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  1. AU="Lipfert, Jan"
  2. AU="Sauchuk, Alina L"
  3. AU="Cosaert, Theo"
  4. AU="Gonella, Paulo M."
  5. AU="Liu, Zhe J"
  6. AU="Sanchayan Sinha"
  7. AU="Ahmadi, Parimah"
  8. AU="Hufert, F T" AU="Hufert, F T"
  9. AU="Maximilian Radtke"
  10. AU="Hinchliffe, Rod F" AU="Hinchliffe, Rod F"
  11. AU="Pourdowlat, Guitti"
  12. AU="Kurskoy Аndrey Yu."
  13. AU="Kuo, Albert"
  14. AU="Haustraete, Eglantine"
  15. AU="Li, Ziying"
  16. AU="Kimura, Kasane"
  17. AU="Gleeson, Sarah"
  18. AU="Hong, Ki Hyun"
  19. AU="Adalbert, V’kovski Philip"
  20. AU="Witte, Martin D"
  21. AU=Sun Yuan
  22. AU=Khan Zeashan Hameed AU=Khan Zeashan Hameed
  23. AU=Andrade D M
  24. AU="Miyata, Fumika"
  25. AU="Ahmad Rizal"
  26. AU="Aponte, Nelson"
  27. AU=Manfredonia Ilaria
  28. AU="Ryu, Jae Sung"
  29. AU="Lo, Bernard"
  30. AU="Pandya, Hardi"
  31. AU="Evans, J Anthony"
  32. AU="Chang, Hanxuan" AU="Chang, Hanxuan"
  33. AU="Bellamy, Kyle" AU="Bellamy, Kyle"
  34. AU="Jensen, Kara L"
  35. AU=Wang Yun
  36. AU=Seimiya H
  37. AU="Victor Babos, Diego"
  38. AU="Giuseppe Sergi"
  39. AU="Nackers, Elke"
  40. AU=Grobler Chistine
  41. AU="Norman H. L. Chiu"
  42. AU="Ioannis Politis"
  43. AU="Scott Nugent"
  44. AU="Sepideh MONSEF"
  45. AU="Wang, Zhaoqi"

Suchergebnis

Treffer 1 - 10 von insgesamt 115

Suchoptionen

  1. Buch ; Online ; Dissertation / Habilitation: Phase transitions in linear polymers

    Kolbeck, Pauline Julika [Verfasser] / Lipfert, Jan [Akademischer Betreuer]

    fundamental mechanisms and biotechnological & biomedical applications

    2024  

    Verfasserangabe Pauline Julika Kolbeck ; Betreuer: Jan Lipfert
    Schlagwörter Biowissenschaften, Biologie ; Life Science, Biology
    Thema/Rubrik (Code) sg570
    Sprache Englisch
    Verlag Universitätsbibliothek der Ludwig-Maximilians-Universität
    Erscheinungsort München
    Dokumenttyp Buch ; Online ; Dissertation / Habilitation
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  2. Buch ; Online ; Dissertation / Habilitation: DNA Nanostructures as Nanomechanical Tools

    Kauert, Dominik [Verfasser] / Seidel, Ralf [Gutachter] / Lipfert, Jan [Gutachter]

    2024  

    Verfasserangabe Dominik Kauert ; Gutachter: Ralf Seidel, Jan Lipfert
    Schlagwörter Biowissenschaften, Biologie ; Life Science, Biology
    Thema/Rubrik (Code) sg570
    Sprache Englisch
    Verlag Universitätsbibliothek Leipzig
    Erscheinungsort Leipzig
    Dokumenttyp Buch ; Online ; Dissertation / Habilitation
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  3. Artikel ; Online: Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments.

    Kolbeck, Pauline J / Tišma, Miloš / Analikwu, Brian T / Vanderlinden, Willem / Dekker, Cees / Lipfert, Jan

    Nucleic acids research

    2024  Band 52, Heft 1, Seite(n) 59–72

    Abstract: DNA stores our genetic information and is ubiquitous in applications, where it interacts with binding partners ranging from small molecules to large macromolecular complexes. Binding is modulated by mechanical strains in the molecule and can change local ...

    Abstract DNA stores our genetic information and is ubiquitous in applications, where it interacts with binding partners ranging from small molecules to large macromolecular complexes. Binding is modulated by mechanical strains in the molecule and can change local DNA structure. Frequently, DNA occurs in closed topological forms where topology and supercoiling add a global constraint to the interplay of binding-induced deformations and strain-modulated binding. Here, we present a quantitative model with a straight-forward numerical implementation of how the global constraints introduced by DNA topology modulate binding. We focus on fluorescent intercalators, which unwind DNA and enable direct quantification via fluorescence detection. Our model correctly describes bulk experiments using plasmids with different starting topologies, different intercalators, and over a broad range of intercalator and DNA concentrations. We demonstrate and quantitatively model supercoiling-dependent binding in a single-molecule assay, where we directly observe the different intercalator densities going from supercoiled to nicked DNA. The single-molecule assay provides direct access to binding kinetics and DNA supercoil dynamics. Our model has broad implications for the detection and quantification of DNA, including the use of psoralen for UV-induced DNA crosslinking to quantify torsional tension in vivo, and for the modulation of DNA binding in cellular contexts.
    Mesh-Begriff(e) DNA ; DNA, Superhelical ; Fluorescence ; Intercalating Agents/chemistry ; Plasmids/genetics
    Chemische Substanzen DNA (9007-49-2) ; DNA, Superhelical ; Intercalating Agents
    Sprache Englisch
    Erscheinungsdatum 2024-01-24
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad1055
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    Zs.A 1067: Hefte anzeigen Standort:
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  4. Artikel ; Online: Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging.

