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  1. Article ; Online: Characterizing single-molecule dynamics of viral RNA-dependent RNA polymerases with multiplexed magnetic tweezers.

    Kuijpers, Louis / van Laar, Theo / Janissen, Richard / Dekker, Nynke H

    STAR protocols

    2022  Volume 3, Issue 3, Page(s) 101606

    Abstract: Multiplexed single-molecule magnetic tweezers (MT) have recently been employed to probe the RNA synthesis dynamics of RNA-dependent RNA polymerases (RdRp). Here, we present a protocol for simultaneously probing the RNA synthesis dynamics of hundreds of ... ...

    Abstract Multiplexed single-molecule magnetic tweezers (MT) have recently been employed to probe the RNA synthesis dynamics of RNA-dependent RNA polymerases (RdRp). Here, we present a protocol for simultaneously probing the RNA synthesis dynamics of hundreds of single polymerases with MT. We describe the preparation of a dsRNA construct for probing single RdRp kinetics. We then detail the measurement of RdRp RNA synthesis kinetics using MT. The protocol is suitable for high-throughput probing of RdRp-targeting antiviral compounds for mechanistic function and efficacy. For complete details on the use and execution of this protocol, please refer to Janissen et al. (2021).
    MeSH term(s) Antiviral Agents ; Kinetics ; Magnetic Phenomena ; RNA, Double-Stranded ; RNA-Dependent RNA Polymerase
    Chemical Substances Antiviral Agents ; RNA, Double-Stranded ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
    Language English
    Publishing date 2022-08-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2022.101606
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint.

    Sánchez, Humberto / Liu, Zhaowei / van Veen, Edo / van Laar, Theo / Diffley, John F X / Dekker, Nynke H

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 6735

    Abstract: Chromatin replication involves the assembly and activity of the replisome within the nucleosomal landscape. At the core of the replisome is the Mcm2-7 complex (MCM), which is loaded onto DNA after binding to the Origin Recognition Complex (ORC). In yeast, ...

    Abstract Chromatin replication involves the assembly and activity of the replisome within the nucleosomal landscape. At the core of the replisome is the Mcm2-7 complex (MCM), which is loaded onto DNA after binding to the Origin Recognition Complex (ORC). In yeast, ORC is a dynamic protein that diffuses rapidly along DNA, unless halted by origin recognition sequences. However, less is known about the dynamics of ORC proteins in the presence of nucleosomes and attendant consequences for MCM loading. To address this, we harnessed an in vitro single-molecule approach to interrogate a chromatinized origin of replication. We find that ORC binds the origin of replication with similar efficiency independently of whether the origin is chromatinized, despite ORC mobility being reduced by the presence of nucleosomes. Recruitment of MCM also proceeds efficiently on a chromatinized origin, but subsequent movement of MCM away from the origin is severely constrained. These findings suggest that chromatinized origins in yeast are essential for the local retention of MCM, which may facilitate subsequent assembly of the replisome.
    MeSH term(s) Origin Recognition Complex/genetics ; Origin Recognition Complex/metabolism ; Nucleosomes ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Cell Cycle Proteins/metabolism ; DNA/metabolism ; DNA Replication ; Minichromosome Maintenance Proteins/genetics ; Minichromosome Maintenance Proteins/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Replication Origin
    Chemical Substances Origin Recognition Complex ; Nucleosomes ; Cell Cycle Proteins ; DNA (9007-49-2) ; Minichromosome Maintenance Proteins (EC 3.6.4.12) ; Saccharomyces cerevisiae Proteins
    Language English
    Publishing date 2023-10-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-42524-8
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  3. Article ; Online: Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation.

    Ramírez Montero, Daniel / Sánchez, Humberto / van Veen, Edo / van Laar, Theo / Solano, Belén / Diffley, John F X / Dekker, Nynke H

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 2082

    Abstract: The eukaryotic replicative helicase CMG centrally orchestrates the replisome and leads the way at the front of replication forks. Understanding the motion of CMG on the DNA is therefore key to our understanding of DNA replication. In vivo, CMG is ... ...

    Abstract The eukaryotic replicative helicase CMG centrally orchestrates the replisome and leads the way at the front of replication forks. Understanding the motion of CMG on the DNA is therefore key to our understanding of DNA replication. In vivo, CMG is assembled and activated through a cell-cycle-regulated mechanism involving 36 polypeptides that has been reconstituted from purified proteins in ensemble biochemical studies. Conversely, single-molecule studies of CMG motion have thus far relied on pre-formed CMG assembled through an unknown mechanism upon overexpression of individual constituents. Here, we report the activation of CMG fully reconstituted from purified yeast proteins and the quantification of its motion at the single-molecule level. We observe that CMG can move on DNA in two ways: by unidirectional translocation and by diffusion. We demonstrate that CMG preferentially exhibits unidirectional translocation in the presence of ATP, whereas it preferentially exhibits diffusive motion in the absence of ATP. We also demonstrate that nucleotide binding halts diffusive CMG independently of DNA melting. Taken together, our findings support a mechanism by which nucleotide binding allows newly assembled CMG to engage with the DNA within its central channel, halting its diffusion and facilitating the initial DNA melting required to initiate DNA replication.
    MeSH term(s) Eukaryota/metabolism ; Nucleotides ; DNA Replication ; DNA Helicases/metabolism ; DNA/metabolism ; Adenosine Triphosphate/metabolism
    Chemical Substances Nucleotides ; DNA Helicases (EC 3.6.4.-) ; DNA (9007-49-2) ; Adenosine Triphosphate (8L70Q75FXE)
    Language English
    Publishing date 2023-04-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-37093-9
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  4. Article: A Biophysics Toolbox for Reliable Data Acquisition and Processing in Integrated Force-Confocal Fluorescence Microscopy.

    Liu, Zhaowei / van Veen, Edo / Sánchez, Humberto / Solano, Belén / Palmero Moya, Francisco J / McCluskey, Kaley A / Ramírez Montero, Daniel / van Laar, Theo / Dekker, Nynke H

    ACS photonics

    2024  Volume 11, Issue 4, Page(s) 1592–1603

    Abstract: Integrated single-molecule force-fluorescence spectroscopy setups allow for simultaneous fluorescence imaging and mechanical force manipulation and measurements on individual molecules, providing comprehensive dynamic and spatiotemporal information. Dual- ...

    Abstract Integrated single-molecule force-fluorescence spectroscopy setups allow for simultaneous fluorescence imaging and mechanical force manipulation and measurements on individual molecules, providing comprehensive dynamic and spatiotemporal information. Dual-beam optical tweezers (OT) combined with a confocal scanning microscope form a force-fluorescence spectroscopy apparatus broadly used to investigate various biological processes, in particular, protein:DNA interactions. Such experiments typically involve imaging of fluorescently labeled proteins bound to DNA and force spectroscopy measurements of trapped individual DNA molecules. Here, we present a versatile state-of-the-art toolbox including the preparation of protein:DNA complex samples, design of a microfluidic flow cell incorporated with OT, automation of OT-confocal scanning measurements, and the development and implementation of a streamlined data analysis package for force and fluorescence spectroscopy data processing. Its components can be adapted to any commercialized or home-built dual-beam OT setup equipped with a confocal scanning microscope, which will facilitate single-molecule force-fluorescence spectroscopy studies on a large variety of biological systems.
    Language English
    Publishing date 2024-03-18
    Publishing country United States
    Document type Journal Article
    ISSN 2330-4022
    ISSN 2330-4022
    DOI 10.1021/acsphotonics.3c01739
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: SMC complexes can traverse physical roadblocks bigger than their ring size.

    Pradhan, Biswajit / Barth, Roman / Kim, Eugene / Davidson, Iain F / Bauer, Benedikt / van Laar, Theo / Yang, Wayne / Ryu, Je-Kyung / van der Torre, Jaco / Peters, Jan-Michael / Dekker, Cees

    Cell reports

    2022  Volume 41, Issue 3, Page(s) 111491

    Abstract: Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in vitro single-molecule ...

    Abstract Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in vitro single-molecule visualization to show that nucleosomes, RNA polymerase, and dCas9 pose virtually no barrier to loop extrusion by yeast condensin. We find that even DNA-bound nanoparticles as large as 200 nm, much bigger than the SMC ring size, also translocate into DNA loops during extrusion by condensin and cohesin. This even occurs for a single-chain version of cohesin in which the ring-forming subunits are covalently linked and cannot open to entrap DNA. The data show that SMC-driven loop extrusion has surprisingly little difficulty in accommodating large roadblocks into the loop. The findings also show that the extruded DNA does not pass through the SMC ring (pseudo)topologically, hence pointing to a nontopological mechanism for DNA loop extrusion.
    MeSH term(s) Nucleosomes ; Cell Cycle Proteins ; Chromatin ; Nanoparticles ; Saccharomyces cerevisiae
    Chemical Substances Nucleosomes ; Cell Cycle Proteins ; Chromatin
    Language English
    Publishing date 2022-10-17
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2022.111491
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: High-throughput, high-force probing of DNA-protein interactions with magnetic tweezers.

    Berghuis, Bojk A / Köber, Mariana / van Laar, Theo / Dekker, Nynke H

    Methods (San Diego, Calif.)

    2016  Volume 105, Page(s) 90–98

    Abstract: Recent advances in high-throughput single-molecule magnetic tweezers have paved the way for obtaining information on individual molecules as well as ensemble-averaged behavior in a single assay. Here we describe how to design robust high-throughput ... ...

    Abstract Recent advances in high-throughput single-molecule magnetic tweezers have paved the way for obtaining information on individual molecules as well as ensemble-averaged behavior in a single assay. Here we describe how to design robust high-throughput magnetic tweezers assays that specifically require application of high forces (>20pN) for prolonged periods of time (>1000s). We elaborate on the strengths and limitations of the typical construct types that can be used and provide a step-by-step guide towards a high tether yield assay based on two examples. Firstly, we discuss a DNA hairpin assay where force-induced strand separation triggers a tight interaction between DNA-binding protein Tus and its binding site Ter, where forces up to 90pN for hundreds of seconds were required to dissociate Tus from Ter. Secondly, we show how the LTag helicase of Simian virus 40 unwinds dsDNA, where a load of 36pN optimizes the assay readout. The approaches detailed here provide guidelines for the high-throughput, quantitative study of a wide range of DNA-protein interactions.
    Language English
    Publishing date 2016-08-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2016.03.025
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: CAF-1 deposits newly synthesized histones during DNA replication using distinct mechanisms on the leading and lagging strands.

    Rouillon, Clément / Eckhardt, Bruna V / Kollenstart, Leonie / Gruss, Fabian / Verkennis, Alexander E E / Rondeel, Inge / Krijger, Peter H L / Ricci, Giulia / Biran, Alva / van Laar, Theo / Delvaux de Fenffe, Charlotte M / Luppens, Georgiana / Albanese, Pascal / Sato, Koichi / Scheltema, Richard A / de Laat, Wouter / Knipscheer, Puck / Dekker, Nynke H / Groth, Anja /
    Mattiroli, Francesca

    Nucleic acids research

    2023  Volume 51, Issue 8, Page(s) 3770–3792

    Abstract: During every cell cycle, both the genome and the associated chromatin must be accurately replicated. Chromatin Assembly Factor-1 (CAF-1) is a key regulator of chromatin replication, but how CAF-1 functions in relation to the DNA replication machinery is ... ...

    Abstract During every cell cycle, both the genome and the associated chromatin must be accurately replicated. Chromatin Assembly Factor-1 (CAF-1) is a key regulator of chromatin replication, but how CAF-1 functions in relation to the DNA replication machinery is unknown. Here, we reveal that this crosstalk differs between the leading and lagging strand at replication forks. Using biochemical reconstitutions, we show that DNA and histones promote CAF-1 recruitment to its binding partner PCNA and reveal that two CAF-1 complexes are required for efficient nucleosome assembly under these conditions. Remarkably, in the context of the replisome, CAF-1 competes with the leading strand DNA polymerase epsilon (Polϵ) for PCNA binding. However, CAF-1 does not affect the activity of the lagging strand DNA polymerase Delta (Polδ). Yet, in cells, CAF-1 deposits newly synthesized histones equally on both daughter strands. Thus, on the leading strand, chromatin assembly by CAF-1 cannot occur simultaneously to DNA synthesis, while on the lagging strand these processes may be coupled. We propose that these differences may facilitate distinct parental histone recycling mechanisms and accommodate the inherent asymmetry of DNA replication.
    MeSH term(s) Histones/metabolism ; Proliferating Cell Nuclear Antigen/genetics ; Proliferating Cell Nuclear Antigen/metabolism ; Chromatin Assembly Factor-1/genetics ; Chromatin Assembly Factor-1/metabolism ; Chromatin/genetics ; DNA Replication ; DNA/genetics
    Chemical Substances Histones ; Proliferating Cell Nuclear Antigen ; Chromatin Assembly Factor-1 ; Chromatin ; DNA (9007-49-2)
    Language English
    Publishing date 2023-03-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad171
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  8. Article ; Online: DNA replication origins retain mobile licensing proteins.

    Sánchez, Humberto / McCluskey, Kaley / van Laar, Theo / van Veen, Edo / Asscher, Filip M / Solano, Belén / Diffley, John F X / Dekker, Nynke H

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 1908

    Abstract: DNA replication in eukaryotes initiates at many origins distributed across each chromosome. Origins are bound by the origin recognition complex (ORC), which, with Cdc6 and Cdt1, recruits and loads the Mcm2-7 (MCM) helicase as an inactive double hexamer ... ...

    Abstract DNA replication in eukaryotes initiates at many origins distributed across each chromosome. Origins are bound by the origin recognition complex (ORC), which, with Cdc6 and Cdt1, recruits and loads the Mcm2-7 (MCM) helicase as an inactive double hexamer during G1 phase. The replisome assembles at the activated helicase in S phase. Although the outline of replisome assembly is understood, little is known about the dynamics of individual proteins on DNA and how these contribute to proper complex formation. Here we show, using single-molecule optical trapping and confocal microscopy, that yeast ORC is a mobile protein that diffuses rapidly along DNA. Origin recognition halts this search process. Recruitment of MCM molecules in an ORC- and Cdc6-dependent fashion results in slow-moving ORC-MCM intermediates and MCMs that rapidly scan the DNA. Following ATP hydrolysis, salt-stable loading of MCM single and double hexamers was seen, both of which exhibit salt-dependent mobility. Our results demonstrate that effective helicase loading relies on an interplay between protein diffusion and origin recognition, and suggest that MCM is stably loaded onto DNA in multiple forms.
    MeSH term(s) Algorithms ; Binding Sites/genetics ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; DNA Replication/genetics ; DNA, Fungal/genetics ; DNA, Fungal/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Minichromosome Maintenance Proteins/genetics ; Minichromosome Maintenance Proteins/metabolism ; Models, Genetic ; Origin Recognition Complex/genetics ; Origin Recognition Complex/metabolism ; Protein Binding ; Replication Origin/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
    Chemical Substances CDC6 protein, S cerevisiae ; Cell Cycle Proteins ; DNA, Fungal ; DNA-Binding Proteins ; Origin Recognition Complex ; Saccharomyces cerevisiae Proteins ; TAH11 protein, S cerevisiae ; Minichromosome Maintenance Proteins (EC 3.6.4.12)
    Language English
    Publishing date 2021-03-26
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-22216-x
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  9. Article: Essential validation methods for E. coli strains created by chromosome engineering.

    Tiruvadi Krishnan, Sriram / Moolman, M Charl / van Laar, Theo / Meyer, Anne S / Dekker, Nynke H

    Journal of biological engineering

    2015  Volume 9, Page(s) 11

    Abstract: Background: Chromosome engineering encompasses a collection of homologous recombination-based techniques that are employed to modify the genome of a model organism in a controlled fashion. Such techniques are widely used in both fundamental and ... ...

    Abstract Background: Chromosome engineering encompasses a collection of homologous recombination-based techniques that are employed to modify the genome of a model organism in a controlled fashion. Such techniques are widely used in both fundamental and industrial research to introduce multiple insertions in the same Escherichia coli strain. To date, λ-Red recombination (also known as recombineering) and P1 phage transduction are the most successfully implemented chromosome engineering techniques in E. coli. However, due to errors that can occur during the strain creation process, reliable validation methods are essential upon alteration of a strain's chromosome.
    Results and discussion: Polymerase chain reaction (PCR)-based methods and DNA sequence analysis are rapid and powerful methods to verify successful integration of DNA sequences into a chromosome. Even though these verification methods are necessary, they may not be sufficient in detecting all errors, imposing the requirement of additional validation methods. For example, as extraneous insertions may occur during recombineering, we highlight the use of Southern blotting to detect their presence. These unwanted mutations can be removed via transducing the region of interest into the wild type chromosome using P1 phages. However, in doing so one must verify that both the P1 lysate and the strains utilized are free from contamination with temperate phages, as these can lysogenize inside a cell as a large plasmid. Thus, we illustrate various methods to probe for temperate phage contamination, including cross-streak agar and Evans Blue-Uranine (EBU) plate assays, whereby the latter is a newly reported technique for this purpose in E. coli. Lastly, we discuss methodologies for detecting defects in cell growth and shape characteristics, which should be employed as an additional check.
    Conclusion: The simple, yet crucial validation techniques discussed here can be used to reliably verify any chromosomally engineered E. coli strains for errors such as non-specific insertions in the chromosome, temperate phage contamination, and defects in growth and cell shape. While techniques such as PCR and DNA sequence verification should standardly be performed, we illustrate the necessity of performing these additional assays. The discussed techniques are highly generic and can be easily applied to any type of chromosome engineering.
    Language English
    Publishing date 2015-07-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 2391582-1
    ISSN 1754-1611
    ISSN 1754-1611
    DOI 10.1186/s13036-015-0008-x
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  10. Article ; Online: Invincible DNA tethers: covalent DNA anchoring for enhanced temporal and force stability in magnetic tweezers experiments.

    Janissen, Richard / Berghuis, Bojk A / Dulin, David / Wink, Max / van Laar, Theo / Dekker, Nynke H

    Nucleic acids research

    2014  Volume 42, Issue 18, Page(s) e137

    Abstract: Magnetic tweezers are a powerful single-molecule technique that allows real-time quantitative investigation of biomolecular processes under applied force. High pulling forces exceeding tens of picoNewtons may be required, e.g. to probe the force range of ...

    Abstract Magnetic tweezers are a powerful single-molecule technique that allows real-time quantitative investigation of biomolecular processes under applied force. High pulling forces exceeding tens of picoNewtons may be required, e.g. to probe the force range of proteins that actively transcribe or package the genome. Frequently, however, the application of such forces decreases the sample lifetime, hindering data acquisition. To provide experimentally viable sample lifetimes in the face of high pulling forces, we have designed a novel anchoring strategy for DNA in magnetic tweezers. Our approach, which exploits covalent functionalization based on heterobifunctional poly(ethylene glycol) crosslinkers, allows us to strongly tether DNA while simultaneously suppressing undesirable non-specific adhesion. A complete force and lifetime characterization of these covalently anchored DNA-tethers demonstrates that, compared to more commonly employed anchoring strategies, they withstand 3-fold higher pulling forces (up to 150 pN) and exhibit up to 200-fold higher lifetimes (exceeding 24 h at a constant force of 150 pN). This advance makes it possible to apply the full range of biologically relevant force scales to biomolecular processes, and its straightforward implementation should extend its reach to a multitude of applications in the field of single-molecule force spectroscopy.
    MeSH term(s) Biomechanical Phenomena ; DNA/chemistry ; Magnets ; Polyethylene Glycols/chemistry ; Spectrum Analysis
    Chemical Substances Polyethylene Glycols (3WJQ0SDW1A) ; DNA (9007-49-2)
    Language English
    Publishing date 2014-08-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gku677
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