1
|
Walker-Gibbons R, Zhu X, Behjatian A, Bennett TJD, Krishnan M. Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations. Sci Rep 2024; 14:20582. [PMID: 39232063 PMCID: PMC11375218 DOI: 10.1038/s41598-024-70641-x] [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] [Received: 03/26/2024] [Accepted: 08/20/2024] [Indexed: 09/06/2024] Open
Abstract
Inferring the 3D structure and conformation of disordered biomolecules, e.g., single stranded nucleic acids (ssNAs), remains challenging due to their conformational heterogeneity in solution. Here, we use escape-time electrometry (ETe) to measure with sub elementary-charge precision the effective electrical charge in solution of short to medium chain length ssNAs in the range of 5-60 bases. We compare measurements of molecular effective charge with theoretically calculated values for simulated molecular conformations obtained from Molecular Dynamics simulations using a variety of forcefield descriptions. We demonstrate that the measured effective charge captures subtle differences in molecular structure in various nucleic acid homopolymers of identical length, and also that the experimental measurements can find agreement with computed values derived from coarse-grained molecular structure descriptions such as oxDNA, as well next generation ssNA force fields. We further show that comparing the measured effective charge with calculations for a rigid, charged rod-the simplest model of a nucleic acid-yields estimates of molecular structural dimensions such as linear charge spacings that capture molecular structural trends observed using high resolution structural analysis methods such as X-ray scattering. By sensitively probing the effective charge of a molecule, electrometry provides a powerful dimension supporting inferences of molecular structural and conformational properties, as well as the validation of biomolecular structural models. The overall approach holds promise for a high throughput, microscopy-based biomolecular analytical approach offering rapid screening and inference of molecular 3D conformation, and operating at the single molecule level in solution.
Collapse
Affiliation(s)
- Rowan Walker-Gibbons
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Xin Zhu
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Ali Behjatian
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Timothy J D Bennett
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Madhavi Krishnan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
- The Kavli Institute for Nanoscience Discovery, Sherrington Road, Oxford, OX1 3QU, UK.
| |
Collapse
|
2
|
Zülske T, Attou A, Groß L, Hörl D, Harz H, Wedemann G. Nucleosome spacing controls chromatin spatial structure and accessibility. Biophys J 2024; 123:847-857. [PMID: 38419332 PMCID: PMC10995425 DOI: 10.1016/j.bpj.2024.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/31/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024] Open
Abstract
Recent research highlights the significance of the three-dimensional structure of chromatin in regulating various cellular processes, particularly transcription. This is achieved through dynamic chromatin structures that facilitate long-range contacts and control spatial accessibility. Chromatin consists of DNA and a variety of proteins, of which histones play an essential structural role by forming nucleosomes. Extensive experimental and theoretical research in recent decades has yielded conflicting results about key factors that regulate the spatial structure of chromatin, which remains enigmatic. By using a computer model that allows us to simulate chromatin volumes containing physiological nucleosome concentrations, we investigated whether nucleosome spacing or nucleosome density is fundamental for three-dimensional chromatin accessibility. Unexpectedly, the regularity of the nucleosome spacing is crucial for determining the accessibility of the chromatin network to diffusive processes, whereas variation in nucleosome concentrations has only minor effects. Using only the basic physical properties of DNA and nucleosomes was sufficient to generate chromatin structures consistent with published electron microscopy data. Contrary to other work, we found that nucleosome density did not substantially alter the properties of chromatin fibers or contact probabilities of genomic loci. No breakup of fiber-like structures was observed at high molar density. These findings challenge previous assumptions and highlight the importance of nucleosome spacing as a key driver of chromatin organization. These results identified changes in nucleosome spacing as a tentative mechanism for altering the spatial chromatin structure and thus genomic functions.
Collapse
Affiliation(s)
- Tilo Zülske
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Aymen Attou
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany; Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Laurens Groß
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - David Hörl
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hartmann Harz
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gero Wedemann
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany.
| |
Collapse
|
3
|
Aldag P, Rutkauskas M, Madariaga-Marcos J, Songailiene I, Sinkunas T, Kemmerich F, Kauert D, Siksnys V, Seidel R. Dynamic interplay between target search and recognition for a Type I CRISPR-Cas system. Nat Commun 2023; 14:3654. [PMID: 37339984 DOI: 10.1038/s41467-023-38790-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/16/2023] [Indexed: 06/22/2023] Open
Abstract
CRISPR-Cas effector complexes enable the defense against foreign nucleic acids and have recently been exploited as molecular tools for precise genome editing at a target locus. To bind and cleave their target, the CRISPR-Cas effectors have to interrogate the entire genome for the presence of a matching sequence. Here we dissect the target search and recognition process of the Type I CRISPR-Cas complex Cascade by simultaneously monitoring DNA binding and R-loop formation by the complex. We directly quantify the effect of DNA supercoiling on the target recognition probability and demonstrate that Cascade uses facilitated diffusion for its target search. We show that target search and target recognition are tightly linked and that DNA supercoiling and limited 1D diffusion need to be considered when understanding target recognition and target search by CRISPR-Cas enzymes and engineering more efficient and precise variants.
Collapse
Affiliation(s)
- Pierre Aldag
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Marius Rutkauskas
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | | | - Inga Songailiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekis ave. 7, Vilnius, 10257, Lithuania
| | - Tomas Sinkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekis ave. 7, Vilnius, 10257, Lithuania
| | - Felix Kemmerich
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Dominik Kauert
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekis ave. 7, Vilnius, 10257, Lithuania.
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany.
| |
Collapse
|
4
|
Attou A, Zülske T, Wedemann G. Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions. Biophys J 2022; 121:4788-4799. [PMID: 36325618 PMCID: PMC9811664 DOI: 10.1016/j.bpj.2022.10.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/12/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
The spatial organization of the eukaryotic genome plays an important role in regulating transcriptional activity. In the nucleus, chromatin forms loops that assemble into fundamental units called topologically associating domains that facilitate or inhibit long-range contacts. These loops are formed and held together by the ring-shaped cohesin protein complex, and this can involve binding of CCCTC-binding factor (CTCF). High-resolution conformation capture experiments provide the frequency at which two DNA fragments physically associate in three-dimensional space. However, technical limitations of this approach, such as low throughput, low resolution, or noise in contact maps, make data interpretation and identification of chromatin intraloop contacts, e.g., between distal regulatory elements and their target genes, challenging. Herein, an existing coarse-grained model of chromatin at single-nucleosome resolution was extended by integrating potentials describing CTCF and cohesin. We performed replica-exchange Monte Carlo simulations with regularly spaced nucleosomes and experimentally determined nucleosome positions in the presence of cohesin-CTCF, as well as depleted systems as controls. In fully extruded loops caused by the presence of cohesin and CTCF, the number of contacts within the formed loops was increased. The number and types of these contacts were impacted by the nucleosome distribution and loop size. Microloops were observed within cohesin-mediated loops due to thermal fluctuations without additional influence of other factors, and the number, size, and shape of microloops were determined by nucleosome distribution and loop size. Nucleosome positions directly affect the spatial structure and contact probability within a loop, with presumed consequences for transcriptional activity.
Collapse
Affiliation(s)
- Aymen Attou
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Tilo Zülske
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Gero Wedemann
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany.
| |
Collapse
|
5
|
A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex. Nat Commun 2022; 13:7460. [PMID: 36460652 PMCID: PMC9718816 DOI: 10.1038/s41467-022-35116-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022] Open
Abstract
CRISPR-Cas effector complexes recognise nucleic acid targets by base pairing with their crRNA which enables easy re-programming of the target specificity in rapidly emerging genome engineering applications. However, undesired recognition of off-targets, that are only partially complementary to the crRNA, occurs frequently and represents a severe limitation of the technique. Off-targeting lacks comprehensive quantitative understanding and prediction. Here, we present a detailed analysis of the target recognition dynamics by the Cascade surveillance complex on a set of mismatched DNA targets using single-molecule supercoiling experiments. We demonstrate that the observed dynamics can be quantitatively modelled as a random walk over the length of the crRNA-DNA hybrid using a minimal set of parameters. The model accurately describes the recognition of targets with single and double mutations providing an important basis for quantitative off-target predictions. Importantly the model intrinsically accounts for observed bias regarding the position and the proximity between mutations and reveals that the seed length for the initiation of target recognition is controlled by DNA supercoiling rather than the Cascade structure.