    Konrad, Sebastian F / Vanderlinden, Willem / Lipfert, Jan

    Biophysical journal

    2022  Band 121, Heft 5, Seite(n) 841–851

    Abstract: Nucleosomes are the basic units of chromatin and critical for storage and expression of eukaryotic genomes. Chromatin accessibility and gene readout are heavily regulated by epigenetic marks, in which post-translational modifications of histones play a ... ...

    Abstract Nucleosomes are the basic units of chromatin and critical for storage and expression of eukaryotic genomes. Chromatin accessibility and gene readout are heavily regulated by epigenetic marks, in which post-translational modifications of histones play a key role. However, the mode of action and the structural implications at the single-molecule level of nucleosomes is still poorly understood. Here we apply a high-throughput atomic force microscopy imaging and analysis pipeline to investigate the conformational landscape of the nucleosome variants three additional methyl groups at lysine 36 of histone H3 (H3K36me3), phosphorylation of H3 histones at serine 10 (H3S10phos), and acetylation of H4 histones at lysines 5, 8, 12, and 16 (H4K5/8/12/16ac). Our data set of more than 25,000 nucleosomes reveals nucleosomal unwrapping steps corresponding to 5-bp DNA. We find that H3K36me3 nucleosomes unwrap significantly more than wild-type nucleosomes and additionally unwrap stochastically from both sides, similar to centromere protein A (CENP-A) nucleosomes and in contrast to the highly anticooperative unwrapping of wild-type nucleosomes. Nucleosomes with H3S10phos or H4K5/8/12/16ac modifications show unwrapping populations similar to wild-type nucleosomes and also retain the same level of anticooperativity. Our findings help to put the mode of action of these modifications into context. Although H3K36me3 likely acts partially by directly affecting nucleosome structure on the single-molecule level, H3S10phos and H4K5/8/12/16ac must predominantly act through higher-order processes. Our analysis pipeline is readily applicable to other nucleosome variants and will facilitate future high-resolution studies of the conformational landscape of nucleoprotein complexes.
    Mesh-Begriff(e) Chromatin/genetics ; Epigenesis, Genetic ; Histones/metabolism ; Lysine/metabolism ; Nucleosomes ; Protein Processing, Post-Translational
    Chemische Substanzen Chromatin ; Histones ; Nucleosomes ; Lysine (K3Z4F929H6)
    Sprache Englisch
    Erscheinungsdatum 2022-01-20
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2022.01.014
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  5. Artikel ; Online: A High-throughput Pipeline to Determine DNA and Nucleosome Conformations by AFM Imaging.

    Konrad, Sebastian F / Vanderlinden, Willem / Lipfert, Jan

    Bio-protocol

    2021  Band 11, Heft 19, Seite(n) e4180

    Abstract: Atomic force microscopy (AFM) is a powerful tool to image macromolecular complexes with nanometer resolution and exquisite single-molecule sensitivity. While AFM imaging is well-established to investigate DNA and nucleoprotein complexes, AFM studies are ... ...

    Abstract Atomic force microscopy (AFM) is a powerful tool to image macromolecular complexes with nanometer resolution and exquisite single-molecule sensitivity. While AFM imaging is well-established to investigate DNA and nucleoprotein complexes, AFM studies are often limited by small datasets and manual image analysis that is slow and prone to user bias. Recently, we have shown that a combination of large scale AFM imaging and automated image analysis of nucleosomes can overcome these previous limitations of AFM nucleoprotein studies. Using our high-throughput imaging and analysis pipeline, we have resolved nucleosome wrapping intermediates with five base pair resolution and revealed how distinct nucleosome variants and environmental conditions affect the unwrapping pathways of nucleosomal DNA. Here, we provide a detailed protocol of our workflow to analyze DNA and nucleosome conformations focusing on practical aspects and experimental parameters. We expect our protocol to drastically enhance AFM analyses of DNA and nucleosomes and to be readily adaptable to a wide variety of other protein and protein-nucleic acid complexes.
    Sprache Englisch
    Erscheinungsdatum 2021-10-05
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2833269-6
    ISSN 2331-8325 ; 2331-8325
    ISSN (online) 2331-8325
    ISSN 2331-8325
    DOI 10.21769/BioProtoc.4180
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  6. Artikel ; Online: Temperature-Dependent Twist of Double-Stranded RNA Probed by Magnetic Tweezer Experiments and Molecular Dynamics Simulations.

