1
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Sangeeta, Bhattacherjee A. Nick Induced Dynamics in Supercoiled DNA Facilitates the Protein Target Search Process. J Phys Chem B 2024; 128:8246-8258. [PMID: 39146491 DOI: 10.1021/acs.jpcb.4c03810] [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: 08/17/2024]
Abstract
A DNA nick, defined as a discontinuity in a double-stranded DNA molecule where the phosphodiester bond between adjacent nucleotides of one strand is absent due to enzyme action, serves as an effective mechanism to alleviate stress in supercoiled DNA. This stress release is essential for the smooth operation of transcriptional machinery. However, the underlying mechanisms and their impact on protein search dynamics, which are crucial for initiating transcription, remain unclear. Through extensive computer simulations, we unravel the molecular picture, demonstrating that intramolecular stress release due to a DNA nick is driven by a combination of writhing and twisting motions, depending on the nick's position. This stress release is quantitatively manifested as a step-like increase in the linking number. Furthermore, we elucidate that the nicked supercoiled minicircles exhibit enhanced torsional dynamics, promoting rapid conformational changes and frequent shifts in the identities of juxtaposed DNA sites on the plectoneme. The dynamics of the juxtaposition sites facilitates communication between protein and DNA, resulting in faster protein diffusion compared with native DNA with the same topology. Our findings highlight the mechanistic intricacies and underscore the importance of DNA nicks in facilitating transcription elongation by actively managing torsional stress during DNA unwinding by the RNA polymerase.
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Affiliation(s)
- Sangeeta
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Arnab Bhattacherjee
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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2
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Lin YY, Brouns T, Kolbeck PJ, Vanderlinden W, Lipfert J. High-yield ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single-molecule manipulation assays. J Biol Chem 2023; 299:104874. [PMID: 37257819 PMCID: PMC10404619 DOI: 10.1016/j.jbc.2023.104874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/08/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023] Open
Abstract
Force and torque spectroscopy have provided unprecedented insights into the mechanical properties, conformational transitions, and dynamics of DNA and DNA-protein complexes, notably nucleosomes. Reliable single-molecule manipulation measurements require, however, specific and stable attachment chemistries to tether the molecules of interest. Here, we present a functionalization strategy for DNA that enables high-yield production of constructs for torsionally constrained and very stable attachment. The method is based on two subsequent PCRs: first ∼380 bp long DNA strands are generated that contain multiple labels, which are used as "megaprimers" in a second PCR to generate ∼kbp long double-stranded DNA constructs with multiple labels at the respective ends. To achieve high-force stability, we use dibenzocyclooctyne-based click chemistry for covalent attachment to the surface and biotin-streptavidin coupling to the bead. The resulting tethers are torsionally constrained and extremely stable under load, with an average lifetime of 70 ± 3 h at 45 pN. The high yield of the approach enables nucleosome reconstitution by salt dialysis on the functionalized DNA, and we demonstrate proof-of-concept measurements on nucleosome assembly statistics and inner turn unwrapping under force. We anticipate that our approach will facilitate a range of studies of DNA interactions and nucleoprotein complexes under forces and torques.
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Affiliation(s)
- Yi-Yun Lin
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Tine Brouns
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Division of Molecular Imaging and Photonics, KU Leuven, Leuven, Belgium
| | - Pauline J Kolbeck
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Willem Vanderlinden
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
| | - Jan Lipfert
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
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3
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Lim W, Randisi F, Doye JPK, Louis AA. The interplay of supercoiling and thymine dimers in DNA. Nucleic Acids Res 2022; 50:2480-2492. [PMID: 35188542 PMCID: PMC8934635 DOI: 10.1093/nar/gkac082] [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: 09/27/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Thymine dimers are a major mutagenic photoproduct induced by UV radiation. While they have been the subject of extensive theoretical and experimental investigations, questions of how DNA supercoiling affects local defect properties, or, conversely, how the presence of such defects changes global supercoiled structure, are largely unexplored. Here, we introduce a model of thymine dimers in the oxDNA forcefield, parametrized by comparison to melting experiments and structural measurements of the thymine dimer induced bend angle. We performed extensive molecular dynamics simulations of double-stranded DNA as a function of external twist and force. Compared to undamaged DNA, the presence of a thymine dimer lowers the supercoiling densities at which plectonemes and bubbles occur. For biologically relevant supercoiling densities and forces, thymine dimers can preferentially segregate to the tips of the plectonemes, where they enhance the probability of a localized tip-bubble. This mechanism increases the probability of highly bent and denatured states at the thymine dimer site, which may facilitate repair enzyme binding. Thymine dimer-induced tip-bubbles also pin plectonemes, which may help repair enzymes to locate damage. We hypothesize that the interplay of supercoiling and local defects plays an important role for a wider set of DNA damage repair systems.
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Affiliation(s)
- Wilber Lim
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Ferdinando Randisi
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
- FabricNano Limited, 192 Drummond St, London NW1 3HP, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
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4
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Hernández N, Soenksen J, Newcombe P, Sandhu M, Barroso I, Wallace C, Asimit JL. The flashfm approach for fine-mapping multiple quantitative traits. Nat Commun 2021; 12:6147. [PMID: 34686674 PMCID: PMC8536717 DOI: 10.1038/s41467-021-26364-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/04/2021] [Indexed: 11/08/2022] Open
Abstract
Joint fine-mapping that leverages information between quantitative traits could improve accuracy and resolution over single-trait fine-mapping. Using summary statistics, flashfm (flexible and shared information fine-mapping) fine-maps signals for multiple traits, allowing for missing trait measurements and use of related individuals. In a Bayesian framework, prior model probabilities are formulated to favour model combinations that share causal variants to capitalise on information between traits. Simulation studies demonstrate that both approaches produce broadly equivalent results when traits have no shared causal variants. When traits share at least one causal variant, flashfm reduces the number of potential causal variants by 30% compared with single-trait fine-mapping. In a Ugandan cohort with 33 cardiometabolic traits, flashfm gave a 20% reduction in the total number of potential causal variants from single-trait fine-mapping. Here we show flashfm is computationally efficient and can easily be deployed across publicly available summary statistics for signals in up to six traits.
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Affiliation(s)
- N Hernández
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - J Soenksen
- Exeter Centre of Excellence for Diabetes Research (EXCEED), University of Exeter Medical School, Exeter, UK
- School of Life Sciences, University of Glasgow, Glasgow, UK
| | - P Newcombe
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - M Sandhu
- Dept of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, UK
| | - I Barroso
- Exeter Centre of Excellence for Diabetes Research (EXCEED), University of Exeter Medical School, Exeter, UK
| | - C Wallace
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
| | - J L Asimit
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK.
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5
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Lee CY, Myong S. Probing steps in DNA transcription using single-molecule methods. J Biol Chem 2021; 297:101086. [PMID: 34403697 PMCID: PMC8441165 DOI: 10.1016/j.jbc.2021.101086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/22/2022] Open
Abstract
Transcriptional regulation is one of the key steps in determining gene expression. Diverse single-molecule techniques have been applied to characterize the stepwise progression of transcription, yielding complementary results. These techniques include, but are not limited to, fluorescence-based microscopy with single or multiple colors, force measuring and manipulating microscopy using magnetic field or light, and atomic force microscopy. Here, we summarize and evaluate these current methodologies in studying and resolving individual steps in the transcription reaction, which encompasses RNA polymerase binding, initiation, elongation, mRNA production, and termination. We also describe the advantages and disadvantages of each method for studying transcription.
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Affiliation(s)
- Chun-Ying Lee
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA; Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, Illinois, USA.