Collapse
|
6
|
Vanderlinden W, Skoruppa E, Kolbeck PJ, Carlon E, Lipfert J. DNA fluctuations reveal the size and dynamics of topological domains. PNAS NEXUS 2022; 1:pgac268. [PMID: 36712371 PMCID: PMC9802373 DOI: 10.1093/pnasnexus/pgac268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022]
Abstract
DNA supercoiling is a key regulatory mechanism that orchestrates DNA readout, recombination, and genome maintenance. DNA-binding proteins often mediate these processes by bringing two distant DNA sites together, thereby inducing (transient) topological domains. In order to understand the dynamics and molecular architecture of protein-induced topological domains in DNA, quantitative and time-resolved approaches are required. Here, we present a methodology to determine the size and dynamics of topological domains in supercoiled DNA in real time and at the single-molecule level. Our approach is based on quantifying the extension fluctuations-in addition to the mean extension-of supercoiled DNA in magnetic tweezers (MT). Using a combination of high-speed MT experiments, Monte Carlo simulations, and analytical theory, we map out the dependence of DNA extension fluctuations as a function of supercoiling density and external force. We find that in the plectonemic regime, the extension variance increases linearly with increasing supercoiling density and show how this enables us to determine the formation and size of topological domains. In addition, we demonstrate how the transient (partial) dissociation of DNA-bridging proteins results in the dynamic sampling of different topological states, which allows us to deduce the torsional stiffness of the plectonemic state and the kinetics of protein-plectoneme interactions. We expect our results to further the understanding and optimization of magnetic tweezer measurements and to enable quantification of the dynamics and reaction pathways of DNA processing enzymes in the context of physiologically relevant forces and supercoiling densities.
Collapse
Affiliation(s)
| | | | - Pauline J Kolbeck
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amalienstrasse 54, 80799 Munich, Germany,Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Enrico Carlon
- Soft Matter and Biophysics, Department of Physics and Astronomy, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | | |
Collapse
|
7
|
Bespalova M, Behjatian A, Karedla N, Walker-Gibbons R, Krishnan M. Opto-Electrostatic Determination of Nucleic Acid Double-Helix Dimensions and the Structure of the Molecule–Solvent Interface. Macromolecules 2022; 55:6200-6210. [PMID: 35910310 PMCID: PMC9330769 DOI: 10.1021/acs.macromol.2c00657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A DNA molecule is
highly electrically charged in solution. The
electrical potential at the molecular surface is known to vary strongly
with the local geometry of the double helix and plays a pivotal role
in DNA–protein interactions. Further out from the molecular
surface, the electrical field propagating into the surrounding electrolyte
bears fingerprints of the three-dimensional arrangement of the charged
atoms in the molecule. However, precise extraction of the structural
information encoded in the electrostatic “far field”
has remained experimentally challenging. Here, we report an optical
microscopy-based approach that detects the field distribution surrounding
a charged molecule in solution, revealing geometric features such
as the radius and the average rise per basepair of the double helix
with up to sub-Angstrom precision, comparable with traditional molecular
structure determination techniques like X-ray crystallography and
nuclear magnetic resonance. Moreover, measurement of the helical radius
furnishes an unprecedented view of both hydration and the arrangement
of cations at the molecule–solvent interface. We demonstrate
that a probe in the electrostatic far field delivers structural and
chemical information on macromolecules, opening up a new dimension
in the study of charged molecules and interfaces in solution.
Collapse
Affiliation(s)
- Maria Bespalova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Ali Behjatian
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Narain Karedla
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Rowan Walker-Gibbons
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Madhavi Krishnan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| |
Collapse
|
8
|
Brandstetter K, Zülske T, Ragoczy T, Hörl D, Guirao-Ortiz M, Steinek C, Barnes T, Stumberger G, Schwach J, Haugen E, Rynes E, Korber P, Stamatoyannopoulos JA, Leonhardt H, Wedemann G, Harz H. Differences in nanoscale organization of regulatory active and inactive human chromatin. Biophys J 2022; 121:977-990. [PMID: 35150617 PMCID: PMC8943813 DOI: 10.1016/j.bpj.2022.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/11/2021] [Accepted: 02/07/2022] [Indexed: 11/25/2022] Open
Abstract
Methodological advances in conformation capture techniques have fundamentally changed our understanding of chromatin architecture. However, the nanoscale organization of chromatin and its cell-to-cell variance are less studied. Analyzing genome-wide data from 733 human cell and tissue samples, we identified 2 prototypical regions that exhibit high or absent hypersensitivity to deoxyribonuclease I, respectively. These regulatory active or inactive regions were examined in the lymphoblast cell line K562 by using high-throughput super-resolution microscopy. In both regions, we systematically measured the physical distance of 2 fluorescence in situ hybridization spots spaced by only 5 kb of DNA. Unexpectedly, the resulting distance distributions range from very compact to almost elongated configurations of more than 200-nm length for both the active and inactive regions. Monte Carlo simulations of a coarse-grained model of these chromatin regions based on published data of nucleosome occupancy in K562 cells were performed to understand the underlying mechanisms. There was no parameter set for the simulation model that can explain the microscopically measured distance distributions. Obviously, the chromatin state given by the strength of internucleosomal interaction, nucleosome occupancy, or amount of histone H1 differs from cell to cell, which results in the observed broad distance distributions. This large variability was not expected, especially in inactive regions. The results for the mechanisms for different distance distributions on this scale are important for understanding the contacts that mediate gene regulation. Microscopic measurements show that the inactive region investigated here is expected to be embedded in a more compact chromatin environment. The simulation results of this region require an increase in the strength of internucleosomal interactions. It may be speculated that the higher density of chromatin is caused by the increased internucleosomal interaction strength.
Collapse
Affiliation(s)
- Katharina Brandstetter
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tilo Zülske
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Tobias Ragoczy
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - David Hörl
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Miguel Guirao-Ortiz
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Clemens Steinek
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Toby Barnes
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Gabriela Stumberger
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jonathan Schwach
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - John A Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, Washington; Department of Genome Sciences, University of Washington, Seattle, Washington; Department of Medicine, Division of Oncology, University of Washington, Seattle, Washington
| | - Heinrich Leonhardt
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gero Wedemann
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany.
| | - Hartmann Harz
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.
| |
Collapse
|
9
|
Wong CK, Tang C, Schreck JS, Doye JPK. Characterizing the free-energy landscapes of DNA origamis. NANOSCALE 2022; 14:2638-2648. [PMID: 35129570 DOI: 10.1039/d1nr05716b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We show how coarse-grained modelling combined with umbrella sampling using distance-based order parameters can be applied to compute the free-energy landscapes associated with mechanical deformations of large DNA nanostructures. We illustrate this approach for the strong bending of DNA nanotubes and the potentially bistable landscape of twisted DNA origami sheets. The homogeneous bending of the DNA nanotubes is well described by the worm-like chain model; for more extreme bending the nanotubes reversibly buckle with the bending deformations localized at one or two "kinks". For a twisted one-layer DNA origami, the twist is coupled to the bending of the sheet giving rise to a free-energy landscape that has two nearly-degenerate minima that have opposite curvatures. By contrast, for a two-layer origami, the increased stiffness with respect to bending leads to a landscape with a single free-energy minimum that has a saddle-like geometry. The ability to compute such landscapes is likely to be particularly useful for DNA mechanotechnology and for understanding stress accumulation during the self-assembly of origamis into higher-order structures.
Collapse
Affiliation(s)
- Chak Kui Wong
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Chuyan Tang
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - John S Schreck
- National Center for Atmospheric Research, Computational and Information Systems Laboratory, 850 Table Mesa Drive, Boulder, CO 80305, USA
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| |
Collapse
|
10
|
Choudhary A, Maffeo C, Aksimentiev A. Multi-resolution simulation of DNA transport through large synthetic nanostructures. Phys Chem Chem Phys 2022; 24:2706-2716. [PMID: 35050282 PMCID: PMC8855663 DOI: 10.1039/d1cp04589j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Modeling and simulation has become an invaluable partner in development of nanopore sensing systems. The key advantage of the nanopore sensing method - the ability to rapidly detect individual biomolecules as a transient reduction of the ionic current flowing through the nanopore - is also its key deficiency, as the current signal itself rarely provides direct information about the chemical structure of the biomolecule. Complementing experimental calibration of the nanopore sensor readout, coarse-grained and all-atom molecular dynamics simulations have been used extensively to characterize the nanopore translocation process and to connect the microscopic events taking place inside the nanopore to the experimentally measured ionic current blockades. Traditional coarse-grained simulations, however, lack the precision needed to predict ionic current blockades with atomic resolution whereas traditional all-atom simulations are limited by the length and time scales amenable to the method. Here, we describe a multi-resolution framework for modeling electric field-driven passage of DNA molecules and nanostructures through to-scale models of synthetic nanopore systems. We illustrate the method by simulating translocation of double-stranded DNA through a solid-state nanopore and a micron-scale slit, capture and translocation of single-stranded DNA in a double nanopore system, and modeling ionic current readout from a DNA origami nanostructure passage through a nanocapillary. We expect our multi-resolution simulation framework to aid development of the nanopore field by providing accurate, to-scale modeling capability to research laboratories that do not have access to leadership supercomputer facilities.
Collapse
Affiliation(s)
- Adnan Choudhary
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
11
|
Jambrec D, Gebala M. DNA Electrostatics: From Theory to Application. ChemElectroChem 2022. [DOI: 10.1002/celc.202101415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Daliborka Jambrec
- Analytische Chemie – Elektroanalytik & Sensorik Ruhr-Universität Bochum Universitätsstr. 150 D-44780 Bochum Germany
| | - Magdalena Gebala
- Department of Biochemistry Stanford University Stanford 94305, CA USA
| |
Collapse
|
12
|
Fortais A, Loukiantchenko E, Dalnoki-Veress K. Writhing and hockling instabilities in twisted elastic fibers. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:149. [PMID: 34905133 DOI: 10.1140/epje/s10189-021-00135-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 10/06/2021] [Indexed: 06/14/2023]
Abstract
The buckling and twisting of slender, elastic fibers is a deep and well-studied field. A slender elastic rod that is twisted with respect to a fixed end will spontaneously form a loop, or hockle, to relieve the torsional stress that builds. Further twisting results in the formation of plectonemes-a helical excursion in the fiber that extends with additional twisting. Here we use an idealized, micron-scale experiment to investigate the energy stored, and subsequently released, by hockles and plectonemes as they are pulled apart, in analogy with force spectroscopy studies of DNA and protein folding. Hysteresis loops in the snapping and unsnapping inform the stored energy in the twisted fiber structures.
Collapse
Affiliation(s)
- Adam Fortais
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4M1, Canada
| | - Elsie Loukiantchenko
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4M1, Canada
| | - Kari Dalnoki-Veress
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4M1, Canada.
- UMR CNRS Gulliver 7083, ESPCI Paris, PSL Research University, 75005, Paris, France.
| |
Collapse
|
13
|
Aldag P, Welzel F, Jakob L, Schmidbauer A, Rutkauskas M, Fettes F, Grohmann D, Seidel R. Probing the stability of the SpCas9-DNA complex after cleavage. Nucleic Acids Res 2021; 49:12411-12421. [PMID: 34792162 PMCID: PMC8643700 DOI: 10.1093/nar/gkab1072] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas9 is a ribonucleoprotein complex that sequence-specifically binds and cleaves double-stranded DNA. Wildtype Cas9 and its nickase and cleavage-incompetent mutants have been used in various biological techniques due to their versatility and programmable specificity. Cas9 has been shown to bind very stably to DNA even after cleavage of the individual DNA strands, inhibiting further turnovers and considerably slowing down in-vivo repair processes. This poses an obstacle in genome editing applications. Here, we employed single-molecule magnetic tweezers to investigate the binding stability of different Streptococcus pyogenes Cas9 variants after cleavage by challenging them with supercoiling. We find that different release mechanisms occur depending on which DNA strand is cleaved. After initial target strand cleavage, supercoils are only removed after the collapse of the R-loop. We identified several states with different stabilities of the R-loop. Most importantly, we find that the post-cleavage state of Cas9 exhibits a higher stability than the pre-cleavage state. After non-target strand cleavage, supercoils are immediately but slowly released by swiveling of the non-target strand around Cas9 bound to the target strand. Consequently, Cas9 and its non-target strand nicking mutant stay stably bound to the DNA for many hours even at elevated torsional stress.
Collapse
Affiliation(s)
- Pierre Aldag
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Fabian Welzel
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Leonhard Jakob
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, Regensburg 93053, Germany
| | - Andreas Schmidbauer
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, Regensburg 93053, Germany
| | - Marius Rutkauskas
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Fergus Fettes
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| | - Dina Grohmann
- Institute of Microbiology & Archaea Centre, Single-Molecule Biochemistry Lab, University of Regensburg, Regensburg 93053, Germany
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, University of Leipzig, Leipzig 04103, Germany
| |
Collapse
|
14
|
Salerno D, Marrano CA, Cassina V, Cristofalo M, Shao Q, Finzi L, Mantegazza F, Dunlap D. Nanomechanics of negatively supercoiled diaminopurine-substituted DNA. Nucleic Acids Res 2021; 49:11778-11786. [PMID: 34718727 PMCID: PMC8599871 DOI: 10.1093/nar/gkab982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Single molecule experiments have demonstrated a progressive transition from a B- to an L-form helix as DNA is gently stretched and progressively unwound. The particular sequence of a DNA segment defines both base stacking and hydrogen bonding that affect the partitioning and conformations of the two phases. Naturally or artificially modified bases alter H-bonds and base stacking and DNA with diaminopurine (DAP) replacing adenine was synthesized to produce linear fragments with triply hydrogen-bonded DAP:T base pairs. Both unmodified and DAP-substituted DNA transitioned from a B- to an L-helix under physiological conditions of mild tension and unwinding. This transition avoids writhing and the ease of this transition may prevent cumbersome topological rearrangements in genomic DNA that would require topoisomerase activity to resolve. L-DNA displayed about tenfold lower persistence length than B-DNA. However, left-handed DAP-substituted DNA was twice as stiff as unmodified L-DNA. Unmodified DNA and DAP-substituted DNA have very distinct mechanical characteristics at physiological levels of negative supercoiling and tension.
Collapse
Affiliation(s)
- Domenico Salerno
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - Claudia Adriana Marrano
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - Valeria Cassina
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - Matteo Cristofalo
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - Qing Shao
- Department of Physics, Emory University, Atlanta, GA USA
| | - Laura Finzi
- Department of Physics, Emory University, Atlanta, GA USA
| | - Francesco Mantegazza
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, Università di Milano-Bicocca, via R. Follereau 3, Vedano al Lambro (MB), Italy
| | - David Dunlap
- Department of Physics, Emory University, Atlanta, GA USA
| |
Collapse
|
15
|
Piccolo JG, Méndez Harper J, McCalla D, Xu W, Miller S, Doan J, Kovari D, Dunlap D, Finzi L. Force spectroscopy with electromagnetic tweezers. JOURNAL OF APPLIED PHYSICS 2021; 130:134702. [PMID: 38681504 PMCID: PMC11055633 DOI: 10.1063/5.0060276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/07/2021] [Indexed: 05/01/2024]
Abstract
Force spectroscopy using magnetic tweezers (MTs) is a powerful method to probe the physical characteristics of single polymers. Typically, molecules are functionalized for specific attachment to a glass surface at one end and a micrometer-scale paramagnetic bead at the other end. By applying an external magnetic field, multiple molecules can be stretched and twisted simultaneously without exposure to potentially damaging radiation. The majority of MTs utilize mobile, permanent magnets to produce forces on the beads (and the molecule under test). However, translating and rotating the permanent magnets may require expensive precision actuators, limit the rate at which force can be changed, and may induce vibrations that disturb tether dynamics and bead tracking. Alternatively, the magnetic field can be produced with an electromagnet, which allows fast force modulation and eliminates motor-associated vibration. Here, we describe a low-cost quadrapolar electromagnetic tweezer design capable of manipulating DNA-tethered MyOne paramagnetic beads with forces as high as 15 pN. The solid-state nature of the generated B-field modulated along two axes is convenient for accessing the range of forces and torques relevant for studying the activity of DNA motor enzymes like polymerases and helicases. Our design specifically leverages technology available at an increasing number of university maker spaces and student-run machine shops. Thus, it is an accessible tool for undergraduate education that is applicable to a wide range of biophysical research questions.
Collapse
Affiliation(s)
- Joseph G. Piccolo
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - Joshua Méndez Harper
- Department of Earth Science, University of Oregon, 1272 University of Oregon, Eugene, Oregon 97403, USA
| | - Derrica McCalla
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - Wenxuan Xu
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - Sam Miller
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - Jessie Doan
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - Dan Kovari
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - David Dunlap
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - Laura Finzi
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| |
Collapse
|
16
|
Qian J, Xu W, Dunlap D, Finzi L. Single-molecule insights into torsion and roadblocks in bacterial transcript elongation. Transcription 2021; 12:219-231. [PMID: 34719335 PMCID: PMC8632135 DOI: 10.1080/21541264.2021.1997315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
During transcription, RNA polymerase (RNAP) translocates along the helical template DNA while maintaining high transcriptional fidelity. However, all genomes are dynamically twisted, writhed, and decorated by bound proteins and motor enzymes. In prokaryotes, proteins bound to DNA, specifically or not, frequently compact DNA into conformations that may silence genes by obstructing RNAP. Collision of RNAPs with these architectural proteins, may result in RNAP stalling and/or displacement of the protein roadblock. It is important to understand how rapidly transcribing RNAPs operate under different levels of supercoiling or in the presence of roadblocks. Given the broad range of asynchronous dynamics exhibited by transcriptional complexes, single-molecule assays, such as atomic force microscopy, fluorescence detection, optical and magnetic tweezers, etc. are well suited for detecting and quantifying activity with adequate spatial and temporal resolution. Here, we summarize current understanding of the effects of torsion and roadblocks on prokaryotic transcription, with a focus on single-molecule assays that provide real-time detection and readout.
Collapse
Affiliation(s)
- Jin Qian
- Emory University, Atlanta, GA, USA
| | | | | | | |
Collapse
|
17
|
Radiation-Induced Effect on Spin-Selective Electron Transfer through Self-Assembled Monolayers of ds-DNA. MAGNETOCHEMISTRY 2021. [DOI: 10.3390/magnetochemistry7070098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Stability of the DNA molecule is essential for the proper functioning and sustainability of all living organisms. In this study, we investigate the effect of gamma radiation (γ-radiation) on spin-selective electron transfer through double strand (ds)DNA molecules. Self-assembled monolayers (SAMs) of 21-base long DNA are prepared on Au-coated Ni thin film. We measure the spin polarization (%) of the SAMs of ds-DNA using the spin-dependent electrochemical technique. We use a Cs-based γ-radiation source to expose the SAMs of ds-DNA immobilized on thin films for various time intervals ranging from 0–30 min. The susceptibility of DNA to γ-radiation is measured by spin-dependent electrochemistry. We observe that the efficiency of spin filtering by ds-DNA gradually decreases when exposure (to γ-radiation) time increases, and drops below 1% after 30 min of exposure. The change in spin polarization value is related either to the conformational perturbation in DNA or to structural damage in DNA molecules caused by ionizing radiation.
Collapse
|
18
|
WASP: a software package for correctly characterizing the topological development of ribbon structures. Sci Rep 2021; 11:1527. [PMID: 33452342 PMCID: PMC7811023 DOI: 10.1038/s41598-020-80851-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/17/2020] [Indexed: 11/09/2022] Open
Abstract
We introduce the Writhe Application Software Package (WASP) which can be used to characterisze the topology of ribbon structures, the underlying mathematical model of DNA, Biopolymers, superfluid vorticies, elastic ropes and magnetic flux ropes. This characterization is achieved by the general twist–writhe decomposition of both open and closed ribbons, in particular through a quantity termed the polar writhe. We demonstrate how this decomposition is far more natural and straightforward than artificial closure methods commonly utilized in DNA modelling. In particular, we demonstrate how the decomposition of the polar writhe into local and non-local components distinctly characterizes the local helical structure and knotting/linking of the ribbon. This decomposition provides additional information not given by alternative approaches. As example applications, the WASP routines are used to characterise the evolving topology (writhe) of DNA minicircle and open ended plectoneme formation magnetic/optical tweezer simulations, and it is shown that the decomponsition into local and non-local components is particularly important for the detection of plectonemes. Finally it is demonstrated that a number of well known alternative writhe expressions are actually simplifications of the polar writhe measure.
Collapse
|
19
|
Songailiene I, Rutkauskas M, Sinkunas T, Manakova E, Wittig S, Schmidt C, Siksnys V, Seidel R. Decision-Making in Cascade Complexes Harboring crRNAs of Altered Length. Cell Rep 2019; 28:3157-3166.e4. [PMID: 31533038 PMCID: PMC6859484 DOI: 10.1016/j.celrep.2019.08.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/21/2019] [Accepted: 08/09/2019] [Indexed: 12/24/2022] Open
Abstract
The multi-subunit type I CRISPR-Cas surveillance complex Cascade uses its crRNA to recognize dsDNA targets. Recognition involves DNA unwinding and base-pairing between the crRNA spacer region and a complementary DNA strand, resulting in formation of an R-loop structure. The modular Cascade architecture allows assembly of complexes containing crRNAs with altered spacer lengths that promise increased target specificity in emerging biotechnological applications. Here we produce type I-E Cascade complexes containing crRNAs with up to 57-nt-long spacers. We show that these complexes form R-loops corresponding to the designed target length, even for the longest spacers tested. Furthermore, the complexes can bind their targets with much higher affinity compared with the wild-type form. However, target recognition and the subsequent Cas3-mediated DNA cleavage do not require extended R-loops but already occur for wild-type-sized R-loops. These findings set important limits for specificity improvements of type I CRISPR-Cas systems.
Collapse
Affiliation(s)
- Inga Songailiene
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Marius Rutkauskas
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| | - Tomas Sinkunas
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Elena Manakova
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania
| | - Sabine Wittig
- HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Carla Schmidt
- HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Vilnius 10257, Lithuania.
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany.
| |
Collapse
|
20
|
Krivoy A, Rutkauskas M, Kuznedelov K, Musharova O, Rouillon C, Severinov K, Seidel R. Primed CRISPR adaptation in Escherichia coli cells does not depend on conformational changes in the Cascade effector complex detected in Vitro. Nucleic Acids Res 2019; 46:4087-4098. [PMID: 29596641 PMCID: PMC5934681 DOI: 10.1093/nar/gky219] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/14/2018] [Indexed: 11/13/2022] Open
Abstract
In type I CRISPR-Cas systems, primed adaptation of new spacers into CRISPR arrays occurs when the effector Cascade-crRNA complex recognizes imperfectly matched targets that are not subject to efficient CRISPR interference. Thus, primed adaptation allows cells to acquire additional protection against mobile genetic elements that managed to escape interference. Biochemical and biophysical studies suggested that Cascade-crRNA complexes formed on fully matching targets (subject to efficient interference) and on partially mismatched targets that promote primed adaption are structurally different. Here, we probed Escherichia coli Cascade-crRNA complexes bound to matched and mismatched DNA targets using a magnetic tweezers assay. Significant differences in complex stabilities were observed consistent with the presence of at least two distinct conformations. Surprisingly, in vivo analysis demonstrated that all mismatched targets stimulated robust primed adaptation irrespective of conformational states observed in vitro. Our results suggest that primed adaptation is a direct consequence of a reduced interference efficiency and/or rate and is not a consequence of distinct effector complex conformations on target DNA.
Collapse
Affiliation(s)
- Andrey Krivoy
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| | - Marius Rutkauskas
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| | - Konstantin Kuznedelov
- Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Olga Musharova
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Christophe Rouillon
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| | - Konstantin Severinov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Waksman Institute, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.,Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig 04103, Germany
| |
Collapse
|
21
|
Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA. Biophys J 2019; 116:1394-1405. [PMID: 30954211 DOI: 10.1016/j.bpj.2019.03.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/12/2019] [Indexed: 01/17/2023] Open
Abstract
DNA intercalators bind nucleic acids by stacking between adjacent basepairs. This causes a considerable elongation of the DNA backbone as well as untwisting of the double helix. In the past few years, single-molecule mechanical experiments have become a common tool to characterize these deformations and to quantify important parameters of the intercalation process. Parameter extraction typically relies on the neighbor-exclusion model, in which a bound intercalator prevents intercalation into adjacent sites. Here, we challenge the neighbor-exclusion model by carefully quantifying and modeling the force-extension and twisting behavior of single ethidium-complexed DNA molecules. We show that only an anticooperative ethidium binding that allows for a disfavored but nonetheless possible intercalation into nearest-neighbor sites can consistently describe the mechanical behavior of intercalator-bound DNA. At high ethidium concentrations and elevated mechanical stress, this causes an almost complete occupation of nearest-neighbor sites and almost a doubling of the DNA contour length. We furthermore show that intercalation into nearest-neighbor sites needs to be considered when estimating intercalator parameters from zero-stress elongation and twisting data. We think that the proposed anticooperative binding mechanism may also be applicable to other intercalating molecules.
Collapse
|
22
|
Erlenbach N, Grünewald C, Krstic B, Heckel A, Prisner TF. "End-to-end" stacking of small dsRNA. RNA (NEW YORK, N.Y.) 2019; 25:239-246. [PMID: 30404925 PMCID: PMC6348986 DOI: 10.1261/rna.068130.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/06/2018] [Indexed: 05/08/2023]
Abstract
PELDOR (pulsed electron-electron double resonance) is an established method to study intramolecular distances and can give evidence for conformational changes and flexibilities. However, it can also be used to study intermolecular interactions as for example oligerimization. Here, we used PELDOR to study the "end-to-end" stacking of small double-stranded (ds) RNAs. For this study, the dsRNA molecules were only singly labeled with the spin label TPA to avoid multispin effects and to measure only the intermolecular stacking interactions. It can be shown that small dsRNAs tend to assemble to rod-like structures due to π-π interactions between the base pairs at the end of the strands. On the one hand, these interactions can influence or complicate measurements aimed at the determining of the structure and dynamics of the dsRNA molecule itself. On the other hand, it can be interesting to study such intermolecular stacking interactions in more detail, as for example their dependence on ion concentration. We quantitatively determined the stacking probability as a function of the monovalent NaCl salt and the dsRNA concentration. From these data, the dissociation constant Kd was deduced and found to depend on the ratio between the NaCl salt and dsRNA concentrations. Additionally, the distances and distance distributions obtained predict a model for the stacking geometry of dsRNAs. Introducing a nucleotide overhangs at one end of the dsRNA molecule restricts the stacking to the other end, leading only to dimer formations. Introducing such an overhang at both ends of the dsRNA molecule fully suppresses stacking, as we demonstrate by PELDOR experiments quantitatively.
Collapse
Affiliation(s)
- Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Bisera Krstic
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
| |
Collapse
|
23
|
Min Y, Purohit PK. Discontinuous growth of DNA plectonemes due to atomic scale friction. SOFT MATTER 2018; 14:7759-7770. [PMID: 30209494 PMCID: PMC6158071 DOI: 10.1039/c8sm00852c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We develop a model to explain discontinuities in the increase of the length of a DNA plectoneme when the DNA filament is continuously twisted under tension. We account for DNA elasticity, electrostatic interactions and entropic effects due to thermal fluctuation. We postulate that a corrugated energy landscape that contains energy barriers is the cause of jumps in the length of the plectoneme as the number of turns is increased. Thus, our model is similar to the Prandtl-Tomlinson model of atomic scale friction. The existence of a corrugated energy landscape can be justified due to the close proximity of the neighboring pieces of DNA in a plectoneme. We assume the corrugated energy landscape to be sinusoidal since the plectoneme has a periodic helical structure and rotation of the bead is a form of periodic motion. We perform calculations with different tensile forces and ionic concentrations, and show that rotation-extension curves manifest stair-step shapes under relatively high ionic concentrations and high forces. We show that the jump in the plectonemic growth is caused by the flattening of the energy barrier in the corrugated landscape.
Collapse
Affiliation(s)
- Yifei Min
- Graduate Group in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Prashant K. Purohit
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA. Tel.:+215 898 3870; Fax: +215 573 6334.
| |
Collapse
|
24
|
Zhou MH, Meng WL, Zhang CY, Li XB, Wu JZ, Zhang NH. The pH-dependent elastic properties of nanoscale DNA films and the resultant bending signals for microcantilever biosensors. SOFT MATTER 2018; 14:3028-3039. [PMID: 29637943 DOI: 10.1039/c7sm01883e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The diverse mechanical properties of nanoscale DNA films on solid substrates have a close correlation with complex detection signals of micro-/nano-devices. This paper is devoted to formulating several multiscale models to study the effect of pH-dependent ionic inhomogeneity on the graded elastic properties of nanoscale DNA films and the resultant bending deflections of microcantilever biosensors. First, a modified inverse Debye length is introduced to improve the classical Poisson-Boltzmann equation for the electrical potential of DNA films to consider the inhomogeneous effect of hydrogen ions. Second, the graded characteristics of the particle distribution are taken into consideration for an improvement in Parsegian's mesoscopic potential for both attraction-dominated and repulsion-dominated films. Third, by the improved interchain interaction potential and the thought experiment about the compression of a macroscopic continuum DNA bar, we investigate the diversity of the elastic properties of single-stranded DNA (ssDNA) films due to pH variations. The relevant theoretical predictions quantitatively or qualitatively agree well with the relevant DNA experiments on the electrical potential, film thickness, condensation force, elastic modulus, and microcantilever deflections. The competition between attraction and repulsion among the fixed charges and the free ions endows the DNA film with mechanical properties such as a remarkable size effect and a non-monotonic behavior, and a negative elastic modulus is first revealed in the attraction-dominated ssDNA film. There exists a transition between the pH-sensitive parameter interval and the pH-insensitive one for the bending signals of microcantilevers, which is predominated by the initial stress effect in the DNA film.
Collapse
Affiliation(s)
- Mei-Hong Zhou
- Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Institute of Applied Mathematics and Mechanics, Shanghai University, Shanghai 200072, China
| | | | | | | | | | | |
Collapse
|
25
|
Wieczór M, Czub J. How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1. Nucleic Acids Res 2017. [PMID: 28633355 PMCID: PMC5737604 DOI: 10.1093/nar/gkx534] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA. For the first time, we describe the spontaneous formation of a sequence-specific native protein-DNA complex in atomistic detail, and study the mechanism by which proteins avoid off-target binding while retaining high affinity for target sites. Our calculated free energy landscapes reproduce the thermodynamics of sequence-specific binding, while statistical approaches allow for a comprehensive description of intermediate stages of complex formation.
Collapse
Affiliation(s)
- Milosz Wieczór
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| |
Collapse
|
26
|
Kriegel F, Ermann N, Forbes R, Dulin D, Dekker NH, Lipfert J. Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers. Nucleic Acids Res 2017; 45:5920-5929. [PMID: 28460037 PMCID: PMC5449586 DOI: 10.1093/nar/gkx280] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/28/2017] [Indexed: 12/14/2022] Open
Abstract
The mechanical properties of DNA fundamentally constrain and enable the storage and transmission of genetic information and its use in DNA nanotechnology. Many properties of DNA depend on the ionic environment due to its highly charged backbone. In particular, both theoretical analyses and direct single-molecule experiments have shown its bending stiffness to depend on salt concentration. In contrast, the salt-dependence of the twist stiffness of DNA is much less explored. Here, we employ optimized multiplexed magnetic torque tweezers to study the torsional stiffness of DNA under varying salt conditions as a function of stretching force. At low forces (<3 pN), the effective torsional stiffness is ∼10% smaller for high salt conditions (500 mM NaCl or 10 mM MgCl2) compared to lower salt concentrations (20 mM NaCl and 100 mM NaCl). These differences, however, can be accounted for by taking into account the known salt dependence of the bending stiffness. In addition, the measured high-force (6.5 pN) torsional stiffness values of C = 103 ± 4 nm are identical, within experimental errors, for all tested salt concentration, suggesting that the intrinsic torsional stiffness of DNA does not depend on salt.
Collapse
Affiliation(s)
- Franziska Kriegel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Niklas Ermann
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Ruaridh Forbes
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - David Dulin
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.,Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Hartmannstrasse 14, 91052 Erlangen, Germany
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| |
Collapse
|
27
|
Zavadlav J, Podgornik R, Praprotnik M. Order and interactions in DNA arrays: Multiscale molecular dynamics simulation. Sci Rep 2017; 7:4775. [PMID: 28684875 PMCID: PMC5500594 DOI: 10.1038/s41598-017-05109-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/06/2017] [Indexed: 11/21/2022] Open
Abstract
While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.
Collapse
Affiliation(s)
- Julija Zavadlav
- Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia.,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia.,Chair of Computational Science, ETH Zurich, Clausiusstrasse 33, CH-8092, Zurich, Switzerland
| | - Rudolf Podgornik
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia. .,Theoretical Physics Department, J. Stefan Institute, Jamova c. 39, SI-1000, Ljubljana, Slovenia.
| | - Matej Praprotnik
- Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia. .,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000, Ljubljana, Slovenia.
| |
Collapse
|
28
|
Saurabh S, Lansac Y, Jang YH, Glaser MA, Clark NA, Maiti PK. Understanding the origin of liquid crystal ordering of ultrashort double-stranded DNA. Phys Rev E 2017; 95:032702. [PMID: 28415169 DOI: 10.1103/physreve.95.032702] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Indexed: 06/07/2023]
Abstract
Recent experiments have shown that short double-stranded DNA (dsDNA) fragments having six- to 20-base pairs exhibit various liquid crystalline phases. This violates the condition of minimum molecular shape anisotropy that analytical theories demand for liquid crystalline ordering. It has been hypothesized that the liquid crystalline ordering is the result of end-to-end stacking of dsDNA to form long supramolecular columns which satisfy the shape anisotropy criterion necessary for ordering. To probe the thermodynamic feasibility of this process, we perform molecular dynamics simulations on ultrashort (four base pair long) dsDNA fragments, quantify the strong end-to-end attraction between them, and demonstrate that the nematic ordering of the self-assembled stacked columns is retained for a large range of temperature and salt concentration.
Collapse
Affiliation(s)
- Suman Saurabh
- Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
- GREMAN, Université François Rabelais, CNRS UMR 7347, 37200 Tours, France
| | - Yves Lansac
- GREMAN, Université François Rabelais, CNRS UMR 7347, 37200 Tours, France
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| | - Yun Hee Jang
- Department of Energy Systems Engineering, DGIST, Daegu 42988, Korea
| | - Matthew A Glaser
- Department of Physics and Liquid Crystal Materials Research Center, University of Colorado, Boulder, Colorado 80309, USA
| | - Noel A Clark
- Department of Physics and Liquid Crystal Materials Research Center, University of Colorado, Boulder, Colorado 80309, USA
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
29
|
Rutkauskas M, Krivoy A, Szczelkun MD, Rouillon C, Seidel R. Single-Molecule Insight Into Target Recognition by CRISPR-Cas Complexes. Methods Enzymol 2016; 582:239-273. [PMID: 28062037 DOI: 10.1016/bs.mie.2016.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ribonucleoprotein (RNP) complexes from CRISPR-Cas systems have attracted enormous interest since they can be easily and flexibly reprogrammed to target any desired locus for genome engineering and gene regulation applications. Basis for the programmability is a short RNA (crRNA) inside these complexes that recognizes the target nucleic acid by base pairing. For CRISPR-Cas systems that target double-stranded DNA this results in local DNA unwinding and formation of a so-called R-loop structure. Here we provide an overview how this target recognition mechanism can be dissected in great detail at the level of a single molecule. Specifically, we demonstrate how magnetic tweezers are applied to measure the local DNA unwinding at the target in real time. To this end we introduce the technique and the measurement principle. By studying modifications of the consensus target sequence, we show how different sequence elements contribute to the target recognition mechanism. From these data, a unified target recognition mechanism can be concluded for the RNPs Cascade and Cas9 from types I and II CRISPR-Cas systems. R-loop formation is hereby initiated on the target at an upstream element, called protospacer adjacent motif (PAM), from which the R-loop structure zips directionally toward the PAM-distal end of the target. At mismatch positions, the R-loop propagation stalls and further propagation competes with collapse of the structure. Upon full R-loop zipping conformational changes within the RNPs trigger degradation of the DNA target. This represents a shared labor mechanism in which zipping between nucleic acid strands is the actual target recognition mechanism while sensing of the R-loop arrival at the PAM-distal end just verifies the success of the full zipping.
Collapse
Affiliation(s)
- M Rutkauskas
- Molecular Biophysics Group, Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany
| | - A Krivoy
- Molecular Biophysics Group, Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany; Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - M D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - C Rouillon
- Molecular Biophysics Group, Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany.
| | - R Seidel
- Molecular Biophysics Group, Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany.
| |
Collapse
|
30
|
O' Lee DJ, Danilowicz C, Rochester C, Kornyshev AA, Prentiss M. Evidence of protein-free homology recognition in magnetic bead force-extension experiments. Proc Math Phys Eng Sci 2016; 472:20160186. [PMID: 27493568 PMCID: PMC4971244 DOI: 10.1098/rspa.2016.0186] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Earlier theoretical studies have proposed that the homology-dependent pairing of large tracts of dsDNA may be due to physical interactions between homologous regions. Such interactions could contribute to the sequence-dependent pairing of chromosome regions that may occur in the presence or the absence of double-strand breaks. Several experiments have indicated the recognition of homologous sequences in pure electrolytic solutions without proteins. Here, we report single-molecule force experiments with a designed 60 kb long dsDNA construct; one end attached to a solid surface and the other end to a magnetic bead. The 60 kb constructs contain two 10 kb long homologous tracts oriented head to head, so that their sequences match if the two tracts fold on each other. The distance between the bead and the surface is measured as a function of the force applied to the bead. At low forces, the construct molecules extend substantially less than normal, control dsDNA, indicating the existence of preferential interaction between the homologous regions. The force increase causes no abrupt but continuous unfolding of the paired homologous regions. Simple semi-phenomenological models of the unfolding mechanics are proposed, and their predictions are compared with the data.
Collapse
Affiliation(s)
- D J O' Lee
- Department of Chemistry , Imperial College London , London SW7 2AZ, UK
| | - C Danilowicz
- Department of Physics , Harvard University, Cambridge , MA 02138, USA
| | - C Rochester
- Department of Chemistry , Imperial College London , London SW7 2AZ, UK
| | - A A Kornyshev
- Department of Chemistry , Imperial College London , London SW7 2AZ, UK
| | - M Prentiss
- Department of Physics , Harvard University, Cambridge , MA 02138, USA
| |
Collapse
|
31
|
Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers. J Struct Biol 2016; 197:26-36. [PMID: 27368129 DOI: 10.1016/j.jsb.2016.06.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/06/2016] [Accepted: 06/28/2016] [Indexed: 11/21/2022]
Abstract
Nucleic acids are central to the storage and transmission of genetic information. Mechanical properties, along with their sequence, both enable and fundamentally constrain the biological functions of DNA and RNA. For small deformations from the equilibrium conformations, nucleic acids are well described by an isotropic elastic rod model. However, external forces and torsional strains can induce conformational changes, giving rise to a complex force-torque phase diagram. This review focuses on magnetic tweezers as a powerful tool to precisely determine both the elastic parameters and conformational transitions of nucleic acids under external forces and torques at the single-molecule level. We review several variations of magnetic tweezers, in particular conventional magnetic tweezers, freely orbiting magnetic tweezers and magnetic torque tweezers, and discuss their characteristic capabilities. We then describe the elastic rod model for DNA and RNA and discuss conformational changes induced by mechanical stress. The focus lies on the responses to torque and twist, which are crucial in the mechanics and interactions of nucleic acids and can directly be measured using magnetic tweezers. We conclude by highlighting several recent studies of nucleic acid-protein and nucleic acid-small-molecule interactions as further applications of magnetic tweezers and give an outlook of some exciting developments to come.
Collapse
|
32
|
TrmBL2 from Pyrococcus furiosus Interacts Both with Double-Stranded and Single-Stranded DNA. PLoS One 2016; 11:e0156098. [PMID: 27214207 PMCID: PMC4877046 DOI: 10.1371/journal.pone.0156098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/08/2016] [Indexed: 12/12/2022] Open
Abstract
In many hyperthermophilic archaea the DNA binding protein TrmBL2 or one of its homologues is abundantly expressed. TrmBL2 is thought to play a significant role in modulating the chromatin architecture in combination with the archaeal histone proteins and Alba. However, its precise physiological role is poorly understood. It has been previously shown that upon binding TrmBL2 covers double-stranded DNA, which leads to the formation of a thick and fibrous filament. Here we investigated the filament formation process as well as the stabilization of DNA by TrmBL2 from Pyroccocus furiosus in detail. We used magnetic tweezers that allow to monitor changes of the DNA mechanical properties upon TrmBL2 binding on the single-molecule level. Extended filaments formed in a cooperative manner and were considerably stiffer than bare double-stranded DNA. Unlike Alba, TrmBL2 did not form DNA cross-bridges. The protein was found to bind double- and single-stranded DNA with similar affinities. In mechanical disruption experiments of DNA hairpins this led to stabilization of both, the double- (before disruption) and the single-stranded (after disruption) DNA forms. Combined, these findings suggest that the biological function of TrmBL2 is not limited to modulating genome architecture and acting as a global repressor but that the protein acts additionally as a stabilizer of DNA secondary structure.
Collapse
|
33
|
Lepage T, Képès F, Junier I. Thermodynamics of long supercoiled molecules: insights from highly efficient Monte Carlo simulations. Biophys J 2016; 109:135-43. [PMID: 26153710 DOI: 10.1016/j.bpj.2015.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 05/26/2015] [Accepted: 06/02/2015] [Indexed: 12/21/2022] Open
Abstract
Supercoiled DNA polymer models for which the torsional energy depends on the total twist of molecules (Tw) are a priori well suited for thermodynamic analysis of long molecules. So far, nevertheless, the exact determination of Tw in these models has been based on a computation of the writhe of the molecules (Wr) by exploiting the conservation of the linking number, Lk=Tw+Wr, which reflects topological constraints coming from the helical nature of DNA. Because Wr is equal to the number of times the main axis of a DNA molecule winds around itself, current Monte Carlo algorithms have a quadratic time complexity, O(L(2)), with respect to the contour length (L) of the molecules. Here, we present an efficient method to compute Tw exactly, leading in principle to algorithms with a linear complexity, which in practice is O(L(1.2)). Specifically, we use a discrete wormlike chain that includes the explicit double-helix structure of DNA and where the linking number is conserved by continuously preventing the generation of twist between any two consecutive cylinders of the discretized chain. As an application, we show that long (up to 21 kbp) linear molecules stretched by mechanical forces akin to magnetic tweezers contain, in the buckling regime, multiple and branched plectonemes that often coexist with curls and helices, and whose length and number are in good agreement with experiments. By attaching the ends of the molecules to a reservoir of twists with which these can exchange helix turns, we also show how to compute the torques in these models. As an example, we report values that are in good agreement with experiments and that concern the longest molecules that have been studied so far (16 kbp).
Collapse
Affiliation(s)
- Thibaut Lepage
- Institute of Systems and Synthetic Biology, Genopole, CNRS, University of Évry, Évry, France; Laboratoire Adaptation et Pathogénie des Micro-organismes-UMR 5163, Université Grenoble 1, CNRS, Grenoble, France
| | - François Képès
- Institute of Systems and Synthetic Biology, Genopole, CNRS, University of Évry, Évry, France; Department of BioEngineering, Imperial College London, London, United Kingdom
| | - Ivan Junier
- Laboratoire Adaptation et Pathogénie des Micro-organismes-UMR 5163, Université Grenoble 1, CNRS, Grenoble, France; Centre for Genomic Regulation (CRG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
34
|
Snodin BEK, Randisi F, Mosayebi M, Šulc P, Schreck JS, Romano F, Ouldridge TE, Tsukanov R, Nir E, Louis AA, Doye JPK. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. J Chem Phys 2016; 142:234901. [PMID: 26093573 DOI: 10.1063/1.4921957] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na(+)] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.
Collapse
Affiliation(s)
- Benedict E K Snodin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ferdinando Randisi
- Life Sciences Interface Doctoral Training Center, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Majid Mosayebi
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Petr Šulc
- Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - John S Schreck
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Thomas E Ouldridge
- Department of Mathematics, Imperial College, 180 Queen's Gate, London SW7 2AZ, United Kingdom
| | - Roman Tsukanov
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eyal Nir
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| |
Collapse
|
35
|
Daldrop P, Brutzer H, Huhle A, Kauert DJ, Seidel R. Extending the range for force calibration in magnetic tweezers. Biophys J 2016; 108:2550-2561. [PMID: 25992733 DOI: 10.1016/j.bpj.2015.04.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/10/2015] [Accepted: 04/14/2015] [Indexed: 12/11/2022] Open
Abstract
Magnetic tweezers are a wide-spread tool used to study the mechanics and the function of a large variety of biomolecules and biomolecular machines. This tool uses a magnetic particle and a strong magnetic field gradient to apply defined forces to the molecule of interest. Forces are typically quantified by analyzing the lateral fluctuations of the biomolecule-tethered particle in the direction perpendicular to the applied force. Since the magnetic field pins the anisotropy axis of the particle, the lateral fluctuations follow the geometry of a pendulum with a short pendulum length along and a long pendulum length perpendicular to the field lines. Typically, the short pendulum geometry is used for force calibration by power-spectral-density (PSD) analysis, because the movement of the bead in this direction can be approximated by a simple translational motion. Here, we provide a detailed analysis of the fluctuations according to the long pendulum geometry and show that for this direction, both the translational and the rotational motions of the particle have to be considered. We provide analytical formulas for the PSD of this coupled system that agree well with PSDs obtained in experiments and simulations and that finally allow a faithful quantification of the magnetic force for the long pendulum geometry. We furthermore demonstrate that this methodology allows the calibration of much larger forces than the short pendulum geometry in a tether-length-dependent manner. In addition, the accuracy of determination of the absolute force is improved. Our force calibration based on the long pendulum geometry will facilitate high-resolution magnetic-tweezers experiments that rely on short molecules and large forces, as well as highly parallelized measurements that use low frame rates.
Collapse
Affiliation(s)
- Peter Daldrop
- Institute for Molecular Cell Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Hergen Brutzer
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Alexander Huhle
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Dominik J Kauert
- Institute for Molecular Cell Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Ralf Seidel
- Institute for Molecular Cell Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany; Biotechnology Center, Technische Universität Dresden, Dresden, Germany; Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany.
| |
Collapse
|
36
|
Yoo J, Aksimentiev A. Improved Parameterization of Amine–Carboxylate and Amine–Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields. J Chem Theory Comput 2015; 12:430-43. [DOI: 10.1021/acs.jctc.5b00967] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jejoong Yoo
- Center for the Physics of
Living Cells, Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Center for the Physics of
Living Cells, Department of Physics, University of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| |
Collapse
|
37
|
Suma A, Rosa A, Micheletti C. Pore Translocation of Knotted Polymer Chains: How Friction Depends on Knot Complexity. ACS Macro Lett 2015; 4:1420-1424. [PMID: 35614794 DOI: 10.1021/acsmacrolett.5b00747] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Knots can affect the capability of polymers to translocate through narrow pores in complex and counterintuitive ways that are still relatively unexplored. We report here on a systematic theoretical and computational investigation of the driven translocation of flexible chains accommodating a large repertoire of knots trapped at the pore entrance. These include composite knots, which are the most common form of spontaneous entanglement in long polymers. Two unexpected results emerge from this study. First, the high force translocation compliance does not decrease systematically with knot complexity. Second, the response of composite knots is so dependent on the order of their factor knots, that their hindrance can even be lower than some of their prime components. We show that the resulting rich and seemingly disparate phenomenology can be captured in a seamless framework based on the mechanism by which the tractive force is propagated along and past the knots. The quantitative scheme can be viably used for predictive purposes and, hence, ought to be useful in applicative contexts, too.
Collapse
Affiliation(s)
- Antonio Suma
- SISSA, International School for Advanced
Studies, via Bonomea 265, I-34136 Trieste, Italy
| | - Angelo Rosa
- SISSA, International School for Advanced
Studies, via Bonomea 265, I-34136 Trieste, Italy
| | - Cristian Micheletti
- SISSA, International School for Advanced
Studies, via Bonomea 265, I-34136 Trieste, Italy
| |
Collapse
|
38
|
Michieletto D, Marenduzzo D, Orlandini E. Topological patterns in two-dimensional gel electrophoresis of DNA knots. Proc Natl Acad Sci U S A 2015; 112:E5471-7. [PMID: 26351668 PMCID: PMC4603474 DOI: 10.1073/pnas.1506907112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. Although there is a large body of experimental work that allows us to accurately separate different topoisomers of a molecule, a full theoretical understanding of these experiments has not yet been achieved. Here we show that the mobility of DNA knots depends crucially and subtly on the physical properties of the gel and, in particular, on the presence of dangling ends. The topological interactions between these and DNA molecules can be described in terms of an "entanglement number" and yield a nonmonotonic mobility at moderate fields. Consequently, in 2D electrophoresis, gel bands display a characteristic arc pattern; this turns into a straight line when the density of dangling ends vanishes. We also provide a novel framework to accurately predict the shape of such arcs as a function of molecule length and topological complexity, which may be used to inform future experiments.
Collapse
Affiliation(s)
- Davide Michieletto
- Department of Physics and Complexity Science, University of Warwick, Coventry CV4 7AL, United Kingdom;
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione, Istituto Nazionale di Fisica Nucleare, Universitá di Padova, 35131 Padova, Italy
| |
Collapse
|
39
|
Müller O, Kepper N, Schöpflin R, Ettig R, Rippe K, Wedemann G. Changing chromatin fiber conformation by nucleosome repositioning. Biophys J 2015; 107:2141-50. [PMID: 25418099 DOI: 10.1016/j.bpj.2014.09.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 09/11/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022] Open
Abstract
Chromatin conformation is dynamic and heterogeneous with respect to nucleosome positions, which can be changed by chromatin remodeling complexes in the cell. These molecular machines hydrolyze ATP to translocate or evict nucleosomes, and establish loci with regularly and more irregularly spaced nucleosomes as well as nucleosome-depleted regions. The impact of nucleosome repositioning on the three-dimensional chromatin structure is only poorly understood. Here, we address this issue by using a coarse-grained computer model of arrays of 101 nucleosomes considering several chromatin fiber models with and without linker histones, respectively. We investigated the folding of the chain in dependence of the position of the central nucleosome by changing the length of the adjacent linker DNA in basepair steps. We found in our simulations that these translocations had a strong effect on the shape and properties of chromatin fibers: i), Fiber curvature and flexibility at the center were largely increased and long-range contacts between distant nucleosomes on the chain were promoted. ii), The highest destabilization of the fiber conformation occurred for a nucleosome shifted by two basepairs from regular spacing, whereas effects of linker DNA changes of ?10 bp in phase with the helical twist of DNA were minimal. iii), A fiber conformation can stabilize a regular spacing of nucleosomes inasmuch as favorable stacking interactions between nucleosomes are facilitated. This can oppose nucleosome translocations and increase the energetic costs for chromatin remodeling. Our computational modeling framework makes it possible to describe the conformational heterogeneity of chromatin in terms of nucleosome positions, and thus advances theoretical models toward a better understanding of how genome compaction and access are regulated within the cell.
Collapse
Affiliation(s)
- Oliver Müller
- Institute for Applied Computer Science, University of Applied Sciences Stralsund, Stralsund, Germany
| | - Nick Kepper
- Deutsches Krebsforschungszentrum and BioQuant, Heidelberg, Germany
| | - Robert Schöpflin
- Institute for Applied Computer Science, University of Applied Sciences Stralsund, Stralsund, Germany
| | - Ramona Ettig
- Deutsches Krebsforschungszentrum and BioQuant, Heidelberg, Germany
| | - Karsten Rippe
- Deutsches Krebsforschungszentrum and BioQuant, Heidelberg, Germany
| | - Gero Wedemann
- Institute for Applied Computer Science, University of Applied Sciences Stralsund, Stralsund, Germany.
| |
Collapse
|
40
|
Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection. Cell Rep 2015; 10:1534-1543. [PMID: 25753419 DOI: 10.1016/j.celrep.2015.01.067] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/09/2015] [Accepted: 01/28/2015] [Indexed: 11/21/2022] Open
Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against foreign nucleic acids. In type I CRISPR-Cas systems, invading DNA is detected by a large ribonucleoprotein surveillance complex called Cascade. The crRNA component of Cascade is used to recognize target sites in foreign DNA (protospacers) by formation of an R-loop driven by base-pairing complementarity. Using single-molecule supercoiling experiments with near base-pair resolution, we probe here the mechanism of R-loop formation and detect short-lived R-loop intermediates on off-target sites bearing single mismatches. We show that R-loops propagate directionally starting from the protospacer-adjacent motif (PAM). Upon reaching a mismatch, R-loop propagation stalls and collapses in a length-dependent manner. This unambiguously demonstrates that directional zipping of the R-loop accomplishes efficient target recognition by rapidly rejecting binding to off-target sites with PAM-proximal mutations. R-loops that reach the protospacer end become locked to license DNA degradation by the auxiliary Cas3 nuclease/helicase without further target verification.
Collapse
|
41
|
Lipfert J, van Oene MM, Lee M, Pedaci F, Dekker NH. Torque spectroscopy for the study of rotary motion in biological systems. Chem Rev 2014; 115:1449-74. [PMID: 25541648 DOI: 10.1021/cr500119k] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for NanoScience (CeNS), Ludwig-Maximilian-University Munich , Amalienstrasse 54, 80799 Munich, Germany
| | | | | | | | | |
Collapse
|
42
|
Maffeo C, Yoo J, Comer J, Wells DB, Luan B, Aksimentiev A. Close encounters with DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:413101. [PMID: 25238560 PMCID: PMC4207370 DOI: 10.1088/0953-8984/26/41/413101] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.
Collapse
Affiliation(s)
- C Maffeo
- Department of Physics, University of Illinois, Urbana, IL, USA
| | | | | | | | | | | |
Collapse
|
43
|
Si W, Zhang Y, Wu G, Sha J, Liu L, Chen Y. DNA sequencing technology based on nanopore sensors by theoretical calculations and simulations. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11434-014-0622-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
44
|
Di Stefano M, Tubiana L, Di Ventra M, Micheletti C. Driving knots on DNA with AC/DC electric fields: topological friction and memory effects. SOFT MATTER 2014; 10:6491-6498. [PMID: 25048107 DOI: 10.1039/c4sm00160e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The dynamical properties of entangled polyelectrolytes are investigated theoretically and computationally for a proposed novel micromanipulation setup. Specifically, we investigate the effects of DC and AC electric fields acting longitudinally on knotted DNA chains, modelled as semiflexible chains of charged beads, under mechanical tension. We consider various experimentally accessible values of the field amplitude and frequency as well as several of the simplest knot types. In particular, we consider both torus and twist knots because they are respectively known to be able or unable to slide along macroscopic threads and ropes. Strikingly, this qualitative distinction disappears in this microscopic context because all the considered knot types acquire a systematic drift in the direction of the electric force. Notably, the knot drift velocity and diffusion coefficient in zero field (both measurable also experimentally) can be used to define a characteristic "frictional" lengthscale for the various knot types. This previously unexplored length provides valuable information on the extent of self-interactions in the nominal knotted region. It is finally observed that the motion of a knot can effectively follow the AC field only if the driving period is larger than the knot relaxation time (for which the self-diffusion time provides an upper bound). These results suggest that salient aspects of the intrinsic dynamics of knots in DNA chains could be probed experimentally by means of external, time-dependent electric fields.