    Dohnalová, Hana / Seifert, Mona / Matoušková, Eva / Klein, Misha / Papini, Flávia S / Lipfert, Jan / Dulin, David / Lankaš, Filip

    The journal of physical chemistry. B

    2024  Band 128, Heft 3, Seite(n) 664–675

    Abstract: RNA plays critical roles in the transmission and regulation of genetic information and is increasingly used in biomedical and biotechnological applications. Functional RNAs contain extended double-stranded regions, and the structure of double-stranded ... ...

    Abstract RNA plays critical roles in the transmission and regulation of genetic information and is increasingly used in biomedical and biotechnological applications. Functional RNAs contain extended double-stranded regions, and the structure of double-stranded RNA (dsRNA) has been revealed at high resolution. However, the dependence of the properties of the RNA double helix on environmental effects, notably temperature, is still poorly understood. Here, we use single-molecule magnetic tweezer measurements to determine the dependence of the dsRNA twist on temperature. We find that dsRNA unwinds with increasing temperature, even more than DNA, with Δ
    Mesh-Begriff(e) RNA, Double-Stranded ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; Temperature ; RNA/chemistry ; DNA/chemistry ; Magnetic Phenomena
    Chemische Substanzen RNA, Double-Stranded ; RNA (63231-63-0) ; DNA (9007-49-2)
    Sprache Englisch
    Erscheinungsdatum 2024-01-10
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c06280
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  7. Artikel ; Online: High-yield ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single-molecule manipulation assays.

    Lin, Yi-Yun / Brouns, Tine / Kolbeck, Pauline J / Vanderlinden, Willem / Lipfert, Jan

    The Journal of biological chemistry

    2023  Band 299, Heft 7, Seite(n) 104874

    Abstract: Force and torque spectroscopy have provided unprecedented insights into the mechanical properties, conformational transitions, and dynamics of DNA and DNA-protein complexes, notably nucleosomes. Reliable single-molecule manipulation measurements require, ...

    Abstract Force and torque spectroscopy have provided unprecedented insights into the mechanical properties, conformational transitions, and dynamics of DNA and DNA-protein complexes, notably nucleosomes. Reliable single-molecule manipulation measurements require, however, specific and stable attachment chemistries to tether the molecules of interest. Here, we present a functionalization strategy for DNA that enables high-yield production of constructs for torsionally constrained and very stable attachment. The method is based on two subsequent PCRs: first ∼380 bp long DNA strands are generated that contain multiple labels, which are used as "megaprimers" in a second PCR to generate ∼kbp long double-stranded DNA constructs with multiple labels at the respective ends. To achieve high-force stability, we use dibenzocyclooctyne-based click chemistry for covalent attachment to the surface and biotin-streptavidin coupling to the bead. The resulting tethers are torsionally constrained and extremely stable under load, with an average lifetime of 70 ± 3 h at 45 pN. The high yield of the approach enables nucleosome reconstitution by salt dialysis on the functionalized DNA, and we demonstrate proof-of-concept measurements on nucleosome assembly statistics and inner turn unwrapping under force. We anticipate that our approach will facilitate a range of studies of DNA interactions and nucleoprotein complexes under forces and torques.
    Mesh-Begriff(e) Nucleosomes ; DNA/chemistry ; Mechanical Phenomena ; Biophysical Phenomena ; Polymerase Chain Reaction
    Chemische Substanzen Nucleosomes ; DNA (9007-49-2)
    Sprache Englisch
    Erscheinungsdatum 2023-05-29
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2023.104874
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    Uc I Zs.108: Hefte anzeigen Standort:
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  8. Buch ; Online ; Dissertation / Habilitation: Probing protein interfaces in health and disease by single-molecule magnetic tweezers force spectroscopy

    Gruber, Sophia [Verfasser] / Lipfert, Jan [Akademischer Betreuer]

    2022  

    Verfasserangabe Sophia Gruber ; Betreuer: Jan Lipfert
    Schlagwörter Medizin, Gesundheit ; Medicine, Health
    Thema/Rubrik (Code) sg610
    Sprache Englisch
    Verlag Universitätsbibliothek der Ludwig-Maximilians-Universität
    Erscheinungsort München
    Dokumenttyp Buch ; Online ; Dissertation / Habilitation
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  9. Buch ; Online ; Dissertation / Habilitation: High-resolution single-molecule spectroscopy to probe conformational dynamics of proteins

    Gebhardt, Christian [Verfasser] / Lipfert, Jan [Akademischer Betreuer]

    2022  

    Verfasserangabe Christian Gebhardt ; Betreuer: Jan Lipfert
    Schlagwörter Biowissenschaften, Biologie ; