaction of BstHU with single molecules of DNA in arbitrary states of supercoiling. BstHU clearly distinguishes under- and overwound substrates, breaking the characteristic symmetry in the elastic response of bare DNA. We demonstrate that BstHU shifts the preferred linking number of the complex, consistent with a model in which bound proteins untwist the double helix. The model qualitatively explains various features, such as overall compaction and weaker dependence on supercoiling, by a softening of the DNA to twist and bending. Previously reported reversal of binding effects at protein concentrations above a threshold also extends to supercoiling. All observed effects are highly sensitive to salt concentrations. Their range and magnitude lend HU great versatility in dynamically altering the physical properties and organization of the nucleoid.
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Affiliation(s)
- BERNHARD SCHNURR
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
- Skirball Institute of Biomolecular Medicine, Program in Molecular Pathogenesis, NYU School of Medicine, New York, NY 10016, USA
| | - CONSTANTINOS VORGIAS
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimiopolis — Zographou, 157 84 Athens, Greece
| | - JOEL STAVANS
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
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14
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Lionberger TA, Demurtas D, Witz G, Dorier J, Lillian T, Meyhöfer E, Stasiak A. Cooperative kinking at distant sites in mechanically stressed DNA. Nucleic Acids Res 2011; 39:9820-32. [PMID: 21917856 PMCID: PMC3239204 DOI: 10.1093/nar/gkr666] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In cells, DNA is routinely subjected to significant levels of bending and twisting. In some cases, such as under physiological levels of supercoiling, DNA can be so highly strained, that it transitions into non-canonical structural conformations that are capable of relieving mechanical stress within the template. DNA minicircles offer a robust model system to study stress-induced DNA structures. Using DNA minicircles on the order of 100 bp in size, we have been able to control the bending and torsional stresses within a looped DNA construct. Through a combination of cryo-EM image reconstructions, Bal31 sensitivity assays and Brownian dynamics simulations, we have been able to analyze the effects of biologically relevant underwinding-induced kinks in DNA on the overall shape of DNA minicircles. Our results indicate that strongly underwound DNA minicircles, which mimic the physical behavior of small regulatory DNA loops, minimize their free energy by undergoing sequential, cooperative kinking at two sites that are located about 180° apart along the periphery of the minicircle. This novel form of structural cooperativity in DNA demonstrates that bending strain can localize hyperflexible kinks within the DNA template, which in turn reduces the energetic cost to tightly loop DNA.
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Affiliation(s)
- Troy A Lionberger
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA.
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15
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Koh J, Shkel I, Saecker RM, Record MT. Nonspecific DNA binding and bending by HUαβ: interfaces of the three binding modes characterized by salt-dependent thermodynamics. J Mol Biol 2011; 410:241-67. [PMID: 21513716 DOI: 10.1016/j.jmb.2011.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/01/2011] [Accepted: 04/01/2011] [Indexed: 10/18/2022]
Abstract
Previous isothermal titration calorimetry (ITC) and Förster resonance energy transfer studies demonstrated that Escherichia coli HU(αβ) binds nonspecifically to duplex DNA in three different binding modes: a tighter-binding 34-bp mode that interacts with DNA in large (>34 bp) gaps between bound proteins, reversibly bending it by 140(o) and thereby increasing its flexibility, and two weaker, modestly cooperative small site-size modes (10 bp and 6 bp) that are useful for filling gaps between bound proteins shorter than 34 bp. Here we use ITC to determine the thermodynamics of these binding modes as a function of salt concentration, and we deduce that DNA in the 34-bp mode is bent around-but not wrapped on-the body of HU, in contrast to specific binding of integration host factor. Analyses of binding isotherms (8-bp, 15-bp, and 34-bp DNA) and initial binding heats (34-bp, 38-bp, and 160-bp DNA) reveal that all three modes have similar log-log salt concentration derivatives of the binding constants (Sk(i)) even though their binding site sizes differ greatly; the most probable values of Sk(i) on 34-bp DNA or larger DNA are -7.5±0.5. From the similarity of Sk(i) values, we conclude that the binding interfaces of all three modes involve the same region of the arms and saddle of HU. All modes are entropy-driven, as expected for nonspecific binding driven by the polyelectrolyte effect. The bent DNA 34-bp mode is most endothermic, presumably because of the cost of HU-induced DNA bending, while the 6-bp mode is modestly exothermic at all salt concentrations examined. Structural models consistent with the observed Sk(i) values are proposed.
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Affiliation(s)
- Junseock Koh
- Program in Biophysics, University of Wisconsin-Madison, Madison, WI 53706, USA.
