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Shepherd JW, Guilbaud S, Zhou Z, Howard JAL, Burman M, Schaefer C, Kerrigan A, Steele-King C, Noy A, Leake MC. Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA. Nat Commun 2024; 15:2748. [PMID: 38553446 PMCID: PMC10980717 DOI: 10.1038/s41467-024-47126-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 03/21/2024] [Indexed: 04/02/2024] Open
Abstract
Biopolymer topology is critical for determining interactions inside cell environments, exemplified by DNA where its response to mechanical perturbation is as important as biochemical properties to its cellular roles. The dynamic structures of chiral biopolymers exhibit complex dependence with extension and torsion, however the physical mechanisms underpinning the emergence of structural motifs upon physiological twisting and stretching are poorly understood due to technological limitations in correlating force, torque and spatial localization information. We present COMBI-Tweez (Combined Optical and Magnetic BIomolecule TWEEZers), a transformative tool that overcomes these challenges by integrating optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy, demonstrated on single DNA molecules, that can controllably form and visualise higher order structural motifs including plectonemes. This technology combined with cutting-edge MD simulations provides quantitative insight into complex dynamic structures relevant to DNA cellular processes and can be adapted to study a range of filamentous biopolymers.
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Affiliation(s)
- Jack W Shepherd
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
- Department of Biology, University of York, York, YO10 5DD, England
| | - Sebastien Guilbaud
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Zhaokun Zhou
- Guangdong Provincial Key Lab of Robotics and Intelligent System, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jamieson A L Howard
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Matthew Burman
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Charley Schaefer
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Adam Kerrigan
- The York-JEOL Nanocentre, University of York, York, YO10 5BR, England
| | - Clare Steele-King
- Bioscience Technology Facility, University of York, York, YO10 5DD, England
| | - Agnes Noy
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Mark C Leake
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England.
- Department of Biology, University of York, York, YO10 5DD, England.
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2
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Wilkinson M, Wilkinson OJ, Feyerherm C, Fletcher EE, Wigley DB, Dillingham MS. Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub. eLife 2022; 11:e83409. [PMID: 36533901 PMCID: PMC9836394 DOI: 10.7554/elife.83409] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/18/2022] [Indexed: 12/23/2022] Open
Abstract
Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, we present biochemical and structural analysis of two phage proteins, gp5.9 and Abc2, which target the DNA break resection complex RecBCD. These exemplify two contrasting mechanisms for control of DNA break repair in which the RecBCD complex is either inhibited or co-opted for the benefit of the invading phage. Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site. Gp5.9 adopts a parallel coiled-coil architecture that is unprecedented for a natural DNA mimic protein. In contrast, binding of Abc2 does not substantially affect the biochemical activities of isolated RecBCD. The RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products.
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Affiliation(s)
- Martin Wilkinson
- Section of Structural Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College LondonLondonUnited Kingdom
| | - Oliver J Wilkinson
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Connie Feyerherm
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Emma E Fletcher
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
| | - Dale B Wigley
- Section of Structural Biology, Department of Infectious Disease, Faculty of Medicine, Imperial College LondonLondonUnited Kingdom
| | - Mark S Dillingham
- DNA:protein Interactions Unit, School of Biochemistry, University of BristolBristolUnited Kingdom
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3
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Yadav S, Senapati S, Kumar S, Gahlaut SK, Singh JP. GLAD Based Advanced Nanostructures for Diversified Biosensing Applications: Recent Progress. BIOSENSORS 2022; 12:1115. [PMID: 36551082 PMCID: PMC9775079 DOI: 10.3390/bios12121115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Glancing angle deposition (GLAD) is a technique for the fabrication of sculpted micro- and nanostructures under the conditions of oblique vapor flux incident and limited adatom diffusion. GLAD-based nanostructures are emerging platforms with broad sensing applications due to their high sensitivity, enhanced optical and catalytic properties, periodicity, and controlled morphology. GLAD-fabricated nanochips and substrates for chemical and biosensing applications are replacing conventionally used nanomaterials due to their broad scope, ease of fabrication, controlled growth parameters, and hence, sensing abilities. This review focuses on recent advances in the diverse nanostructures fabricated via GLAD and their applications in the biomedical field. The effects of morphology and deposition conditions on GLAD structures, their biosensing capability, and the use of these nanostructures for various biosensing applications such as surface plasmon resonance (SPR), fluorescence, surface-enhanced Raman spectroscopy (SERS), and colorimetric- and wettability-based bio-detection will be discussed in detail. GLAD has also found diverse applications in the case of molecular imaging techniques such as fluorescence, super-resolution, and photoacoustic imaging. In addition, some in vivo applications, such as drug delivery, have been discussed. Furthermore, we will also provide an overview of the status of GLAD technology as well as future challenges associated with GLAD-based nanostructures in the mentioned areas.
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Affiliation(s)
- Sarjana Yadav
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Sneha Senapati
- School of Interdisciplinary Research, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Samir Kumar
- Department of Electronics and Information Engineering, Korea University, Sejong 30019, Republic of Korea
| | - Shashank K. Gahlaut
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Jitendra P. Singh
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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4
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Ozaslan D, Byrd AK, Belachew B, Raney KD. Alignment of helicases on single-stranded DNA increases activity. Methods Enzymol 2022; 672:29-54. [PMID: 35934480 PMCID: PMC9421817 DOI: 10.1016/bs.mie.2022.03.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Helicases function in most biological processes that utilize RNA or DNA nucleic acids including replication, recombination, repair, transcription, splicing, and translation. They are motor proteins that bind ATP and then catalyze hydrolysis to release energy which is transduced for conformational changes. Different conformations correspond to different steps in a process that results in movement of the enzyme along the nucleic acid track in a unidirectional manner. Some helicases such as DEAD-box helicases do not translocate, but these enzymes transduce chemical energy from ATP hydrolysis to unwind secondary structure in DNA or RNA. Some helicases function as monomers while others assemble into defined structures, either dimers or higher order oligomers. Dda helicase from bacteriophage T4 and NS3 helicase domain from the hepatitis C virus are examples of monomeric helicases. These helicases can bind to single-stranded DNA in a manner that appears like train engines on a track. When monomeric helicases align on DNA, the activity of the enzymes increases. Helicase activity can include the rate of duplex unwinding and the total number of base pairs melted during a single binding event or processivity. Dda and NS3h are considered as having low processivity, unwinding fewer than 50 base pairs per binding event. Here, we report fusing two molecules of NS3h molecules together through genetically linking the C-terminus of one molecule to the N-terminus of a second NS3h molecule. We observed increased processivity relative to NS3h possibly arising from the increased probability that at least one of the helicases will completely unwind the DNA prior to dissociation. The dimeric enzyme also binds DNA more like the full-length NS3 helicase. Finally, the dimer can displace streptavidin from biotin-labeled oligonucleotide, whereas monomeric NS3h cannot.
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Affiliation(s)
- Deniz Ozaslan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
| | - Binyam Belachew
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
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5
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Bianco PR. Insight into the biochemical mechanism of DNA helicases provided by bulk-phase and single-molecule assays. Methods 2021; 204:348-360. [PMID: 34896247 PMCID: PMC9534331 DOI: 10.1016/j.ymeth.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022] Open
Abstract
There are multiple assays available that can provide insight into the biochemical mechanism of DNA helicases. For the first 22 years since their discovery, bulk-phase assays were used. These include gel-based, spectrophotometric, and spectrofluorometric assays that revealed many facets of these enzymes. From 2001, single-molecule studies have contributed additional insight into these DNA nanomachines to reveal details on energy coupling, step size, processivity as well as unique aspects of individual enzyme behavior that were masked in the averaging inherent in ensemble studies. In this review, important aspects of the study of helicases are discussed including beginning with active, nuclease-free enzyme, followed by several bulk-phase approaches that have been developed and still find widespread use today. Finally, two single-molecule approaches are discussed, and the resulting findings are related to the results obtained in bulk-phase studies.
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Affiliation(s)
- Piero R Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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6
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Ravi Kumara GS, Seo YJ. Polymerase-mediated synthesis of p-vinylaniline-coupled fluorescent DNA for the sensing of nucleolin protein- c-myc G-quadruplex interactions. Org Biomol Chem 2021; 19:5788-5793. [PMID: 34085078 DOI: 10.1039/d1ob00863c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this paper we report the synthesis of two deoxyuridine derivatives (dUCN2, dUPy)-featuring p-vinylaniline-based fluorophores linked through a propargyl unit at the 5' position-that function as molecular rotors. This probing system proved to be useful for the sensing of gene regulation arising from interactions between this G-quadruplex and nucleolin.
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Affiliation(s)
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea.
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7
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Dos Santos Á, Fili N, Pearson DS, Hari-Gupta Y, Toseland CP. High-throughput mechanobiology: Force modulation of ensemble biochemical and cell-based assays. Biophys J 2021; 120:631-641. [PMID: 33453266 PMCID: PMC7896026 DOI: 10.1016/j.bpj.2020.12.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/25/2020] [Accepted: 12/17/2020] [Indexed: 11/27/2022] Open
Abstract
Mechanobiology is focused on how the physical forces and mechanical properties of proteins, cells, and tissues contribute to physiology and disease. Although the response of proteins and cells to mechanical stimuli is critical for function, the tools to probe these activities are typically restricted to single-molecule manipulations. Here, we have developed a novel microplate reader assay to encompass mechanical measurements with ensemble biochemical and cellular assays, using a microplate lid modified with magnets. This configuration enables multiple static magnetic tweezers to function simultaneously across the microplate, thereby greatly increasing throughput. We demonstrate the broad applicability and versatility through in vitro and in cellulo approaches. Overall, our methodology allows, for the first time (to our knowledge), ensemble biochemical and cell-based assays to be performed under force in high-throughput format. This approach substantially increases the availability of mechanobiology measurements.
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Affiliation(s)
- Ália Dos Santos
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Natalia Fili
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - David S Pearson
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Yukti Hari-Gupta
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Christopher P Toseland
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom.
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8
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Phase separation by ssDNA binding protein controlled via protein-protein and protein-DNA interactions. Proc Natl Acad Sci U S A 2020; 117:26206-26217. [PMID: 33020264 PMCID: PMC7584906 DOI: 10.1073/pnas.2000761117] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cells must rapidly and efficiently react to DNA damage to avoid its harmful consequences. Here we report a molecular mechanism that gives rise to a model of how bacterial cells mobilize DNA repair proteins for timely response to genomic stress and initiation of DNA repair upon exposure of single-stranded DNA. We found that bacterial single-stranded DNA binding protein (SSB), a central player in genome metabolism, can undergo dynamic phase separation under physiological conditions. SSB condensates can store a wide array of DNA repair proteins that specifically interact with SSB. However, elevated levels of single-stranded DNA during genomic stress can dissolve SSB condensates, enabling rapid mobilization of SSB and SSB-interacting proteins to sites of DNA damage. Bacterial single-stranded (ss)DNA-binding proteins (SSB) are essential for the replication and maintenance of the genome. SSBs share a conserved ssDNA-binding domain, a less conserved intrinsically disordered linker (IDL), and a highly conserved C-terminal peptide (CTP) motif that mediates a wide array of protein−protein interactions with DNA-metabolizing proteins. Here we show that the Escherichia coli SSB protein forms liquid−liquid phase-separated condensates in cellular-like conditions through multifaceted interactions involving all structural regions of the protein. SSB, ssDNA, and SSB-interacting molecules are highly concentrated within the condensates, whereas phase separation is overall regulated by the stoichiometry of SSB and ssDNA. Together with recent results on subcellular SSB localization patterns, our results point to a conserved mechanism by which bacterial cells store a pool of SSB and SSB-interacting proteins. Dynamic phase separation enables rapid mobilization of this protein pool to protect exposed ssDNA and repair genomic loci affected by DNA damage.
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9
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Wilkinson OJ, Carrasco C, Aicart-Ramos C, Moreno-Herrero F, Dillingham MS. Bulk and single-molecule analysis of a bacterial DNA2-like helicase-nuclease reveals a single-stranded DNA looping motor. Nucleic Acids Res 2020; 48:7991-8005. [PMID: 32621607 PMCID: PMC7430649 DOI: 10.1093/nar/gkaa562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/12/2020] [Accepted: 06/19/2020] [Indexed: 11/14/2022] Open
Abstract
DNA2 is an essential enzyme involved in DNA replication and repair in eukaryotes. In a search for homologues of this protein, we identified and characterised Geobacillus stearothermophilus Bad, a bacterial DNA helicase-nuclease with similarity to human DNA2. We show that Bad contains an Fe-S cluster and identify four cysteine residues that are likely to co-ordinate the cluster by analogy to DNA2. The purified enzyme specifically recognises ss-dsDNA junctions and possesses ssDNA-dependent ATPase, ssDNA binding, ssDNA endonuclease, 5' to 3' ssDNA translocase and 5' to 3' helicase activity. Single molecule analysis reveals that Bad is a processive DNA motor capable of moving along DNA for distances of >4 kb at a rate of ∼200 bp per second at room temperature. Interestingly, as reported for the homologous human and yeast DNA2 proteins, the DNA unwinding activity of Bad is cryptic and can be unmasked by inactivating the intrinsic nuclease activity. Strikingly, our experiments show that the enzyme loops DNA while translocating, which is an emerging feature of processive DNA unwinding enzymes. The bacterial Bad enzymes will provide an excellent model system for understanding the biochemical properties of DNA2-like helicase-nucleases and DNA looping motor proteins in general.
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Affiliation(s)
- Oliver J Wilkinson
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Carolina Carrasco
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Mark S Dillingham
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
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10
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Kumari S, Halder S, Aggrawal R, Sundar G, Saha SK. Effect of gemini surfactants on binding interactions of Coumarin 485 with calf thymus deoxyribonucleic acid in presence of nanotubes of β-cyclodextrin. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Chisty LT, Quaglia D, Webb MR. Fluorescent single-stranded DNA-binding protein from Plasmodium falciparum as a biosensor for single-stranded DNA. PLoS One 2018; 13:e0193272. [PMID: 29466468 PMCID: PMC5821389 DOI: 10.1371/journal.pone.0193272] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/07/2018] [Indexed: 11/30/2022] Open
Abstract
Single-stranded DNA (ssDNA) is a product of many cellular processes that involve double-stranded DNA, for example during DNA replication and repair, and is formed transiently in many others. Measurement of ssDNA formation is fundamental for understanding many such processes. The availability of a fluorescent biosensor for the determination of single-stranded DNA provides an important route to achieve this. Single-stranded DNA binding proteins (SSBs) protect ssDNA from degradation, but can be displaced to allow processing of the ssDNA. Their tight binding of ssDNA means that they are very good candidates for the development of a biosensor. Previously, the single stranded DNA binding protein from Escherichia coli, labeled with a fluorophore, (DCC-EcSSB) was developed and used for this purpose. However, the multiple binding modes of this protein meant that interpretation of DCC-EcSSB fluorescence was potentially complex in terms of determining the amount of ssDNA. Here, we present an improved biosensor, developed using the tetrameric SSB from Plasmodium falciparum as a new scaffold for fluorophore attachment. Each subunit of this tetrameric SSB was labeled with a diethylaminocoumarin fluorophore at a single site on its surface, such that there is a very large, 20-fold, fluorescence increase when it binds to ssDNA. This adduct can be used as a biosensor to report ssDNA formation. Because SSB from this organism has a single mode of binding ssDNA, namely 65-70 bases per tetramer, over a wide range of conditions, the fluorescent SSB allows simple quantitation of ssDNA. The binding is fast, possibly diffusion controlled, and tight (dissociation constant for DCC-PfSSB <5 pM). Its suitability for real-time assays of ssDNA formation was demonstrated by measurement of AddAB helicase activity, unwinding double-stranded DNA.
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12
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Cook A, Hari-Gupta Y, Toseland CP. Application of the SSB biosensor to study in vitro transcription. Biochem Biophys Res Commun 2018; 496:820-825. [PMID: 29378185 PMCID: PMC5811048 DOI: 10.1016/j.bbrc.2018.01.147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 01/24/2018] [Indexed: 01/09/2023]
Abstract
Gene expression, catalysed by RNA polymerases (RNAP), is one of the most fundamental processes in living cells. The majority of methods to quantify mRNA are based upon purification of the nucleic acid which leads to experimental inaccuracies and loss of product, or use of high cost dyes and sensitive spectrophotometers. Here, we describe the use of a fluorescent biosensor based upon the single stranded binding (SSB) protein. In this study, the SSB biosensor showed similar binding properties to mRNA, to that of its native substrate, single-stranded DNA (ssDNA). We found the biosensor to be reproducible with no associated loss of product through purification, or the requirement for expensive dyes. Therefore, we propose that the SSB biosensor is a useful tool for comparative measurement of mRNA yield following in vitro transcription. Single-stranded binding protein can bind mRNA similar to single-stranded DNA. The biosensor MDCC-SSB can be used to quantify mRNA yield from in vitro transcription. Myosin VI motor activity is required for in vitro and in vivo transcription.
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Affiliation(s)
- Alexander Cook
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Yukti Hari-Gupta
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
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13
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Schweigert C, Gaß N, Wagenknecht HA, Unterreiner AN. Significant Fluorescence Enhancement ofN,N-Dimethylaminobenzophenone after Embedding as a C-Nucleoside in DNA. CHEMPHOTOCHEM 2017. [DOI: 10.1002/cptc.201700183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Caroline Schweigert
- Institute of Physical Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 2 76131 Karlsruhe Germany
| | - Nadine Gaß
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Andreas-Neil Unterreiner
- Institute of Physical Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 2 76131 Karlsruhe Germany
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14
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Mills M, Harami GM, Seol Y, Gyimesi M, Martina M, Kovács ZJ, Kovács M, Neuman KC. RecQ helicase triggers a binding mode change in the SSB-DNA complex to efficiently initiate DNA unwinding. Nucleic Acids Res 2017; 45:11878-11890. [PMID: 29059328 PMCID: PMC5714189 DOI: 10.1093/nar/gkx939] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/29/2017] [Accepted: 10/09/2017] [Indexed: 11/12/2022] Open
Abstract
The single-stranded DNA binding protein (SSB) of Escherichia coli plays essential roles in maintaining genome integrity by sequestering ssDNA and mediating DNA processing pathways through interactions with DNA-processing enzymes. Despite its DNA-sequestering properties, SSB stimulates the DNA processing activities of some of its binding partners. One example is the genome maintenance protein RecQ helicase. Here, we determine the mechanistic details of the RecQ-SSB interaction using single-molecule magnetic tweezers and rapid kinetic experiments. Our results reveal that the SSB-RecQ interaction changes the binding mode of SSB, thereby allowing RecQ to gain access to ssDNA and facilitating DNA unwinding. Conversely, the interaction of RecQ with the SSB C-terminal tail increases the on-rate of RecQ-DNA binding and has a modest stimulatory effect on the unwinding rate of RecQ. We propose that this bidirectional communication promotes efficient DNA processing and explains how SSB stimulates rather than inhibits RecQ activity.
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Affiliation(s)
- Maria Mills
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gábor M. Harami
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Máté Gyimesi
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Máté Martina
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Zoltán J. Kovács
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Mihály Kovács
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Pavankumar TL, Exell JC, Kowalczykowski SC. Direct Fluorescent Imaging of Translocation and Unwinding by Individual DNA Helicases. Methods Enzymol 2016; 581:1-32. [PMID: 27793277 DOI: 10.1016/bs.mie.2016.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The unique translocation and DNA unwinding properties of DNA helicases can be concealed by the stochastic behavior of enzyme molecules within the necessarily large populations used in ensemble experiments. With recent technological advances, the direct visualization of helicases acting on individual DNA molecules has contributed significantly to the current understanding of their mechanisms of action and biological functions. The combination of single-molecule techniques that enable both manipulation of individual protein or DNA molecules and visualization of their actions has made it possible to literally see novel and unique biochemical characteristics that were previously masked. Here, we describe the execution and use of single-molecule fluorescence imaging techniques, focusing on methods that include optical trapping in conjunction with epifluorescent imaging, and also surface immobilization in conjunction with total internal reflection fluorescence visualization. Combined with microchannel flow cells and microfluidic control, these methods allow individual fluorescently labeled protein and DNA molecules to be imaged and tracked, affording measurement of DNA unwinding and translocation at single-molecule resolution.
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Affiliation(s)
| | - J C Exell
- University of California, Davis, CA, United States
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16
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Gyimesi M, Harami GM, Kocsis ZS, Kovács M. Recent adaptations of fluorescence techniques for the determination of mechanistic parameters of helicases and translocases. Methods 2016; 108:24-39. [PMID: 27133766 DOI: 10.1016/j.ymeth.2016.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/22/2016] [Accepted: 04/25/2016] [Indexed: 01/11/2023] Open
Abstract
Helicases and translocases are nucleic acid (NA)-based molecular motors that use the free energy liberated during the nucleoside triphosphate (NTP, usually ATP) hydrolysis cycle for unidirectional translocation along their NA (DNA, RNA or heteroduplex) substrates. Determination of the kinetic and thermodynamic parameters of their mechanoenzymatic cycle serves as a basis for the exploration of their physiological behavior and various cellular functions. Here we describe how recent adaptations of fluorescence-based solution kinetic methods can be used to determine practically all important mechanistic parameters of NA-based motor proteins. We outline practically useful analysis procedures for equilibrium, steady-state and transient kinetic data. This analysis can be used to quantitatively characterize the enzymatic steps of the NTP hydrolytic cycle, the binding site size, stoichiometry and energetics of protein-NA interactions, the rate and processivity of translocation along and unwinding of NA strands, and the mechanochemical coupling between these processes. The described methods yield insights into the functional role of the enzymes, and also greatly aid the design and interpretation of single-molecule experiments as well as the engineering of enzymatic properties for biotechnological applications.
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Affiliation(s)
- Máté Gyimesi
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary.
| | - Gábor M Harami
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary.
| | - Zsuzsa S Kocsis
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary.
| | - Mihály Kovács
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117 Budapest, Hungary.
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17
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Yu C, Tan HY, Choi M, Stanenas AJ, Byrd AK, D Raney K, Cohan CS, Bianco PR. SSB binds to the RecG and PriA helicases in vivo in the absence of DNA. Genes Cells 2016; 21:163-84. [PMID: 26766785 DOI: 10.1111/gtc.12334] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/24/2015] [Indexed: 11/27/2022]
Abstract
The E. coli single-stranded DNA-binding protein (SSB) binds to the fork DNA helicases RecG and PriA in vitro. Typically for binding to occur, 1.3 m ammonium sulfate must be present, bringing into question the validity of these results as these are nonphysiological conditions. To determine whether SSB can bind to these helicases, we examined binding in vivo. First, using fluorescence microscopy, we show that SSB localizes PriA and RecG to the vicinity of the inner membrane in the absence of DNA damage. Localization requires that SSB be in excess over the DNA helicases and the SSB C-terminus and both PriA and RecG be present. Second, using the purification of tagged complexes, our results show that SSB binds to PriA and RecG in vivo, in the absence of DNA. We propose that this may be the 'storage form' of RecG and PriA. We further propose that when forks stall, RecG and PriA are targeted to the fork by SSB, which, by virtue of its high affinity for single-stranded DNA, allows these helicases to outcompete other proteins. This ensures their actions in the early stages of the rescue of stalled replication forks.
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Affiliation(s)
- Cong Yu
- Department of Biochemistry, University at Buffalo, Buffalo, NY, 14214, USA.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA
| | - Hui Yin Tan
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA.,Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY, 14214, USA
| | - Meerim Choi
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA.,Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY, 14214, USA
| | - Adam J Stanenas
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA.,Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY, 14214, USA
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, slot 516, Little Rock, AR, 72205, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, slot 516, Little Rock, AR, 72205, USA
| | - Christopher S Cohan
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY, 14214, USA
| | - Piero R Bianco
- Department of Biochemistry, University at Buffalo, Buffalo, NY, 14214, USA.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, 14214, USA.,Center for Single Molecule Biophysics, University at Buffalo, Buffalo, NY, 14214, USA
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18
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Abstract
This article reviews atomic force microscopy (AFM) studies of DNA structure and dynamics and protein-DNA complexes, including recent advances in the visualization of protein-DNA complexes with the use of cutting-edge, high-speed AFM. Special emphasis is given to direct nanoscale visualization of dynamics of protein-DNA complexes. In the area of DNA structure and dynamics, structural studies of local non-B conformations of DNA and the interplay of local and global DNA conformations are reviewed. The application of time-lapse AFM nanoscale imaging of DNA dynamics is illustrated by studies of Holliday junction branch migration. Structure and dynamics of protein-DNA interactions include problems related to site-specific DNA recombination, DNA replication, and DNA mismatch repair. Studies involving the structure and dynamics of chromatin are also described.
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Affiliation(s)
- Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
| | - Luda S. Shlyakhtenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
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19
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Vancraenenbroeck R, Webb MR. A Fluorescent, Reagentless Biosensor for ATP, Based on Malonyl-Coenzyme A Synthetase. ACS Chem Biol 2015; 10:2650-7. [PMID: 26355992 PMCID: PMC4655421 DOI: 10.1021/acschembio.5b00346] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
A fluorescent reagentless biosensor
for ATP has been developed,
based on malonyl-coenzyme A synthetase from Rhodopseudomonas
palustris as the protein scaffold and recognition element.
Two 5-iodoacetamidotetramethylrhodamines were covalently bound to
this protein to provide the readout. This adduct couples ATP binding
to a 3.7-fold increase in fluorescence intensity with excitation at
553 nm and emission at 575 nm. It measures ATP concentrations with
micromolar sensitivity and is highly selective for ATP relative to
ADP. Its ability to monitor enzymatic ATP production or depletion
was demonstrated in steady-state kinetic assays in which ATP is a
product or substrate, respectively.
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Affiliation(s)
- Renée Vancraenenbroeck
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
| | - Martin R. Webb
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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20
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Single-molecule visualization of RecQ helicase reveals DNA melting, nucleation, and assembly are required for processive DNA unwinding. Proc Natl Acad Sci U S A 2015; 112:E6852-61. [PMID: 26540728 DOI: 10.1073/pnas.1518028112] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA helicases are motor proteins that unwind double-stranded DNA (dsDNA) to reveal single-stranded DNA (ssDNA) needed for many biological processes. The RecQ helicase is involved in repairing damage caused by DNA breaks and stalled replication forks via homologous recombination. Here, the helicase activity of RecQ was visualized on single molecules of DNA using a fluorescent sensor that directly detects ssDNA. By monitoring the formation and progression of individual unwinding forks, we observed that both the frequency of initiation and the rate of unwinding are highly dependent on RecQ concentration. We establish that unwinding forks can initiate internally by melting dsDNA and can proceed in both directions at up to 40-60 bp/s. The findings suggest that initiation requires a RecQ dimer, and that continued processive unwinding of several kilobases involves multiple monomers at the DNA unwinding fork. We propose a distinctive model wherein RecQ melts dsDNA internally to initiate unwinding and subsequently assembles at the fork into a distribution of multimeric species, each encompassing a broad distribution of rates, to unwind DNA. These studies define the species that promote resection of DNA, proofreading of homologous pairing, and migration of Holliday junctions, and they suggest that various functional forms of RecQ can be assembled that unwind at rates tailored to the diverse biological functions of RecQ helicase.
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21
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Bell JC, Liu B, Kowalczykowski SC. Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function. eLife 2015; 4:e08646. [PMID: 26381353 PMCID: PMC4652220 DOI: 10.7554/elife.08646] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/18/2015] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli single-stranded DNA (ssDNA) binding protein (SSB) is the defining bacterial member of ssDNA binding proteins essential for DNA maintenance. SSB binds ssDNA with a variable footprint of ∼30-70 nucleotides, reflecting partial or full wrapping of ssDNA around a tetramer of SSB. We directly imaged single molecules of SSB-coated ssDNA using total internal reflection fluorescence (TIRF) microscopy and observed intramolecular condensation of nucleoprotein complexes exceeding expectations based on simple wrapping transitions. We further examined this unexpected property by single-molecule force spectroscopy using magnetic tweezers. In conditions favoring complete wrapping, SSB engages in long-range reversible intramolecular interactions resulting in condensation of the SSB-ssDNA complex. RecO and RecOR, which interact with SSB, further condensed the complex. Our data support the idea that RecOR--and possibly other SSB-interacting proteins-function(s) in part to alter long-range, macroscopic interactions between or throughout nucleoprotein complexes by microscopically altering wrapping and bridging distant sites.
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Affiliation(s)
- Jason C Bell
- Graduate Group in Biochemistry and Molecular Biology, University of California, Davis, Davis, United States
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - Bian Liu
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
- Graduate Group in Biophysics, University of California, Davis, Davis, United States
| | - Stephen C Kowalczykowski
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
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22
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Chandrasekaran S, Sameena Y, Enoch IV. Tuning the binding of coumarin 6 with DNA by molecular encapsulators: effect of β-cyclodextrin and C-hexylpyrogallol[4]arene. J Mol Recognit 2015; 27:640-52. [PMID: 25277088 DOI: 10.1002/jmr.2387] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/01/2014] [Accepted: 05/01/2014] [Indexed: 01/03/2023]
Abstract
We report in this paper that the binding of coumarin 6 (C6) to DNA can be tuned by complexing it with host structures, viz. β-cyclodextrin (β-CD) and C-hexylpyrogallol-4-arene (C-HPA). Because host molecules are used as carriers of small molecules onto target sites, the exposed part of the guest molecule needs to be found out, and the relationship between the host : guest ratio and the mode of binding with the target macromolecule, that is, the DNA needs to be analyzed, in order to comprehend the preferred binding moiety and tune the binding. In this paper, the formation of the inclusion complex of C6 with β-CD and with C-HPA is studied by UV-visible, fluorescence, 2D rotating-frame nuclear Overhauser effect correlation spectroscopy and diffusion-ordered spectroscopy nuclear magnetic resonance spectra and molecular modeling. C6 forms a 1:1 complex with β-CD and a 1:2 complex with C-HPA. The studies on the protonation of C6 in the presence and the absence of the host molecules suggest that the chromone part of C6 is outside the β-CD molecule, whereas it is fully covered by C-HPA. The binding of C6 with calf thymus DNA (ctDNA) occurs through intercalation and hydrogen bonding, and the host-guest structures remain intact on binding with ctDNA. The oxygens of the C6 molecules are exposed when inside the host molecules and aid in the hydrogen bonding with DNA.
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23
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Green M, Gilhooly NS, Abedeen S, Scott DJ, Dillingham MS, Soultanas P. Engineering a reagentless biosensor for single-stranded DNA to measure real-time helicase activity in Bacillus. Biosens Bioelectron 2014; 61:579-86. [PMID: 24953846 PMCID: PMC4103019 DOI: 10.1016/j.bios.2014.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/28/2014] [Accepted: 06/03/2014] [Indexed: 10/27/2022]
Abstract
Single-stranded DNA-binding protein (SSB) is a well characterized ubiquitous and essential bacterial protein involved in almost all aspects of DNA metabolism. Using the Bacillus subtilis SSB we have generated a reagentless SSB biosensor that can be used as a helicase probe in B. subtilis and closely related gram positive bacteria. We have demonstrated the utility of the probe in a DNA unwinding reaction using a helicase from Bacillus and for the first time, characterized the B. subtilis SSB's DNA binding mode switching and stoichiometry. The importance of SSB in DNA metabolism is not limited to simply binding and protecting ssDNA during DNA replication, as previously thought. It interacts with an array of partner proteins to coordinate many different aspects of DNA metabolism. In most cases its interactions with partner proteins is species-specific and for this reason, knowing how to produce and use cognate reagentless SSB biosensors in different bacteria is critical. Here we explain how to produce a B. subtilis SSB probe that exhibits 9-fold fluorescence increase upon binding to single stranded DNA and can be used in all related gram positive firmicutes which employ drastically different DNA replication and repair systems than the widely studied Escherichia coli. The materials to produce the B. subtilis SSB probe are commercially available, so the methodology described here is widely available unlike previously published methods for the E. coli SSB.
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Affiliation(s)
- Matthew Green
- School of Chemistry, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Neville S Gilhooly
- School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Shahriar Abedeen
- School of Chemistry, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - David J Scott
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, UK
| | - Mark S Dillingham
- School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Panos Soultanas
- School of Chemistry, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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24
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The role of encapsulation by β-cyclodextrin in the interaction of raloxifene with macromolecular targets: a study by spectroscopy and molecular modeling. J Biol Phys 2014; 40:347-67. [PMID: 25073419 DOI: 10.1007/s10867-014-9355-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 05/21/2014] [Indexed: 10/25/2022] Open
Abstract
We report the binding of the drug raloxifene with Calf thymus DNA (ctDNA) and bovine serum albumin (BSA) in the presence and absence of β-cyclodextrin (β-CD) and explain the influence of β-cyclodextrin on the binding of the drug to macromolecules. UV-Vis absorption, fluorescence, proton nuclear magnetic resonance and two-dimensional rotating-frame nuclear overhauser effect spectroscopic techniques are used to study the stoichiometry and the binding strength of the complexes. Molecular modeling is used in combination with other techniques to propose the structure of the inclusion complex and the interaction with ctDNA. The Stern-Volmer quenching constants of the interaction of raloxifene with ctDNA in aqueous and in β-CD solution are compared. The competition for binding of ctDNA with raloxifene and Methylene Blue is studied. The apparent binding constant and the number of binding sites for the binding of raloxifene with BSA in aqueous solution are significantly different from those in the presence of β-CD. The influence of β-CD on the binding of the small molecules with biological macromolecules is discussed. We infer that the binding strengths between raloxifene and macromolecules, viz., ctDNA and BSA are influenced by the β-CD encapsulation. These results may suggest new ways to tune the drug binding to biomacromolecules by encapsulating specific moieties of drugs.
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25
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Host–guest association of coumarin 343 with β-cyclodextrin and C-hexylpyrogallol[4]arene: opposite fluorescent behavior and prototropic characteristics. J INCL PHENOM MACRO 2014. [DOI: 10.1007/s10847-014-0380-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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26
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Fluorescent biosensors: design and application to motor proteins. EXPERIENTIA SUPPLEMENTUM (2012) 2014; 105:25-47. [PMID: 25095989 DOI: 10.1007/978-3-0348-0856-9_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Reagentless biosensors are single molecular species that report the concentration of a specific target analyte, while having minimal impact on the system being studied. This chapter reviews such biosensors with emphasis on the ones that use fluorescence as readout and can be used for real-time assays of concentration changes with reasonably high time resolution and sensitivity. Reagentless biosensors can be designed with different types of recognition elements, particularly specific binding proteins and nucleic acids, including aptamers. Different ways are described in which a fluorescence signal can be used to report the target concentration. These include the use of single, environmentally sensitive fluorophores; FRET pairs, often used in genetically encoded biosensors; and pairs of identical fluorophores that undergo reversible stacking interactions to change fluorescence intensity. The applications of these biosensors in different types of real-time assays with motor proteins are described together with some specific examples. These encompass regulation and mechanism of motor proteins, using both steady-state assays and single-turnover measurements.
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27
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Chisty LT, Toseland CP, Fili N, Mashanov GI, Dillingham MS, Molloy JE, Webb MR. Monomeric PcrA helicase processively unwinds plasmid lengths of DNA in the presence of the initiator protein RepD. Nucleic Acids Res 2013; 41:5010-23. [PMID: 23535146 PMCID: PMC3643603 DOI: 10.1093/nar/gkt194] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The helicase PcrA unwinds DNA during asymmetric replication of plasmids, acting with an initiator protein, in our case RepD. Detailed kinetics of PcrA activity were measured using bulk solution and a single-molecule imaging technique to investigate the oligomeric state of the active helicase complex, its processivity and the mechanism of unwinding. By tethering either DNA or PcrA to a microscope coverslip surface, unwinding of both linear and natural circular plasmid DNA by PcrA/RepD was followed in real-time using total internal reflection fluorescence microscopy. Visualization was achieved using a fluorescent single-stranded DNA-binding protein. The single-molecule data show that PcrA, in combination with RepD, can unwind plasmid lengths of DNA in a single run, and that PcrA is active as a monomer. Although the average rate of unwinding was similar in single-molecule and bulk solution assays, the single-molecule experiments revealed a wide distribution of unwinding speeds by different molecules. The average rate of unwinding was several-fold slower than the PcrA translocation rate on single-stranded DNA, suggesting that DNA unwinding may proceed via a partially passive mechanism. However, the fastest dsDNA unwinding rates measured in the single-molecule unwinding assays approached the PcrA translocation speed measured on ssDNA.
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Affiliation(s)
- Liisa T Chisty
- MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
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28
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Kozlov AG, Galletto R, Lohman TM. SSB-DNA binding monitored by fluorescence intensity and anisotropy. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 922:55-83. [PMID: 22976177 DOI: 10.1007/978-1-62703-032-8_4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Fluorescence methods have proven to be extremely useful tools for quantitative studies of the equilibria and kinetics of protein-DNA interactions. If the protein contains tryptophan (Trp), as is often the case, and there is a change in intrinsic Trp fluorescence of the protein, one can use this change in signal (quenching/enhancement) to monitor binding. One can also attach an extrinsic fluorophore to either the protein or the DNA and monitor binding due to a change in fluorescence intensity or a change in fluorescence anisotropy. Such equilibrium studies can provide important quantitative information on stoichiometries (occluded site size, number of binding sites) and energetics (affinities and cooperativities) of the interactions. This information is needed to understand the mechanisms of protein-DNA interactions. A critical aspect of such approaches for systems that have non-unity stoichiometries (e.g., a protein that binds multiple ligands) is knowledge of the relationship between the change in fluorescence signal (intensity or anisotropy) and the average extent of binding. Here we describe procedures for using fluorescence approaches to examine the stoichiometries and equilibrium binding affinities of Escherichia coli single-stranded DNA-binding protein (SSB) and Deinococcus radiodurans SSB with long polymeric ssDNA to determine an occluded site size. We also provide examples of studies of SSB binding to shorter oligonucleotides to demonstrate analysis and fitting of the data to an appropriate model (monitoring fluorescence intensity or anisotropy) to obtain quantitative estimates of equilibrium binding parameters. We emphasize that the solution conditions (especially salt concentration and type) can influence not only the binding affinity, but also the mode by which an SSB oligomer binds ssDNA.
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Affiliation(s)
- Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
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29
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Abstract
First discovered in the 1970s, DNA helicases were initially described as enzymes that use chemical energy to separate (i.e., to unwind) the complementary strands of DNA. Because helicases are ubiquitous, display a range of fascinating biochemical activities, and are involved in all aspects of DNA metabolism, defects in human helicases are linked to a variety of genetic disorders, and helicase research continues to be important in understanding the molecular basis of DNA replication, recombination, and repair. The purpose of this book is to organize this information and to update the traditional view of these enzymes, because it is now evident that not all helicases possess bona fide strand separation activity and may function instead as energy-dependent switches or translocases. In this chapter, we will first discuss the biochemical and structural features of DNA-the lattice on which helicases operate-and its cellular organization. We will then provide a historical overview of helicases, starting from their discovery and classification, leading to their structures, mechanisms, and biomedical significance. Finally, we will highlight several key advances and developments in helicase research, and summarize some remaining questions and active areas of investigation. The subsequent chapters will discuss these topics and others in greater detail and are written by experts of these respective fields.
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Affiliation(s)
- Colin G Wu
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
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30
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Bell JC, Plank JL, Dombrowski CC, Kowalczykowski SC. Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA. Nature 2012; 491:274-8. [PMID: 23103864 PMCID: PMC4112059 DOI: 10.1038/nature11598] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 09/20/2012] [Indexed: 01/14/2023]
Abstract
Escherichia coli RecA is the defining member of a ubiquitous class of DNA strand exchange proteins that are essential for homologous recombination, a pathway that maintains genomic integrity by repairing broken DNA1. To function, filaments of RecA must nucleate and grow on single-stranded DNA (ssDNA) in direct competition with ssDNA-binding protein (SSB), which rapidly binds and continuously sequesters ssDNA, kinetically blocking RecA assembly2,3. This dynamic self-assembly on a DNA lattice, in competition with another protein, is unique for the RecA-family relative to other filament-forming proteins such as actin and tubulin. The complexity of this process has hindered our understanding of RecA filament assembly because ensemble measurements cannot reliably distinguish between the nucleation and growth phases, despite extensive and diverse attempts2–5. Previous single-molecule assays have measured nucleation and growth of RecA—and its eukaryotic homolog RAD51—on naked dsDNA and ssDNA6–12; however, the template for RecA self-assembly in vivo is SSB-coated ssDNA3. Using single-molecule microscopy, we directly visualized RecA filament assembly on single molecules of SSB-coated ssDNA, simultaneously measuring nucleation and growth. We establish that a dimer of RecA is required for nucleation, followed by growth of the filament through monomer addition, consistent with the finding that nucleation, but not growth, is modulated by nucleotide and magnesium ion cofactors. Filament growth is bidirectional, albeit faster in the 5′→3′ direction. Both nucleation and growth are repressed at physiological conditions, highlighting the essential role of recombination mediators in potentiating assembly in vivo. We define a two-step kinetic mechanism where RecA nucleates on transiently exposed ssDNA during SSB sliding and/or partial dissociation (i.e., DNA unwrapping) and then grows. We further demonstrate that the recombination mediator protein pair, RecOR, accelerates both RecA nucleation and filament growth, and that introduction of RecF further stimulates RecA nucleation.
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Affiliation(s)
- Jason C Bell
- Department of Microbiology, University of California, Davis, California 95616, USA
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31
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Arbore C, Lewis LM, Webb MR. Kinetic mechanism of initiation by RepD as a part of asymmetric, rolling circle plasmid unwinding. Biochemistry 2012; 51:3684-93. [PMID: 22463759 PMCID: PMC3340939 DOI: 10.1021/bi300172p] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Some bacterial plasmids carry antibiotic resistance genes and replicate by an asymmetric, rolling circle mechanism, in which replication of the two strands is not concurrent. Initiation of this replication occurs via an initiator protein that nicks one DNA strand at the double-stranded origin of replication. In this work, RepD protein from the staphylococcal plasmid pC221 carries this function and allows PcrA helicase to bind and begin unwinding the plasmid DNA. This work uses whole plasmid constructs as well as oligonucleotide-based mimics of parts of the origin to examine the initiation reaction. It investigates the phenomenon that nicking, although required to open a single-stranded region at the origin and so allow PcrA to bind, is not required for another function of RepD, namely to increase the processivity of PcrA, allowing it to unwind plasmid lengths of DNA. A kinetic mechanism of RepD initiation is presented, showing rapid binding of the origin DNA. The rate of nicking varies with the structure of the DNA but can occur with a rate constant of >25 s(-1) at 30 °C. The equilibrium constant of the nicking reaction, which involves a transesterification to form a phosphotyrosine bond within the RepD active site, is close to unity.
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Affiliation(s)
- Claudia Arbore
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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32
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Shlyakhtenko LS, Lushnikov AY, Miyagi A, Lyubchenko YL. Specificity of binding of single-stranded DNA-binding protein to its target. Biochemistry 2012; 51:1500-9. [PMID: 22304461 DOI: 10.1021/bi201863z] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Single-stranded DNA-binding proteins (SSBs) bind single-stranded DNA (ssDNA) and participate in all genetic processes involving ssDNA, such as replication, recombination, and repair. Here we applied atomic force microscopy to directly image SSB-DNA complexes under various conditions. We used the hybrid DNA construct methodology in which the ssDNA segment is conjugated to the DNA duplex. The duplex part of the construct plays the role of a marker, allowing unambiguous identification of specific and nonspecific SSB-DNA complexes. We designed hybrid DNA substrates with 5'- and 3'-ssDNA termini to clarify the role of ssDNA polarity on SSB loading. The hybrid substrates, in which two duplexes are connected with ssDNA, were the models for gapped DNA substrates. We demonstrated that Escherichia coli SSB binds to ssDNA ends and internal ssDNA regions with the same efficiency. However, the specific recognition by ssDNA requires the presence of Mg(2+) cations or a high ionic strength. In the absence of Mg(2+) cations and under low-salt conditions, the protein is capable of binding DNA duplexes. In addition, the number of interprotein interactions increases, resulting in the formation of clusters on double-stranded DNA. This finding suggests that the protein adopts different conformations depending on ionic strength, and specific recognition of ssDNA by SSB requires a high ionic strength or the presence of Mg(2+) cations.
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Affiliation(s)
- Luda S Shlyakhtenko
- University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
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33
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Gyimesi M, Harami GM, Sarlós K, Hazai E, Bikádi Z, Kovács M. Complex activities of the human Bloom's syndrome helicase are encoded in a core region comprising the RecA and Zn-binding domains. Nucleic Acids Res 2012; 40:3952-63. [PMID: 22253018 PMCID: PMC3351180 DOI: 10.1093/nar/gks008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bloom's syndrome DNA helicase (BLM), a member of the RecQ family, is a key player in homologous recombination (HR)-based error-free DNA repair processes. During HR, BLM exerts various biochemical activities including single-stranded (ss) DNA translocation, separation and annealing of complementary DNA strands, disruption of complex DNA structures (e.g. displacement loops) and contributes to quality control of HR via clearance of Rad51 nucleoprotein filaments. We performed a quantitative mechanistic analysis of truncated BLM constructs that are shorter than the previously identified minimal functional module. Surprisingly, we found that a BLM construct comprising only the two conserved RecA domains and the Zn2+-binding domain (residues 642–1077) can efficiently perform all mentioned HR-related activities. The results demonstrate that the Zn2+-binding domain is necessary for functional interaction with DNA. We show that the extensions of this core, including the winged-helix domain and the strand separation hairpin identified therein in other RecQ-family helicases, are not required for mechanochemical activity per se and may instead play modulatory roles and mediate protein–protein interactions.
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Affiliation(s)
- Máté Gyimesi
- Department of Biochemistry, ELTE-MTA Momentum Motor Enzymology Research Group, Eötvös University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
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34
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Abstract
Helicases are an important and much studied group of enzymes that generally couple ATP hydrolysis to the separation of strands of base-paired nucleic acids. Studying their biochemistry at different levels of organization requires assays that measure the progress of the reaction in different ways. One such method makes use of the single-stranded DNA-binding protein (SSB) from Escherichia coli. This is used as a protein framework to produce a "reagentless biosensor," making use of its tight and specific binding of single-stranded DNA. The attachment of a fluorophore to this protein produces a signal in response to that binding. Thus the (G26C)SSB, labeled with a diethylaminocoumarin, gives a ~5-fold fluorescence increase on binding to single-stranded DNA and this can be used to assay the progress of helicase action along double-stranded DNA. A protocol for this is described along with a variant that can be used to follow the unwinding on a single molecule scale.
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35
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Bianco PR, Stanenas AJ, Liu J, Cohan CS. Fluorescent single-stranded DNA-binding proteins enable in vitro and in vivo studies. Methods Mol Biol 2012; 922:235-244. [PMID: 22976191 PMCID: PMC5862424 DOI: 10.1007/978-1-62703-032-8_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Fluorescent single-stranded DNA-binding proteins (SSB) that have a defined number of fluorophores per tetramer are invaluable tools to understand biochemical mechanism and biological function. Here, we describe the purification of fluorescent SSB chimeras with a unique number of fluorescent subunits incorporated per tetramer. We describe the use of these tetramers to enable clear visualization of SSB in vivo. Purified chimeras also facilitate single molecule studies (Liu et al., Protein Sci 20:1005-1020, 2011).
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Affiliation(s)
- Piero R Bianco
- Center for Single Molecule Biophysics, Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, USA.
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36
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Abstract
The development of novel fluorescence methods for the detection of key biomolecules is of great interest, both in basic research and in drug discovery. Particularly relevant and widespread molecules in cells are ADP and GDP, which are the products of a large number of cellular reactions, including reactions catalysed by nucleoside triphosphatases and kinases. Previously, biosensors for ADP were developed in this laboratory, based on fluorophore adducts with the bacterial actin homologue ParM. It is shown in the present study that one of these biosensors, tetramethylrhodamine–ParM, can also monitor GDP. The biosensor can be used to measure micromolar concentrations of GDP on the background of millimolar concentrations of GTP. The fluorescence response of the biosensor is fast, the response time being <0.2 s. Thus the biosensor allows real-time measurements of GTPase and GTP-dependent kinase reactions. Applications of the GDP biosensor are exemplified with two different GTPases, measuring the rates of GTP hydrolysis and nucleotide exchange.
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37
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Yeeles JTP, van Aelst K, Dillingham MS, Moreno-Herrero F. Recombination hotspots and single-stranded DNA binding proteins couple DNA translocation to DNA unwinding by the AddAB helicase-nuclease. Mol Cell 2011; 42:806-16. [PMID: 21700225 DOI: 10.1016/j.molcel.2011.04.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/03/2011] [Accepted: 04/11/2011] [Indexed: 12/24/2022]
Abstract
AddAB is a helicase-nuclease that processes double-stranded DNA breaks for repair by homologous recombination. This process is modulated by Chi recombination hotspots: specific DNA sequences that attenuate the nuclease activity of the translocating AddAB complex to promote downstream recombination. Using a combination of kinetic and imaging techniques, we show that AddAB translocation is not coupled to DNA unwinding in the absence of single-stranded DNA binding proteins because nascent single-stranded DNA immediately re-anneals behind the moving enzyme. However, recognition of recombination hotspot sequences during translocation activates unwinding by coupling these activities, thereby ensuring the downstream formation of single-stranded DNA that is required for RecA-mediated recombinational repair. In addition to their implications for the mechanism of double-stranded DNA break repair, these observations may affect our implementation and interpretation of helicase assays and our understanding of helicase mechanisms in general.
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Affiliation(s)
- Joseph T P Yeeles
- DNA:Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
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38
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Liu J, Choi M, Stanenas AG, Byrd AK, Raney KD, Cohan C, Bianco PR. Novel, fluorescent, SSB protein chimeras with broad utility. Protein Sci 2011; 20:1005-20. [PMID: 21462278 DOI: 10.1002/pro.633] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 03/15/2011] [Accepted: 03/18/2011] [Indexed: 11/09/2022]
Abstract
The Escherichia coli single-stranded DNA binding protein (SSB) is a central player in DNA metabolism where it organizes genome maintenance complexes and stabilizes single-stranded DNA (ssDNA) intermediates generated during DNA processing. Due to the importance of SSB and to facilitate real-time studies, we developed a dual plasmid expression system to produce novel, chimeric SSB proteins. These chimeras, which contain mixtures of histidine-tagged and fluorescent protein(FP)-fusion subunits, are easily purified in milligram quantities and used without further modification, a significant enhancement over previous methods to produce fluorescent SSB. Chimeras retain the functionality of wild type in all assays, demonstrating that SSB function is unaffected by the FPs. We demonstrate the power and utility of these chimeras in single molecule studies providing a great level of insight into the biochemical mechanism of RecBCD. We also utilized the chimeras to show for the first time that RecG and SSB interact in vivo. Consequently, we anticipate that the chimeras described herein will facilitate in vivo, in vitro and single DNA molecule studies using proteins that do not require further modification prior to use.
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Affiliation(s)
- Juan Liu
- Center for Single Molecule Biophysics, Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York 14214, USA
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39
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Norris V. Speculations on the initiation of chromosome replication in Escherichia coli: the dualism hypothesis. Med Hypotheses 2011; 76:706-16. [PMID: 21349650 DOI: 10.1016/j.mehy.2011.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2010] [Revised: 01/23/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
The exact nature of the mechanism that triggers initiation of chromosome replication in the best understood of all organisms, Escherichia coli, remains mysterious. Here, I suggest that this mechanism evolved in response to the problems that arise if chromosome replication does not occur. E. coli is now known to be highly structured. This leads me to propose a mechanism for initiation of replication based on the dynamics of large assemblies of molecules and macromolecules termed hyperstructures. In this proposal, hyperstructures and their constituents are put into two classes, non-equilibrium and equilibrium, that spontaneously separate and that are appropriate for life in either good or bad conditions. Maintaining the right ratio(s) of non-equilibrium to equilibrium hyperstructures is therefore a major challenge for cells. I propose that this maintenance entails a major transfer of material from equilibrium to non-equilibrium hyperstructures once per cell and I further propose that this transfer times the cell cycle. More specifically, I speculate that the dialogue between hyperstructures involves the structuring of water and the condensation of cations and that one of the outcomes of ion condensation on ribosomal hyperstructures and decondensation from the origin hyperstructure is the separation of strands at oriC responsible for triggering initiation of replication. The dualism hypothesis that comes out of these speculations may help integrate models for initiation of replication, chromosome segregation and cell division with the 'prebiotic ecology' scenario of the origins of life.
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Affiliation(s)
- Vic Norris
- AMMIS Laboratory, EA 3829, Department of Biology, University of Rouen, 76821 Mont Saint Aignan, France.
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40
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Direct observation method of individual single-stranded DNA molecules using fluorescent replication protein A. J Fluoresc 2011; 21:1189-94. [PMID: 21225324 DOI: 10.1007/s10895-010-0797-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 12/28/2010] [Indexed: 02/04/2023]
Abstract
Direct observation studies of single molecules have revealed molecular behaviors usually hidden in the ensemble and time-averaging of bulk experiments. Direct single DNA molecule analysis of DNA metabolism reactions such as DNA replication, repair, and recombination is necessary to fully understand these essential processes. Intercalation of fluorescent dyes such as YOYO-1 and SYTOX Orange has been the standard method for observing single molecules of double-stranded DNA (dsDNA), but effective fluorescent dyes for observing single molecules of single-stranded DNA (ssDNA) have not been found. To facilitate direct single-molecule observations of DNA metabolism reactions, it is necessary to establish methods for discriminating ssDNA and dsDNA. To observe ssDNA directly, we prepared a fusion protein consisting of the 70 kDa DNA-binding domain of replication protein A and enhanced yellow fluorescent protein (RPA-YFP). This fusion protein had ssDNA-binding activity. In our experiments, dsDNA was stained by SYTOX Orange and ssDNA by RPA-YFP, and we succeeded in staining ssDNA and dsDNA by using RPA-YFP and SYTOX Orange simultaneously.
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41
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Fili N, Toseland CP, Dillingham MS, Webb MR, Molloy JE. A single-molecule approach to visualize the unwinding activity of DNA helicases. Methods Mol Biol 2011; 778:193-214. [PMID: 21809208 DOI: 10.1007/978-1-61779-261-8_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Almost all aspects of DNA metabolism involve separation of double-stranded DNA catalyzed by helicases. Observation and measurement of the dynamics of these events at the single-molecule level provide important mechanistic details of helicase activity and give the opportunity to probe aspects that are not revealed in bulk solution measurements. The assay, presented here, provides information about helicase unwinding rates and processivity. Visualization is achieved by using a fluorescent single-stranded DNA-binding protein (SSB), which allows the time course of individual DNA unwinding events to be observed using total internal reflection fluorescence microscopy. Observation of a prototypical helicase, Bacillus subtilis AddAB, shows that the unwinding process consists of bursts of unwinding activity, interspersed with periods of pausing.
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Affiliation(s)
- Natalia Fili
- MRC National Institute for Medical Research, London, UK.
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42
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Yeeles JTP, Gwynn EJ, Webb MR, Dillingham MS. The AddAB helicase-nuclease catalyses rapid and processive DNA unwinding using a single Superfamily 1A motor domain. Nucleic Acids Res 2010; 39:2271-85. [PMID: 21071401 PMCID: PMC3064778 DOI: 10.1093/nar/gkq1124] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The oligomeric state of Superfamily I DNA helicases is the subject of considerable and ongoing debate. While models based on crystal structures imply that a single helicase core domain is sufficient for DNA unwinding activity, biochemical data from several related enzymes suggest that a higher order oligomeric species is required. In this work we characterize the helicase activity of the AddAB helicase–nuclease, which is involved in the repair of double-stranded DNA breaks in Bacillus subtilis. We show that the enzyme is functional as a heterodimer of the AddA and AddB subunits, that it is a rapid and processive DNA helicase, and that it catalyses DNA unwinding using one single-stranded DNA motor of 3′→5′ polarity located in the AddA subunit. The AddB subunit contains a second putative ATP-binding pocket, but this does not contribute to the observed helicase activity and may instead be involved in the recognition of recombination hotspot sequences.
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Affiliation(s)
- Joseph T P Yeeles
- DNA-Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
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43
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Toseland CP, Webb MR. Fluorescence tools to measure helicase activity in real time. Methods 2010; 51:259-68. [DOI: 10.1016/j.ymeth.2010.02.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 02/03/2010] [Accepted: 02/12/2010] [Indexed: 11/16/2022] Open
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Abstract
ATP-driven translocation of helicases along DNA can be assayed in several ways. Reagentless biosensors, based on fluorophore-protein adducts, provide convenient ways for real-time assays of both the separation of dsDNA and the hydrolysis of ATP. Single-stranded DNA can be assayed using a modified single-stranded DNA-binding protein (SSB), and phosphate production during ATP hydrolysis can be measured by a modified phosphate-binding protein. Advantages and limitations of these approaches are compared with those of other types of measurements.
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Affiliation(s)
- Martin R Webb
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK
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45
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Fili N, Mashanov GI, Toseland CP, Batters C, Wallace MI, Yeeles JTP, Dillingham MS, Webb MR, Molloy JE. Visualizing helicases unwinding DNA at the single molecule level. Nucleic Acids Res 2010; 38:4448-57. [PMID: 20350930 PMCID: PMC2910053 DOI: 10.1093/nar/gkq173] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
DNA helicases are motor proteins that catalyze the unwinding of double-stranded DNA into single-stranded DNA using the free energy from ATP hydrolysis. Single molecule approaches enable us to address detailed mechanistic questions about how such enzymes move processively along DNA. Here, an optical method has been developed to follow the unwinding of multiple DNA molecules simultaneously in real time. This was achieved by measuring the accumulation of fluorescent single-stranded DNA-binding protein on the single-stranded DNA product of the helicase, using total internal reflection fluorescence microscopy. By immobilizing either the DNA or helicase, localized increase in fluorescence provides information about the rate of unwinding and the processivity of individual enzymes. In addition, it reveals details of the unwinding process, such as pauses and bursts of activity. The generic and versatile nature of the assay makes it applicable to a variety of DNA helicases and DNA templates. The method is an important addition to the single-molecule toolbox available for studying DNA processing enzymes.
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Affiliation(s)
- Natali Fili
- MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
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46
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Kunzelmann S, Morris C, Chavda AP, Eccleston JF, Webb MR. Mechanism of interaction between single-stranded DNA binding protein and DNA. Biochemistry 2010; 49:843-52. [PMID: 20028139 PMCID: PMC2827191 DOI: 10.1021/bi901743k] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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A single-stranded DNA binding protein (SSB), labeled with a fluorophore, interacts with single-stranded DNA (ssDNA), giving a 6-fold increase in fluorescence. The labeled protein is the adduct of the G26C mutant of the homotetrameric SSB from Escherichia coli and a diethylaminocoumarin {N-[2-(iodoacetamido)ethyl]-7-diethylaminocoumarin-3-carboxamide}. This adduct can be used to assay production of ssDNA during separation of double-stranded DNA by helicases. To use this probe effectively, as well as to investigate the interaction between ssDNA and SSB, the fluorescent SSB has been used to develop the kinetic mechanism by which the protein and ssDNA associate and dissociate. Under conditions where ∼70 base lengths of ssDNA wrap around the tetramer, initial association is relatively simple and rapid, possibly diffusion-controlled. The kinetics are similar for a 70-base length of ssDNA, which binds one tetramer, and poly(dT), which could bind several. Under some conditions (high SSB and/or low ionic strength), a second tetramer binds to each 70-base length, but at a rate 2 orders of magnitude slower than the rate of binding of the first tetramer. Dissociation kinetics are complex and greatly accelerated by the presence of free wild-type SSB. The main route of dissociation of the fluorescent SSB·ssDNA complex is via association first with an additional SSB and then dissociation. Comparison of binding data with different lengths of ssDNA gave no evidence of cooperativity between tetramers. Analytical ultracentrifugation was used to determine the dissociation constant for labeled SSB2·dT70 to be 1.1 μM at a high ionic strength (200 mM NaCl). Shorter lengths of ssDNA were tested for binding: only when the length is reduced to 20 bases is the affinity significantly reduced.
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Affiliation(s)
- Simone Kunzelmann
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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47
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Slatter AF, Thomas CD, Webb MR. PcrA helicase tightly couples ATP hydrolysis to unwinding double-stranded DNA, modulated by the initiator protein for plasmid replication, RepD. Biochemistry 2009; 48:6326-34. [PMID: 19473041 PMCID: PMC2776994 DOI: 10.1021/bi900101h] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The plasmid replication initiator protein, RepD, greatly stimulates the ability of the DNA helicase, PcrA, to unwind plasmid lengths of DNA. Unwinding begins at oriD, the double-stranded origin of replication that RepD recognizes and covalently binds to initiate replication. Using a combination of plasmids containing oriD and oligonucleotide structures that mimic parts of oriD, the kinetics of DNA nicking and separation have been determined, along with the coupling ratio between base separation and ATP hydrolysis. At 30 °C, the rate of nicking is 1.0 s−1, and translocation is ∼30 bp s−1. During translocation, the coupling ratio is one ATP hydrolyzed per base pair separated, the same as the value previously reported for ATP hydrolyzed per base moved by PcrA along single-stranded DNA. The data suggest that processivity is high, such that several thousand base-pair plasmids are unwound by a single molecule of PcrA. In the absence of RepD, a single PcrA is unable to separate even short lengths (10 to 40 bp) of double stranded DNA.
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Affiliation(s)
- Andrew F Slatter
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, U.K
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