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6
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Wang Y, Rakela S, Chambers JW, Hua ZC, Muller MT, Nitiss JL, Tse-Dinh YC, Leng F. Kinetic Study of DNA Topoisomerases by Supercoiling-Dependent Fluorescence Quenching. ACS OMEGA 2019; 4:18413-18422. [PMID: 31720544 PMCID: PMC6844113 DOI: 10.1021/acsomega.9b02676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 10/11/2019] [Indexed: 06/10/2023]
Abstract
DNA topoisomerases are essential enzymes for all living organisms and important targets for anticancer drugs and antibiotics. Although DNA topoisomerases have been studied extensively, steady-state kinetics has not been systematically investigated because of the lack of an appropriate assay. Previously, we demonstrated that newly synthesized, fluorescently labeled plasmids pAB1_FL905 and pAB1_FL924 can be used to study DNA topoisomerase-catalyzed reactions by fluorescence resonance energy transfer (FRET) or supercoiling-dependent fluorescence quenching (SDFQ). With the FRET or SDFQ method, we performed steady-state kinetic studies for six different DNA topoisomerases including two type IA enzymes (Escherichia coli and Mycobacterium smegmatis DNA topoisomerase I), two type IB enzymes (human and variola DNA topoisomerase I), and two type IIA enzymes (E. coli DNA gyrase and human DNA topoisomerase IIα). Our results show that all DNA topoisomerases follow the classical Michaelis-Menten kinetics and have unique steady-state kinetic parameters, K M, V max, and k cat. We found that k cat for all topoisomerases are rather low and that such low values may stem from the tight binding of topoisomerases to DNA. Additionally, we confirmed that novobiocin is a competitive inhibitor for adenosine 5'-triphosphate binding to E. coli DNA gyrase, demonstrating the utility of our assay for studying topoisomerase inhibitors.
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Affiliation(s)
- Yunke Wang
- Biomolecular
Sciences Institute, Department of Chemistry & Biochemistry, and Enviromental
and Occupational Health, Robert Stempel College of Public Health &
Social Work, Florida International University, Miami, Florida 33199, United States
- School
of Life Sciences, Nanjing University, Nanjing, Jiangsu Province 210023, P. R. China
| | - Samantha Rakela
- Biomolecular
Sciences Institute, Department of Chemistry & Biochemistry, and Enviromental
and Occupational Health, Robert Stempel College of Public Health &
Social Work, Florida International University, Miami, Florida 33199, United States
| | - Jeremy W. Chambers
- Biomolecular
Sciences Institute, Department of Chemistry & Biochemistry, and Enviromental
and Occupational Health, Robert Stempel College of Public Health &
Social Work, Florida International University, Miami, Florida 33199, United States
| | - Zi-Chun Hua
- School
of Life Sciences, Nanjing University, Nanjing, Jiangsu Province 210023, P. R. China
- Changzhou
High-Tech Research Institute of Nanjing University and Jiangsu TargetPharma
Laboratories Inc., Changzhou, Jiangsu 213164, P. R. China
| | - Mark T. Muller
- TopoGEN,
Inc., Buena Vista, Colorado 81211, United
States
| | - John L. Nitiss
- Pharmaceutical
Sciences Department, College of Pharmacy at Rockford, University of Illinois at Chicago, 1601 Parkview Avenue, N310, Rockford, Illinois 61107, United States
| | - Yuk-Ching Tse-Dinh
- Biomolecular
Sciences Institute, Department of Chemistry & Biochemistry, and Enviromental
and Occupational Health, Robert Stempel College of Public Health &
Social Work, Florida International University, Miami, Florida 33199, United States
| | - Fenfei Leng
- Biomolecular
Sciences Institute, Department of Chemistry & Biochemistry, and Enviromental
and Occupational Health, Robert Stempel College of Public Health &
Social Work, Florida International University, Miami, Florida 33199, United States
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7
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Kim SH, Ganji M, Kim E, van der Torre J, Abbondanzieri E, Dekker C. DNA sequence encodes the position of DNA supercoils. eLife 2018; 7:e36557. [PMID: 30523779 PMCID: PMC6301789 DOI: 10.7554/elife.36557] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022] Open
Abstract
The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes (extended intertwined DNA structures formed upon supercoiling) on individual DNA molecules. Remarkably, our experiments show that the DNA sequence directly encodes the structure of supercoiled DNA by pinning plectonemes at specific sequences. We develop a physical model that predicts that sequence-dependent intrinsic curvature is the key determinant of pinning strength and demonstrate this simple model provides very good agreement with the data. Analysis of several prokaryotic genomes indicates that plectonemes localize directly upstream of promoters, which we experimentally confirm for selected promotor sequences. Our findings reveal a hidden code in the genome that helps to spatially organize the chromosomal DNA.
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Affiliation(s)
- Sung Hyun Kim
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Mahipal Ganji
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Eugene Kim
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Jaco van der Torre
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Elio Abbondanzieri
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
| | - Cees Dekker
- Department of BionanoscienceKavli Institute of Nanoscience, Delft University of TechnologyDelftThe Netherlands
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8
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Seol Y, Neuman KC. Combined Magnetic Tweezers and Micro-mirror Total Internal Reflection Fluorescence Microscope for Single-Molecule Manipulation and Visualization. Methods Mol Biol 2018; 1665:297-316. [PMID: 28940076 PMCID: PMC5672814 DOI: 10.1007/978-1-4939-7271-5_16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Magnetic tweezers is a versatile yet simple single-molecule manipulation technique that has been used to study a broad range of nucleic acids and nucleic acid-based molecular motors. In this chapter, we combine micro-mirror-based total internal reflection microscopy with a magnetic tweezers instrument, permitting simultaneous single-molecule visualization and mechanical manipulation. We provide a simple method to calibrate the evanescent wave penetration depth via supercoiling of DNA with a fluorescent nanodiamond-labeled magnetic bead and a complementary method employing a surface-immobilized fluorescent nanodiamond.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Room 3517, 50 South Drive, Bethesda, 20892, MD, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Room 3517, 50 South Drive, Bethesda, 20892, MD, USA.
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9
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Abstract
Chemogenomics is a comparatively nascent branch dealing with the effects of drugs and chemicals on molecular level systems. With the emergence of this new epoch, the quantity of data sources is also unprecedentedly increasing. Despite having a plethora of a databases, the variation in bioactivity measurement as well as bias toward specific protein studies, varied computational procedures and redundant information make data mining tedious, especially for newcomers in the field. In this chapter, we give an overview of hands-on data collection and domains of applicability from some useful Web-based chemogenomic resources that are accessible with nothing more than a Web browser. This overview can help assist users in acquiring chemogenomic datasets for their project at hand.
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Affiliation(s)
- Rasel Al Mahmud
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Rifat Ara Najnin
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
| | - Ahsan Habib Polash
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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10
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Seol Y, Neuman KC. The dynamic interplay between DNA topoisomerases and DNA topology. Biophys Rev 2016; 8:101-111. [PMID: 28510219 DOI: 10.1007/s12551-016-0240-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/07/2016] [Indexed: 01/03/2023] Open
Abstract
Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, 50 South Dr., Room 3517, Bethesda, MD, 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, 50 South Dr., Room 3517, Bethesda, MD, 20892, USA.
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11
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Abstract
Topological properties of DNA influence its structure and biochemical interactions. Within the cell DNA topology is constantly in flux. Transcription and other essential processes including DNA replication and repair, alter the topology of the genome, while introducing additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases, is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that established the fundamental mechanistic basis of topoisomerase activity, the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases have begun to be explored. In this review we survey established and emerging DNA topology dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD, 20892, U.S.A
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD, 20892, U.S.A
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12
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von Hippel PH, Johnson NP, Marcus AH. Fifty years of DNA "breathing": Reflections on old and new approaches. Biopolymers 2016; 99:923-54. [PMID: 23840028 DOI: 10.1002/bip.22347] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 07/02/2013] [Indexed: 12/20/2022]
Abstract
The coding sequences for genes, and much other regulatory information involved in genome expression, are located 'inside' the DNA duplex. Thus the "macromolecular machines" that read-out this information from the base sequence of the DNA must somehow access the DNA "interior." Double-stranded (ds) DNA is a highly structured and cooperatively stabilized system at physiological temperatures, but is also only marginally stable and undergoes a cooperative "melting phase transition" at temperatures not far above physiological. Furthermore, due to its length and heterogeneous sequence, with AT-rich segments being less stable than GC-rich segments, the DNA genome 'melts' in a multistate fashion. Therefore the DNA genome must also manifest thermally driven structural ("breathing") fluctuations at physiological temperatures that should reflect the heterogeneity of the dsDNA stability near the melting temperature. Thus many of the breathing fluctuations of dsDNA are likely also to be sequence dependent, and could well contain information that should be "readable" and useable by regulatory proteins and protein complexes in site-specific binding reactions involving dsDNA "opening." Our laboratory has been involved in studying the breathing fluctuations of duplex DNA for about 50 years. In this "Reflections" article we present a relatively chronological overview of these studies, starting with the use of simple chemical probes (such as hydrogen exchange, formaldehyde, and simple DNA "melting" proteins) to examine the local stability of the dsDNA structure, and culminating in sophisticated spectroscopic approaches that can be used to monitor the breathing-dependent interactions of regulatory complexes with their duplex DNA targets in "real time."
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Affiliation(s)
- Peter H von Hippel
- Institute of Molecular Biology, University of Oregon, Eugene, OR, 97403; Department of Chemistry, University of Oregon, Eugene, OR, 97403
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13
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The Effect of Dimethyl Sulfoxide on Supercoiled DNA Relaxation Catalyzed by Type I Topoisomerases. BIOMED RESEARCH INTERNATIONAL 2015; 2015:320490. [PMID: 26682217 PMCID: PMC4670693 DOI: 10.1155/2015/320490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/26/2015] [Accepted: 11/01/2015] [Indexed: 11/30/2022]
Abstract
The effects of dimethyl sulfoxide (DMSO) on supercoiled plasmid DNA relaxation catalyzed by two typical type I topoisomerases were investigated in our studies. It is shown that DMSO in a low concentration (less than 20%, v/v) can induce a dose-related enhancement of the relaxation efficiency of Escherichia coli topoisomerase I (type IA). Conversely, obvious inhibitory effect on the activity of calf thymus topoisomerase I (type IB) was observed when the same concentration of DMSO is used. In addition, our studies demonstrate that 20% DMSO has an ability to reduce the inhibitory effect on EcTopo I, which was induced by double-stranded oligodeoxyribonucleotides while the same effect cannot be found in the case of CtTopo I. Moreover, our AFM examinations suggested that DMSO can change the conformation of negatively supercoiled plasmid by creating some locally loose regions in DNA molecules. Combining all the lines of evidence, we proposed that DMSO enhanced EcTopo I relaxation activity by (1) increasing the single-stranded DNA regions for the activities of EcTopo I in the early and middle stages of the reaction and (2) preventing the formation of double-stranded DNA-enzyme complex in the later stage, which can elevate the effective concentration of the topoisomerase in the reaction solution.
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14
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Seol Y, Zhang H, Agama K, Lorence N, Pommier Y, Neuman KC. Single-Molecule Supercoil Relaxation Assay as a Screening Tool to Determine the Mechanism and Efficacy of Human Topoisomerase IB Inhibitors. Mol Cancer Ther 2015; 14:2552-9. [PMID: 26351326 PMCID: PMC4636450 DOI: 10.1158/1535-7163.mct-15-0454] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/27/2015] [Indexed: 11/16/2022]
Abstract
Human nuclear type IB topoisomerase (Top1) inhibitors are widely used and powerful anticancer agents. In this study, we introduce and validate a single-molecule supercoil relaxation assay as a molecular pharmacology tool for characterizing therapeutically relevant Top1 inhibitors. Using this assay, we determined the effects on Top1 supercoil relaxation activity of four Top1 inhibitors; three clinically relevant: camptothecin, LMP-400, LMP-776 (both indenoisoquinoline derivatives), and one natural product in preclinical development, lamellarin-D. Our results demonstrate that Top1 inhibitors have two distinct effects on Top1 activity: a decrease in supercoil relaxation rate and an increase in religation inhibition. The type and magnitude of the inhibition mode depend both on the specific inhibitor and on the topology of the DNA substrate. In general, the efficacy of inhibition is significantly higher with supercoiled than with relaxed DNA substrates. Comparing single-molecule inhibition with cell growth inhibition (IC50) measurements showed a correlation between the binding time of the Top1 inhibitors and their cytotoxic efficacy, independent of the mode of inhibition. This study demonstrates that the single-molecule supercoil relaxation assay is a sensitive method to elucidate the detailed mechanisms of Top1 inhibitors and is relevant for the cellular efficacy of Top1 inhibitors.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, Maryland
| | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Keli Agama
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Nicholas Lorence
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, Maryland.
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15
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Desbois N, Pertuit D, Moretto J, Cachia C, Chauffert B, Bouyer F. cis-Dichloroplatinum(II) complexes tethered to dibenzo[c,h][1,6]naphthyridin-6-ones: Synthesis and cytotoxicity in human cancer cell lines in vitro. Eur J Med Chem 2013; 69:719-27. [DOI: 10.1016/j.ejmech.2013.09.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 09/10/2013] [Accepted: 09/16/2013] [Indexed: 12/22/2022]
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16
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Paik DH, Roskens VA, Perkins TT. Torsionally constrained DNA for single-molecule assays: an efficient, ligation-free method. Nucleic Acids Res 2013; 41:e179. [PMID: 23935118 PMCID: PMC3799452 DOI: 10.1093/nar/gkt699] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Controlled twisting of individual, double-stranded DNA molecules provides a unique method to investigate the enzymes that alter DNA topology. Such twisting requires a single DNA molecule to be torsionally constrained. This constraint is achieved by anchoring the opposite ends of the DNA to two separate surfaces via multiple bonds. The traditional protocol for making such DNA involves a three-way ligation followed by gel purification, a laborious process that often leads to low yield both in the amount of DNA and the fraction of molecules that is torsionally constrained. We developed a simple ligation-free procedure for making torsionally constrained DNA via polymerase chain reaction (PCR). This PCR protocol used two 'megaprimers', 400-base-pair long double-stranded DNA that were labelled with either biotin or digoxigenin. We obtained a relatively high yield of gel-purified DNA (∼500 ng/100 µl of PCR reaction). The final construct in this PCR-based method contains only one labelled strand in contrast to the traditional construct in which both strands of the DNA are labelled. Nonetheless, we achieved a high yield (84%) of torsionally constrained DNA when measured using an optical-trap-based DNA-overstretching assay. This protocol significantly simplifies the application and adoption of torsionally constrained assays to a wide range of single-molecule systems.
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Affiliation(s)
- D Hern Paik
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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17
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Seol Y, Gentry AC, Osheroff N, Neuman KC. Chiral discrimination and writhe-dependent relaxation mechanism of human topoisomerase IIα. J Biol Chem 2013; 288:13695-703. [PMID: 23508957 PMCID: PMC3650406 DOI: 10.1074/jbc.m112.444745] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/04/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Human topoisomerase IIα unlinks catenated chromosomes and preferentially relaxes positive supercoils. RESULTS Supercoil chirality, twist density, and tension determine topoisomerase IIα relaxation rate and processivity. CONCLUSION Strand passage rate is determined by the efficiency of transfer segment capture that is modulated by the topoisomerase C-terminal domains. SIGNIFICANCE Single-molecule measurements reveal the mechanism of chiral discrimination and tension dependence of supercoil relaxation by human topoisomerase IIα. Type IIA topoisomerases (Topo IIA) are essential enzymes that relax DNA supercoils and remove links joining replicated chromosomes. Human topoisomerase IIα (htopo IIα), one of two human isoforms, preferentially relaxes positive supercoils, a feature shared with Escherichia coli topoisomerase IV (Topo IV). The mechanistic basis of this chiral discrimination remains unresolved. To address this important issue, we measured the relaxation of individual supercoiled and "braided" DNA molecules by htopo IIα using a magnetic tweezers-based single-molecule assay. Our study confirmed the chiral discrimination activity of htopo IIα and revealed that the strand passage rate depends on DNA twist, tension on the DNA, and the C-terminal domain (CTD). Similar to Topo IV, chiral discrimination by htopo IIα results from chiral interactions of the CTDs with DNA writhe. In contrast to Topo IV, however, these interactions lead to chiral differences in relaxation rate rather than processivity. Increasing tension or twist disrupts the CTD-DNA interactions with a subsequent loss of chiral discrimination. Together, these results suggest that transfer segment (T-segment) capture is the rate-limiting step in the strand passage cycle. We propose a model for T-segment capture that provides a mechanistic basis for chiral discrimination and provides a coherent explanation for the effects of DNA twist and tension on eukaryotic type IIA topoisomerases.
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Affiliation(s)
- Yeonee Seol
- From the Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Amanda C. Gentry
- the Departments of Biochemistry and Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Neil Osheroff
- the Departments of Biochemistry and Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Keir C. Neuman
- From the Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892 and
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18
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Narros A, Moreno AJ, Likos CN. Effects of Knots on Ring Polymers in Solvents of Varying Quality. Macromolecules 2013; 46:3654-3668. [PMID: 23729865 PMCID: PMC3667624 DOI: 10.1021/ma400308x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 04/03/2013] [Indexed: 11/30/2022]
Abstract
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We employ extensive computer simulations to investigate the conformations
and the interactions of ring polymers under conditions of worsening
solvent quality, in comparison with those for linear polymers. We
determine the dependence of the Θ-temperature on knotedness
by considering ring polymers of different topologies. We establish
a clear decrease of the former upon changing the topology of the polymer
from linear to an unknotted ring and a further decrease of the same
upon introducing trefoil- or 5-fold knots but we find no difference
in the Θ-point between the two knotted molecules. Our results
are based on two independent methods: one considering the scaling
of the gyration radius with molecular weight and one based on the
dependence of the effective interaction on solvent quality. In addition,
we calculate several shape-parameters of the polymers to characterize
linear, unknotted, and knotted topologies in good solvents and in
the proximity of the Θ-point. The shape parameters of the knotted
molecules show an interesting crossover at a degree of polymerization
that depends on the degree of knottedness of the molecule.
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Affiliation(s)
- Arturo Narros
- Faculty of Physics, University of Vienna , Boltzmanngasse 5, A- 1090 Vienna, Austria
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19
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Abstract
In the present article, we review recent computational investigations on the properties of ring polymers in solution. In particular, we focus on effective interactions obtained by means of coarse-graining techniques. We discuss the relative importance of the self-avoidance and the topological contributions in the qualitative features of the effective potential. We extend our previous results on identical rings and determine the effective potential between dissimilar ring polymers of distinct topology and size. The results obtained reveal the dramatic effects of the specific topology on the effective interactions, and hence in the structural correlations, of polymeric systems.
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20
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Seol Y, Hardin AH, Strub MP, Charvin G, Neuman KC. Comparison of DNA decatenation by Escherichia coli topoisomerase IV and topoisomerase III: implications for non-equilibrium topology simplification. Nucleic Acids Res 2013; 41:4640-9. [PMID: 23460205 PMCID: PMC3632123 DOI: 10.1093/nar/gkt136] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Type II topoisomerases are essential enzymes that regulate DNA topology through a strand-passage mechanism. Some type II topoisomerases relax supercoils, unknot and decatenate DNA to below thermodynamic equilibrium. Several models of this non-equilibrium topology simplification phenomenon have been proposed. The kinetic proofreading (KPR) model postulates that strand passage requires a DNA-bound topoisomerase to collide twice in rapid succession with a second DNA segment, implying a quadratic relationship between DNA collision frequency and relaxation rate. To test this model, we used a single-molecule assay to measure the unlinking rate as a function of DNA collision frequency for Escherichia coli topoisomerase IV (topo IV) that displays efficient non-equilibrium topology simplification activity, and for E. coli topoisomerase III (topo III), a type IA topoisomerase that unlinks and unknots DNA to equilibrium levels. Contrary to the predictions of the KPR model, topo IV and topo III unlinking rates were linearly related to the DNA collision frequency. Furthermore, topo III exhibited decatenation activity comparable with that of topo IV, supporting proposed roles for topo III in DNA segregation. This study enables us to rule out the KPR model for non-equilibrium topology simplification. More generally, we establish an experimental approach to systematically control DNA collision frequency.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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21
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A kinetic clutch governs religation by type IB topoisomerases and determines camptothecin sensitivity. Proc Natl Acad Sci U S A 2012; 109:16125-30. [PMID: 22991469 DOI: 10.1073/pnas.1206480109] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Type IB topoisomerases (Top1Bs) relax excessive DNA supercoiling associated with replication and transcription by catalyzing a transient nick in one strand to permit controlled rotation of the DNA about the intact strand. The natural compound camptothecin (CPT) and the cancer chemotherapeutics derived from it, irinotecan and topotecan, are highly specific inhibitors of human nuclear Top1B (nTop1). Previous work on vaccinia Top1B led to an elegant model that describes a straightforward dependence of rotation and religation on the torque caused by supercoiling. Here, we used a single-molecule DNA supercoil relaxation assay to measure the torque dependence of nTop1 and its inhibition by CPT. For comparison, we also examined mitochondrial Top1B and an N-terminal deletion mutant of nTop1. Despite substantial sequence homology in their core domains, nTop1 and mitochondrial Top1B exhibit dramatic differences in sensitivity to torque and CPT, with the N-terminal deletion mutant of nTop1 showing intermediate characteristics. In particular, nTop1 displays nearly torque-independent religation probability, distinguishing it from other Top1B enzymes studied to date. Kinetic modeling reveals a hitherto unobserved torque-independent transition linking the DNA rotation and religation phases of the enzymatic cycle. The parameters of this transition determine the torque sensitivity of religation and the efficiency of CPT binding. This "kinetic clutch" mechanism explains the molecular basis of CPT sensitivity and more generally provides a framework with which to interpret Top1B activity and inhibition.
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22
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[The discussion of the infiltrative model of mathematical knowledge to genetics teaching]. YI CHUAN = HEREDITAS 2011; 33:1279-82. [PMID: 22120086 DOI: 10.3724/sp.j.1005.2011.01279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genetics, the core course of biological field, is an importance major-basic course in curriculum of many majors related with biology. Due to strong theoretical and practical as well as abstract of genetics, it is too difficult to study on genetics for many students. At the same time, mathematics is one of the basic courses in curriculum of the major related natural science, which has close relationship with the establishment, development and modification of genetics. In this paper, to establish the intrinsic logistic relationship and construct the integral knowledge network and to help students improving the analytic, comprehensive and logistic abilities, we applied some mathematical infiltrative model genetic knowledge in genetics teaching, which could help students more deeply learn and understand genetic knowledge.
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Claridge SA, Schwartz JJ, Weiss PS. Electrons, photons, and force: quantitative single-molecule measurements from physics to biology. ACS NANO 2011; 5:693-729. [PMID: 21338175 PMCID: PMC3043607 DOI: 10.1021/nn103298x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 01/10/2011] [Indexed: 05/19/2023]
Abstract
Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution.
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Affiliation(s)
| | | | - Paul S. Weiss
- California NanoSystems Institute
- Department of Chemistry and Biochemistry
- Department of Materials Science and Engineering
- Address correspondence to
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24
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Abstract
Magnetic tweezers provide a versatile tool enabling the precise application of force and torque on -individual biomolecules. These properties make magnetic tweezers uniquely suited for the study of DNA topology and topoisomerases at the single-molecule level. Single-molecule approaches, which are complementary to ensemble biochemical and structural approaches, have provided remarkable insights into the mechanisms of topoisomerase activity and interactions with DNA. Here, we describe how to make single-molecule measurements of topoisomerase activity with a magnetic tweezers instrument. We provide detailed instructions for preparing and characterizing DNA substrates, flow cells, and supercoilable DNA tethers. We then describe magnetic tweezers measurements of supercoil relaxation by single topoisomerases.
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