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16
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Czapla L, Peters JP, Rueter EM, Olson WK, Maher LJ. Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins. J Mol Biol 2011; 409:278-89. [PMID: 21459097 DOI: 10.1016/j.jmb.2011.03.050] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 03/21/2011] [Accepted: 03/24/2011] [Indexed: 11/25/2022]
Abstract
Understanding and predicting the mechanical properties of protein/DNA complexes are challenging problems in biophysics. Certain architectural proteins bind DNA without sequence specificity and strongly distort the double helix. These proteins rapidly bind and unbind, seemingly enhancing the flexibility of DNA as measured by cyclization kinetics. The ability of architectural proteins to overcome DNA stiffness has important biological consequences, but the detailed mechanism of apparent DNA flexibility enhancement by these proteins has not been clear. Here, we apply a novel Monte Carlo approach that incorporates the precise effects of protein on DNA structure to interpret new experimental data for the bacterial histone-like HU protein and two eukaryotic high-mobility group class B (HMGB) proteins binding to ∼200-bp DNA molecules. These data (experimental measurement of protein-induced increase in DNA cyclization) are compared with simulated cyclization propensities to deduce the global structure and binding characteristics of the closed protein/DNA assemblies. The simulations account for all observed (chain length and concentration dependent) effects of protein on DNA behavior, including how the experimental cyclization maxima, observed at DNA lengths that are not an integral helical repeat, reflect the deformation of DNA by the architectural proteins and how random DNA binding by different proteins enhances DNA cyclization to different levels. This combination of experiment and simulation provides a powerful new approach to resolve a long-standing problem in the biophysics of protein/DNA interactions.
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Affiliation(s)
- Luke Czapla
- (1)Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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17
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Xiao B, Zhang H, Johnson RC, Marko JF. Force-driven unbinding of proteins HU and Fis from DNA quantified using a thermodynamic Maxwell relation. Nucleic Acids Res 2011; 39:5568-77. [PMID: 21427084 PMCID: PMC3141252 DOI: 10.1093/nar/gkr141] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Determining numbers of proteins bound to large DNAs is important for understanding their chromosomal functions. Protein numbers may be affected by physical factors such as mechanical forces generated in DNA, e.g. by transcription or replication. We performed single-DNA stretching experiments with bacterial nucleoid proteins HU and Fis, verifying that the force-extension measurements were in thermodynamic equilibrium. We, therefore, could use a thermodynamic Maxwell relation to deduce the change of protein number on a single DNA due to varied force. For the binding of both HU and Fis under conditions studied, numbers of bound proteins decreased as force was increased. Our experiments showed that most of the bound HU proteins were driven off the DNA at 6.3 pN for HU concentrations lower than 150 nM; our HU data were fit well by a statistical-mechanical model of protein-induced bending of DNA. In contrast, a significant amount of Fis proteins could not be forced off the DNA at forces up to 12 pN and Fis concentrations up to 20 nM. This thermodynamic approach may be applied to measure changes in numbers of a wide variety of molecules bound to DNA or other polymers. Force-dependent DNA binding by proteins suggests mechano-chemical mechanisms for gene regulation.
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Affiliation(s)
- Botao Xiao
- Department of Physics and Astronomy, Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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18
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Vitoc CI, Mukerji I. HU binding to a DNA four-way junction probed by Förster resonance energy transfer. Biochemistry 2011; 50:1432-41. [PMID: 21230005 PMCID: PMC4724199 DOI: 10.1021/bi1007589] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The Escherichia coli protein HU is a non-sequence-specific DNA-binding protein that interacts with DNA primarily through electrostatic interactions. In addition to nonspecific binding to linear DNA, HU has been shown to bind with nanomolar affinity to discontinuous DNA substrates, such as repair and recombination intermediates. This work specifically examines the HU-four-way junction (4WJ) interaction using fluorescence spectroscopic methods. The conformation of the junction in the presence of different counterions was investigated by Förster resonance energy transfer (FRET) measurements, which revealed an ion-type conformational dependence, where Na(+) yields the most stacked conformation followed by K(+) and Mg(2+). HU binding induces a greater degree of stacking in the Na(+)-stabilized and Mg(2+)-stabilized junctions but not the K(+)-stabilized junction, which is attributed to differences in the size of the ionic radii and potential differences in ion binding sites. Interestingly, junction conformation modulates binding affinity, where HU exhibits the lowest affinity for the Mg(2+)-stabilized form (24 μM(-1)), which is the least stacked conformation. Protein binding to a mixed population of open and stacked forms of the junction leads to nearly complete formation of a protein-stabilized stacked-X junction. These results strongly support a model in which HU binds to and stabilizes the stacked-X conformation.