Collapse
Affiliation(s)
- Marco Di Stefano
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy.
| | | | | | | |
Collapse
|
45
|
Szczelkun MD, Tikhomirova MS, Sinkunas T, Gasiunas G, Karvelis T, Pschera P, Siksnys V, Seidel R. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc Natl Acad Sci U S A 2014; 111:9798-803. [PMID: 24912165 PMCID: PMC4103346 DOI: 10.1073/pnas.1402597111] [Citation(s) in RCA: 311] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems protect bacteria and archaea from infection by viruses and plasmids. Central to this defense is a ribonucleoprotein complex that produces RNA-guided cleavage of foreign nucleic acids. In DNA-targeting CRISPR-Cas systems, the RNA component of the complex encodes target recognition by forming a site-specific hybrid (R-loop) with its complement (protospacer) on an invading DNA while displacing the noncomplementary strand. Subsequently, the R-loop structure triggers DNA degradation. Although these reactions have been reconstituted, the exact mechanism of R-loop formation has not been fully resolved. Here, we use single-molecule DNA supercoiling to directly observe and quantify the dynamics of torque-dependent R-loop formation and dissociation for both Cascade- and Cas9-based CRISPR-Cas systems. We find that the protospacer adjacent motif (PAM) affects primarily the R-loop association rates, whereas protospacer elements distal to the PAM affect primarily R-loop stability. Furthermore, Cascade has higher torque stability than Cas9 by using a conformational locking step. Our data provide direct evidence for directional R-loop formation, starting from PAM recognition and expanding toward the distal protospacer end. Moreover, we introduce DNA supercoiling as a quantitative tool to explore the sequence requirements and promiscuities of orthogonal CRISPR-Cas systems in rapidly emerging gene-targeting applications.
Collapse
Affiliation(s)
- Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom;
| | - Maria S Tikhomirova
- Institute for Molecular Cell Biology, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany;Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany; and
| | - Tomas Sinkunas
- Department of Protein-Nucleic Acid Interactions, Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Giedrius Gasiunas
- Department of Protein-Nucleic Acid Interactions, Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Tautvydas Karvelis
- Department of Protein-Nucleic Acid Interactions, Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Patrizia Pschera
- Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany; and
| | - Virginijus Siksnys
- Department of Protein-Nucleic Acid Interactions, Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Ralf Seidel
- Institute for Molecular Cell Biology, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany;Biotechnology Center, Technische Universität Dresden, 01062 Dresden, Germany; and
| |
Collapse
|
46
|
O'Lee DJ. Undulations in a weakly interacting mechanically generated molecular braid under tension. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:245101. [PMID: 24848455 DOI: 10.1088/0953-8984/26/24/245101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We consider mechanically generated molecular braids composed of two molecules where long range interactions between them can be considered to be very weak. We describe a model that takes account of the thermal fluctuations of the braid, steric interactions between the molecules, and external mechanical forces. In this model, both sets of ends, of the two molecules, are considered to be separated by a fixed distance much larger than the radius of the braid. One set of ends is rotated to generate a braid of a certain number of pitches (or turns), while the other set remains fixed. This model may describe the situation in which the ends of each molecule are attached to a substrate and a magnetic bead; to the latter a pulling force and rotational torque can be applied. We discuss various aspects of our model. Most importantly, an expression for the free energy is given, from which equations, determining the various geometric parameters of the braid, can be obtained. By numerically solving these equations, we give predictions from the model for the external torque needed to produce a braid with a certain number of turns per bending persistence length, as well as the end to end extension of the two molecules for a given pulling force. Other geometric parameters, as well as the lateral force required to keep the ends of the two molecules apart, are also calculated.
Collapse
Affiliation(s)
- D J O'Lee
- Department of Chemistry, Imperial College London, SW7 2AZ, London, UK
| |
Collapse
|
47
|
Lee DJ. Self-consistent treatment of electrostatics in molecular DNA braiding through external forces. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:062711. [PMID: 25019818 DOI: 10.1103/physreve.89.062711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Indexed: 06/03/2023]
Abstract
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the braid. The system is subjected to an external pulling force, and a moment that induces the braiding. In a model, developed for understanding such a system, we assume that each molecule can be divided into a braided and unbraided section. We also suppose that the DNA is nicked so that there is no constraint of the individual linking numbers of the molecules. Included in the model are steric and electrostatic interactions, thermal fluctuations of the braided and unbraided sections of the molecule, as well as the constraint on the braid linking (catenation) number. We compare two approximations used in estimating the free energy of the braided section. One is where the amplitude of undulations of one molecule with respect to the other is determined only by steric interactions. The other is a self-consistent determination of the mean-squared amplitude of these undulations. In this second approximation electrostatics should play an important role in determining this quantity, as suggested by physical arguments. We see that if the electrostatic interaction is sufficiently large there are indeed notable differences between the two approximations. We go on to test the self-consistent approximation-included in the full model-against experimental data for such a system, and we find good agreement. However, there seems to be a slight left-right-handed braid asymmetry in some of the experimental results. We discuss what might be the origin of this small asymmetry.
Collapse
Affiliation(s)
- Dominic J Lee
- Department of Chemistry, Imperial College London, SW7 2AZ London, United Kingdom
| |
Collapse
|
48
|
Abstract
Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the folding and dynamics of RNA and DNA and their complexes with proteins and with each other cannot be understood without a reasonably sophisticated appreciation of these ions' electrostatic interactions. However, the underlying behavior of the ion atmosphere follows physical rules that are distinct from the rules of site binding that biochemists are most familiar and comfortable with. The main goal of this review is to familiarize nucleic acid experimentalists with the physical concepts that underlie nucleic acid-ion interactions. Throughout, we provide practical strategies for interpreting and analyzing nucleic acid experiments that avoid pitfalls from oversimplified or incorrect models. We briefly review the status of theories that predict or simulate nucleic acid-ion interactions and experiments that test these theories. Finally, we describe opportunities for going beyond phenomenological fits to a next-generation, truly predictive understanding of nucleic acid-ion interactions.
Collapse
Affiliation(s)
- Jan Lipfert
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands;
| | | | | | | |
Collapse
|
49
|
Kesselheim S, Müller W, Holm C. Origin of current blockades in nanopore translocation experiments. PHYSICAL REVIEW LETTERS 2014; 112:018101. [PMID: 24483933 DOI: 10.1103/physrevlett.112.018101] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Indexed: 06/03/2023]
Abstract
We present a detailed investigation of the ionic current in a cylindrical model nanopore in the absence and the presence of a double stranded DNA homopolymer. Our atomistic simulations are capable of reproducing almost exactly the experimental data obtained by Smeets et al., including notably the crossover salt concentration that yields equal current measurements in both situations. We can rule out that the observed current blockade is due to the steric exclusion of charge carriers from the DNA, since for all investigated salt concentrations the charge carrier density is higher when the DNA is present. Calculations using a mean-field electrokinetic model proposed by van Dorp et al. fail quantitatively in predicting this effect. We can relate the shortcomings of the mean-field model to a surface related molecular drag that the ions feel in the presence of the DNA. This drag is independent of the salt concentration and originates from electrostatic, hydrodynamic, and excluded volume interactions.
Collapse
Affiliation(s)
- Stefan Kesselheim
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Wojciech Müller
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Christian Holm
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| |
Collapse
|
50
|
Emanuel M, Lanzani G, Schiessel H. Multiplectoneme phase of double-stranded DNA under torsion. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:022706. [PMID: 24032863 DOI: 10.1103/physreve.88.022706] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/11/2013] [Indexed: 06/02/2023]
Abstract
We use the wormlike chain model to study supercoiling of DNA under tension and torque. The model reproduces experimental data for a broad range of forces, salt concentrations, and contour lengths. We find a plane of first-order phase transitions ending in a smeared-out line of critical points, the multiplectoneme phase, which is characterized by a fast twist-mediated diffusion of plectonemes and a torque that rises after plectoneme formation with increasing linking number. The discovery of this phase at the same time resolves the discrepancies between existing models and experiment.
Collapse
Affiliation(s)
- Marc Emanuel
- Instituut Lorentz voor de Theoretische Natuurkunde, Universiteit Leiden, P. O. Box 9506, NL-2300 RA Leiden, The Netherlands and Institute of Complex Systems II, Forschungszentrum Jülich, Jülich 52425, Germany and Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628CJ Delft, The Netherlands
| | | | | |
Collapse
|