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Affiliation(s)
- Codruta Iulia Vitoc
- Molecular Biology and Biochemistry Department, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459-0175
| | - Ishita Mukerji
- Molecular Biology and Biochemistry Department, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459-0175
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19
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Qaiser D, Khan MS, Singh RD, Khan ZH, Chawla S. Förster's resonance energy transfer between Fullerene C60 and Coumarin C440. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 77:1065-1068. [PMID: 20869302 DOI: 10.1016/j.saa.2010.08.074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 08/09/2010] [Accepted: 08/26/2010] [Indexed: 05/29/2023]
Abstract
The interaction between Coumarin C440 with Fullerene C60 has been studied by fluorescence and time resolved spectroscopic techniques. The Coumarin C440-Fullerene C60 pair shows Forster's resonance energy transfer (FRET) from Coumarin C440 (donor) to Fullerenes C60 (acceptor). The FRET efficiency of this pair increases with the increase of the acceptor concentration. The critical energy transfer distance (R0) at which transfer efficiency is 50% is found to be 34Ǻ. Stern-Volmer plot indicates static as well as dynamic quenching. However, the FRET studies show highest efficiency at the critical stage of dimer formation.
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Affiliation(s)
- Darakhshan Qaiser
- Department of Physics, Jamia Millia Islamia, New Delhi 110025, India.
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20
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Xiao B, Johnson RC, Marko JF. Modulation of HU-DNA interactions by salt concentration and applied force. Nucleic Acids Res 2010; 38:6176-85. [PMID: 20497998 PMCID: PMC2952867 DOI: 10.1093/nar/gkq435] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
HU is one of the most abundant proteins in bacterial chromosomes and participates in nucleoid compaction and gene regulation. We report experiments using DNA stretching that study the dependence of DNA condensation by HU on force, salt and HU concentration. Previous experiments at sub-physiological salt levels revealed that low concentrations of HU could compact DNA, whereas larger HU concentrations formed a DNA-stiffening complex. Here we report that this bimodal binding behavior depends sensitively on salt concentration. Only the compaction mode was observed for 150 mM and higher NaCl levels, i.e. for physiological salt concentrations. Similar results were obtained for the more physiological salt K-glutamate. Real-time studies of dissociation kinetics revealed that HU unbound slowly (minutes to hours under the conditions studied) but completely for salt concentrations at or above 100 mM NaCl; the lifetime of HU complexes was observed to increase with the HU concentration at which the complexes were formed, and to decrease with salt concentration. Higher salt levels of 300 mM NaCl completely eliminated observable HU binding to DNA. Finally, we observed that the dissociation kinetics depend on force applied to the DNA: increased applied force in the sub-piconewton range accelerates dissociation, suggesting a mechanism for DNA tension to regulate chromosome structure and gene expression.
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Affiliation(s)
- Botao Xiao
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA.
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21
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Ghosh D, Bose D, Sarkar D, Chattopadhyay N. Excited-State-Proton-Transfer-Triggered Fluorescence Resonance Energy Transfer: from 2-Naphthylamine to Phenosafranin. J Phys Chem A 2009; 113:10460-5. [DOI: 10.1021/jp9054318] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Debanjana Ghosh
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India
| | - Debosreeta Bose
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India
| | - Deboleena Sarkar
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India
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22
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Czapla L, Swigon D, Olson WK. Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations. J Mol Biol 2008; 382:353-70. [PMID: 18586040 PMCID: PMC2679585 DOI: 10.1016/j.jmb.2008.05.088] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 05/20/2008] [Accepted: 05/26/2008] [Indexed: 11/22/2022]
Abstract
The histone-like HU (heat unstable) protein plays a key role in the organization and regulation of the Escherichia coli genome. The nonspecific nature of HU binding to DNA complicates analysis of the mechanism by which the protein contributes to the looping of DNA. Conventional models of the looping of HU-bound duplexes attribute the changes in biophysical properties of DNA brought about by the random binding of protein to changes in the effective parameters of an ideal helical wormlike chain. Here, we introduce a novel Monte Carlo approach to study the effects of nonspecific HU binding on the configurational properties of DNA directly. We randomly decorated segments of an ideal double-helical DNA with HU molecules that induce the bends and other structural distortions of the double helix find in currently available X-ray structures. We find that the presence of HU at levels approximating those found in the cell reduces the persistence length by roughly threefold compared with that of naked DNA. The binding of protein has particularly striking effects on the cyclization properties of short duplexes, altering the dependence of ring closure on chain length in a way that cannot be mimicked by a simple wormlike model and accumulating at higher-than-expected levels on successfully closed chains. Moreover, the uptake of protein on small minicircles depends on chain length, taking advantage of the HU-induced deformations of DNA structure to facilitate ligation. Circular duplexes with bound HU show much greater propensity than protein-free DNA to exist as negatively supercoiled topoisomers, suggesting a potential role of HU in organizing the bacterial nucleoid. The local bending and undertwisting of DNA by HU, in combination with the number of bound proteins, provide a structural rationale for the condensation of DNA and the observed expression levels of reporter genes in vivo.
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Affiliation(s)
- Luke Czapla
- Department of Chemistry & Chemical Biology, the State University of New Jersey, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, New Jersey 08854
| | - David Swigon
- Department of Mathematics, University of Pittsburgh, 519 Thackeray Hall, Pittsburgh, Pennsylvania 15260
| | - Wilma K. Olson
- Department of Chemistry & Chemical Biology, the State University of New Jersey, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, New Jersey 08854
- BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, New Jersey 08854
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23
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Koh J, Saecker RM, Record MT. DNA binding mode transitions of Escherichia coli HU(alphabeta): evidence for formation of a bent DNA--protein complex on intact, linear duplex DNA. J Mol Biol 2008; 383:324-46. [PMID: 18657548 DOI: 10.1016/j.jmb.2008.07.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Revised: 07/07/2008] [Accepted: 07/08/2008] [Indexed: 10/21/2022]
Abstract
Escherichia coli HU(alphabeta), a major nucleoid-associated protein, organizes chromosomal DNA and facilitates numerous DNA transactions. Using isothermal titration calorimetry, fluorescence resonance energy transfer and a series of DNA lengths (8 bp, 15 bp, 34 bp, 38 bp and 160 bp) we established that HU(alphabeta) interacts with duplex DNA using three different nonspecific binding modes. Both the HU to DNA molar ratio ([HU]/[DNA]) and DNA length dictate the dominant HU binding mode. On sufficiently long DNA (> or =34 bp), at low [HU]/[DNA], HU populates a noncooperative 34 bp binding mode with a binding constant of 2.1+/-0.4x10(6) M(-1), and a binding enthalpy of +7.7+/-0.6 kcal/mol at 15 degrees C and 0.15 M Na(+). With increasing [HU]/[DNA], HU bound in the noncooperative 34 bp mode progressively converts to two cooperative (omega approximately 20) modes with site sizes of 10 bp and 6 bp. These latter modes exhibit smaller binding constants (1.1+/-0.2x10(5) M(-1) for the 10 bp mode, 3.5+/-1.4x10(4) M(-1) for the 6 bp mode) and binding enthalpies (4.2+/-0.3 kcal/mol for the 10 bp mode, -1.6+/-0.3 kcal/mol for the 6 bp mode). As DNA length increases to 34 bp or more at low [HU]/[DNA], the small modes are replaced by the 34 bp binding mode. Fluorescence resonance energy transfer data demonstrate that the 34 bp mode bends DNA by 143+/-6 degrees whereas the 6 bp and 10 bp modes do not. The model proposed in this study provides a novel quantitative and comprehensive framework for reconciling previous structural and solution studies of HU, including single molecule (force extension measurement), fluorescence, and electrophoretic gel mobility-shift assays. In particular, it explains how HU condenses or extends DNA depending on the relative concentrations of HU and DNA.
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Affiliation(s)
- Junseock Koh
- Program in Biophysics, University of Wisconsin, Madison WI 53706, USA
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24
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Benevides JM, Danahy J, Kawakami J, Thomas GJ. Mechanisms of Specific and Nonspecific Binding of Architectural Proteins in Prokaryotic Gene Regulation. Biochemistry 2008; 47:3855-62. [DOI: 10.1021/bi7009426] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James M. Benevides
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| | - Jessica Danahy
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| | - Jessica Kawakami
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| | - George J. Thomas
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
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25
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Das P, Mallick A, Haldar B, Chakrabarty A, Chattopadhyay N. Fluorescence resonance energy transfer from tryptophan in human serum albumin to a bioactive indoloquinolizine system. J CHEM SCI 2007. [DOI: 10.1007/s12039-007-0013-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Mouw KW, Rice PA. Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending protein Hbb. Mol Microbiol 2007; 63:1319-30. [PMID: 17244195 DOI: 10.1111/j.1365-2958.2007.05586.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The genome of the Lyme disease-causing spirochete Borrelia burgdorferi encodes only a single polypeptide from the integration host factor (IHF)/HU or 'DNABII' family of nucleoid-associated proteins - Hbb. DNABII proteins induce large bends in DNA and serve as architectural factors in a variety of prokaryotic cellular processes. We have solved the crystal structure of an Hbb-DNA complex in which the DNA is bent by over 180 degrees . We find that like IHF, Hbb relies exclusively on indirect readout to recognize its cognate site. Additional binding studies show that the sequence preferences of Hbb are related to, yet distinct from those of IHF. Defining these binding characteristics may help to uncover additional roles for Hbb in Borrelia DNA metabolism as well as further our understanding of the mechanism of indirect readout.
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Affiliation(s)
- Kent W Mouw
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
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27
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Sarkar T, Vitoc I, Mukerji I, Hud NV. Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines. Nucleic Acids Res 2007; 35:951-61. [PMID: 17259223 PMCID: PMC1807954 DOI: 10.1093/nar/gkl1093] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Controlling the size and shape of DNA condensates is important in vivo and for the improvement of nonviral gene delivery. Here, we demonstrate that the morphology of DNA condensates, formed under a variety of conditions, is shifted completely from toroids to rods if the bacterial protein HU is present during condensation. HU is a non-sequence-specific DNA binding protein that sharply bends DNA, but alone does not condense DNA into densely packed particles. Less than one HU dimer per 225 bp of DNA is sufficient to completely control condensate morphology when DNA is condensed by spermidine. We propose that rods are favored in the presence of HU because rods contain sharply bent DNA, whereas toroids contain only smoothly bent DNA. The results presented illustrate the utility of naturally derived proteins for controlling the shape of DNA condensates formed in vitro. HU is a highly conserved protein in bacteria that is implicated in the compaction and shaping of nucleoid structure. However, the exact role of HU in chromosome compaction is not well understood. Our demonstration that HU governs DNA condensation in vitro also suggests a mechanism by which HU could act as an architectural protein for bacterial chromosome compaction and organization in vivo.
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Affiliation(s)
- Tumpa Sarkar
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400 and Molecular Biology and Biochemistry Department, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459-0175
| | - Iulia Vitoc
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400 and Molecular Biology and Biochemistry Department, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459-0175
| | - Ishita Mukerji
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400 and Molecular Biology and Biochemistry Department, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459-0175
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400 and Molecular Biology and Biochemistry Department, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459-0175
- *To whom correspondence should be addressed. Tel: +1 404 385 1162; Fax: +1 404 894 2295;
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28
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Kar S, Choi EJ, Guo F, Dimitriadis EK, Kotova SL, Adhya S. Right-handed DNA Supercoiling by an Octameric Form of Histone-like Protein HU. J Biol Chem 2006; 281:40144-53. [PMID: 17062578 DOI: 10.1074/jbc.m605576200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In bacteria, the contribution of global nucleoid organization in determining cellular transcription programs is unclear. Using a mutant form of the most abundant nucleoid-associated protein HU, HUalpha(E38K,V42L), we previously showed that nucleoid remodeling by the mutant protein re-organizes the global transcription pattern. Here, we demonstrate that, unlike the dimeric wild-type HU, HUalpha(E38K,V42L) is an octamer and wraps DNA around its surface. The formation of wrapped nucleoprotein complexes by HUalpha(E38K,V42L) leads to a high degree of DNA condensation. The DNA wrapping is right-handed, which restrains positive supercoils. In vivo, HUalpha(E38K,V42L) shows altered association and distribution patterns with the genetic loci whose transcription are differentially affected in the mutant strain.
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Affiliation(s)
- Sudeshna Kar
- Laboratory of Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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29
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Swinger KK, Rice PA. Structure-based analysis of HU-DNA binding. J Mol Biol 2006; 365:1005-16. [PMID: 17097674 PMCID: PMC1945228 DOI: 10.1016/j.jmb.2006.10.024] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 09/25/2006] [Accepted: 10/07/2006] [Indexed: 11/29/2022]
Abstract
HU and IHF are prokaryotic proteins that induce very large bends in DNA. They are present in high concentrations in the bacterial nucleoid and aid in chromosomal compaction. They also function as regulatory cofactors in many processes, such as site-specific recombination and the initiation of replication and transcription. HU and IHF have become paradigms for understanding DNA bending and indirect readout of sequence. While IHF shows significant sequence specificity, HU binds preferentially to certain damaged or distorted DNAs. However, none of the structurally diverse HU substrates previously studied in vitro is identical with the distorted substrates in the recently published Anabaena HU(AHU)-DNA cocrystal structures. Here, we report binding affinities for AHU and the DNA in the cocrystal structures. The binding free energies for formation of these AHU-DNA complexes range from approximately 10-14.5 kcal/mol, representing K(d) values in the nanomolar to low picomolar range, and a maximum stabilization of at least approximately 6.3 kcal/mol relative to complexes with undistorted, non-specific DNA. We investigated IHF binding and found that appropriate structural distortions can greatly enhance its affinity. On the basis of the coupling of structural and relevant binding data, we estimate the amount of conformational strain in an IHF-mediated DNA kink that is relieved by a nick (at least 0.76 kcal/mol) and pinpoint the location of the strain. We show that AHU has a sequence preference for an A+T-rich region in the center of its DNA-binding site, correlating with an unusually narrow minor groove. This is similar to sequence preferences shown by the eukaryotic nucleosome.
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30
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Ma B, Wang J, Fang X. Fluorescence study of DNA binding and bending by EcoRI DNA methyltransferase. J Phys Chem B 2006; 110:19647-51. [PMID: 17004833 DOI: 10.1021/jp0574293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have applied fluorescence anisotropy and fluorescence resonance energy transfer (FRET) techniques to study the interaction between EcoRI DNA methyltransferase (M.EcoRI) and its target DNA in solution. Upon binding with M.EcoRI, the dsDNA containing GAATTC bends to flip out the second adenine for methylation. The binding affinity of M.EcoRI to two dsDNA fragments (20 and 38 bp) was studied with fluorescence anisotropy. Their binding constants at different temperatures from 20 to 40 degrees C were obtained, and the thermodynamic parameters of binding were derived. The results showed that M.EcoRI had a higher binding affinity to the short dsDNA strand than to the long one, and its binding to DNA was primarily entropy-driven. By labeling the 5' ends of the 20-bp dsDNA with two fluorescent dyes, fluorescein (FAM) and tetramethylrhodamine (TMR), we were able to monitor the enhanced TMR fluorescence in the presence of M.EcoRI. The end-to-end distance of the dsDNA determined from the FRET efficiency was changed from 72.4 to 63.4 A, and the DNA bending angle was estimated as 57.8 degrees .
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Affiliation(s)
- Baocheng Ma
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, PR China
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31
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Dame RT. The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol Microbiol 2005; 56:858-70. [PMID: 15853876 DOI: 10.1111/j.1365-2958.2005.04598.x] [Citation(s) in RCA: 274] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The bacterial chromosomal DNA is folded into a compact structure called nucleoid. The shape and size of this 'body' is determined by a number of factors. Major players are DNA supercoiling, macromolecular crowding and architectural proteins, associated with the nucleoid, which are the topic of this MicroReview. Although many of these proteins were identified more than 25 years ago, the molecular mechanisms involved in the organization and compaction of DNA have only started to become clear in recent years. Many of these new insights can be attributed to the use of recently developed biophysical techniques.
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Affiliation(s)
- Remus T Dame
- Physics of Complex Systems, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, the Netherlands.
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32
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Semsey S, Virnik K, Adhya S. A gamut of loops: meandering DNA. Trends Biochem Sci 2005; 30:334-41. [PMID: 15950878 DOI: 10.1016/j.tibs.2005.04.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Revised: 03/29/2005] [Accepted: 04/22/2005] [Indexed: 11/18/2022]
Abstract
Nucleoprotein complexes comprising short DNA loops (150 base pairs or less) are involved in a wide variety of DNA transactions (e.g. transcription regulation, replication and recombination) in both prokaryotes and eukaryotes, and also can be useful in designing nanostructures. In these higher-order nucleoprotein complexes, proteins bound to spatially separated sites on a DNA interact with each other by looping out the relatively stiff intervening DNA. Recent technological developments have enabled determination of DNA trajectories in a few DNA-loop-containing regulatory complexes. Results show that, in a given system, a specific DNA trajectory is preferred over others.
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Affiliation(s)
- Szabolcs Semsey
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA
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33
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Dame RT, van Mameren J, Luijsterburg MS, Mysiak ME, Janićijević A, Pazdzior G, van der Vliet PC, Wyman C, Wuite GJL. Analysis of scanning force microscopy images of protein-induced DNA bending using simulations. Nucleic Acids Res 2005; 33:e68. [PMID: 15843682 PMCID: PMC1083423 DOI: 10.1093/nar/gni073] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bending of DNA is a feature essential to the function of many DNA-binding proteins. Bending angles can be estimated with a variety of techniques, but most directly from images obtained using scanning force microscopy (SFM). Direct measurement of the bending angle using a tangent method often produces angles that deviate significantly from values obtained using other techniques. Here, we describe the application of SFM in combination with simulations of DNA as a means to estimate protein-induced bending angles in a reliable and unbiased fashion. In this manner, we were able to obtain accurate estimates for the bending angles induced by nuclear factor I, octamer-binding transcription factor 1, the human XPC-Rad23B complex and integration host factor [correction]
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Affiliation(s)
- Remus T Dame
- Physics of Complex Systems, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit De Boelelaan 1081, NL-1081 HV, Amsterdam, The Netherlands.
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Wojtuszewski K, Mukerji I. The HU-DNA binding interaction probed with UV resonance Raman spectroscopy: structural elements of specificity. Protein Sci 2005; 13:2416-28. [PMID: 15322284 PMCID: PMC2280020 DOI: 10.1110/ps.04730204] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The Escherichia coli protein HU functions as an architectural DNA-binding protein by facilitating DNA looping or bending to form multiprotein complexes. Although HU does not recognize a specific DNA sequence, site-specific binding to a number of discontinuous, looped, or bent DNA substrates has been observed. In this study UV resonance Raman (UVRR) spectroscopy is used to identify structural elements associated with low- and high-affinity binding by examining three different HU-DNA complexes. UVRR spectra obtained with an excitation wavelength of 210 nm, which preferentially enhances protein backbone amide vibrations, indicate that HU secondary structure content increases and the protein structure becomes more rigid upon binding to DNA. The increase in alpha-helical content is attributed to the C-terminal helix, which interacts with the DNA and may play a role in binding affinity and specificity. UVRR spectra obtained with a 215 nm excitation wavelength demonstrate that Pro mode intensity at 1455 cm(-1) decreases upon complex formation. This intensity decrease is attributed to the intercalation of Pro residues between DNA base pairs to induce a bend in the DNA, as has been observed previously in the IHF-DNA and HU-DNA cocrystal structures. DNA vibrational modes are also indicative of significant base unstacking and opening of the minor groove upon protein binding, consistent with bending and distortion of the DNA. In all three complexes, A-DNA conformational features are indicated by deoxyribose-phosphate backbone modes. These and other results suggest that protein-induced bending plays an important role in HU site-specific binding and supports a model of a mutually induced fit.
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Affiliation(s)
- Kristi Wojtuszewski
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459-0175, USA
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Abstract
The energetic cost of bending short segments of DNA is very high. This bending is critical for the packaging of DNA and is exploited to regulate many cellular processes. In prokaryotes, IHF and HU are key architectural proteins present at high concentrations. New protein-DNA co-crystal structures, and the adaptation of advanced biophysical and biochemical techniques have led to an improved understanding of how these proteins interact with DNA. These techniques include time-resolved synchrotron X-ray footprinting, differential scanning calorimetry, isothermal titration calorimetry and single-molecule experiments.
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Affiliation(s)
- Kerren K Swinger
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
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Arthanari H, Wojtuszewski K, Mukerji I, Bolton PH. Effects of HU binding on the equilibrium cyclization of mismatched, curved, and normal DNA. Biophys J 2004; 86:1625-31. [PMID: 14990489 PMCID: PMC1303997 DOI: 10.1016/s0006-3495(04)74230-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The effects of HU, the histone-like protein from Escherichia coli, on the equilibrium cyclization of duplex DNAs have been observed as a function of protein concentration and DNA sequence. The results indicate that the presence of HU significantly enhances the extent of cyclization and increases the melting temperature, T(m), of the cyclized form of the DNA by >10 K. The stabilization of equilibrium cyclization by HU binding is at least -1.2 kcal/mol. The results are consistent with two HU homotypic dimers binding to each of the three 29-mer duplexes studied. One of the 29-mer duplexes contains a central dA tract, one contains mismatched sites, and one a conventional sequence. Stepwise or microscopic association constants, determined from the fluorescence data, range from 1.5 to 0.6 micro M(-1). The binding affinity of the HU dimer is strongest for the mismatched duplex and lowest for the dA tract, consistent with HU dimers having a preference for flexible DNA substrates. These results demonstrate the utility of the equilibrium cyclization approach to monitor DNA-protein interactions. These results have been considered along with those previously obtained to refine a model for the interaction of HU with duplex DNA.
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Affiliation(s)
- Haribabu Arthanari
- Chemistry Department, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut, USA
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Sagi D, Friedman N, Vorgias C, Oppenheim AB, Stavans J. Modulation of DNA conformations through the formation of alternative high-order HU-DNA complexes. J Mol Biol 2004; 341:419-28. [PMID: 15276833 DOI: 10.1016/j.jmb.2004.06.023] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Revised: 06/07/2004] [Accepted: 06/07/2004] [Indexed: 11/26/2022]
Abstract
HU is an abundant, highly conserved protein associated with the bacterial chromosome. It belongs to a small class of proteins that includes the eukaryotic proteins TBP, SRY, HMG-I and LEF-I, which bind to DNA non-specifically at the minor groove. HU plays important roles as an accessory architectural factor in a variety of bacterial cellular processes such as DNA compaction, replication, transposition, recombination and gene regulation. In an attempt to unravel the role this protein plays in shaping nucleoid structure, we have carried out fluorescence resonance energy transfer measurements of HU-DNA oligonucleotide complexes, both at the ensemble and single-pair levels. Our results provide direct experimental evidence for concerted DNA bending by HU, and the abrogation of this effect at HU to DNA ratios above about one HU dimer per 10-12 bp. These findings support a model in which a number of HU molecules form an ordered helical scaffold with DNA lying in the periphery. The abrogation of these nucleosome-like structures for high HU to DNA ratios suggests a unique role for HU in the dynamic modulation of bacterial nucleoid structure.
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Affiliation(s)
- Dror Sagi
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot 76100, Israel
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van Noort J, Verbrugge S, Goosen N, Dekker C, Dame RT. Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc Natl Acad Sci U S A 2004; 101:6969-74. [PMID: 15118104 PMCID: PMC406450 DOI: 10.1073/pnas.0308230101] [Citation(s) in RCA: 228] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nucleoid-associated protein HU is one of the most abundant proteins in Escherichia coli and has been suggested to play an important role in bacterial nucleoid organization and regulation. Although the regulatory aspects of HU have been firmly established, much less is understood about the role of HU in shaping the bacterial nucleoid. In both functions (local) modulation of DNA architecture seems an essential feature, but information on the mechanical properties of this type of sequence-independent nucleoprotein complex is scarce. In this study we used magnetic tweezers and atomic force microscopy to quantify HU-induced DNA bending and condensation. Both techniques revealed that HU can have two opposing mechanical effects depending on the protein concentration. At concentrations <100 nM, individual HU dimers induce very flexible bends in DNA that are responsible for DNA compaction up to 50%. At higher HU concentrations, a rigid nucleoprotein filament is formed in which HU appears to arrange helically around the DNA without inducing significant condensation.
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Affiliation(s)
- John van Noort
- Molecular Biophysics, Kavli Institute of Nanoscience, Delft University of Technology, NL-2628 CJ, Delft, The Netherlands.
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Beveridge DL, Dixit SB, Barreiro G, Thayer KM. Molecular dynamics simulations of DNA curvature and flexibility: helix phasing and premelting. Biopolymers 2004; 73:380-403. [PMID: 14755574 DOI: 10.1002/bip.20019] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Recent studies of DNA axis curvature and flexibility based on molecular dynamics (MD) simulations on DNA are reviewed. The MD simulations are on DNA sequences up to 25 base pairs in length, including explicit consideration of counterions and waters in the computational model. MD studies are described for ApA steps, A-tracts, for sequences of A-tracts with helix phasing. In MD modeling, ApA steps and A-tracts in aqueous solution are essentially straight, relatively rigid, and exhibit the characteristic features associated with the B'-form of DNA. The results of MD modeling of A-tract oligonucleotides are validated by close accord with corresponding crystal structure results and nuclear magnetic resonance (NMR) nuclear Overhauser effect (NOE) and residual dipolar coupling (RDC) structures of d(CGCGAATTCGCG) and d(GGCAAAAAACGG). MD simulation successfully accounts for enhanced axis curvature in a set of three sequences with phased A-tracts studied to date. The primary origin of the axis curvature in the MD model is found at those pyrimidine/purine YpR "flexible hinge points" in a high roll, open hinge conformational substate. In the MD model of axis curvature in a DNA sequence with both phased A-tracts and YpR steps, the A-tracts appear to act as positioning elements that make the helix phasing more precise, and key YpR steps in the open hinge state serve as curvature elements. Our simulations on a phased A-tract sequence as a function of temperature show that the MD simulations exhibit a premelting transition in close accord with experiment, and predict that the mechanism involves a B'-to-B transition within A-tracts coupled with the prediction of a transition in key YpR steps from the high roll, open hinge, to a low roll, closed hinge substate. Diverse experimental observations on DNA curvature phenomena are examined in light of the MD model with no serious discrepancies. The collected MD results provide independent support for the "non-A-tract model" of DNA curvature. The "junction model" is indicated to be a special case of the non-A-tract model when there is a Y base at the 5' end of an A-tract. In accord with crystallography, the "ApA wedge model" is not supported by MD.
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Affiliation(s)
- D L Beveridge
- Department of Chemistry, Wesleyan University, Middletown CT 06459, USA.
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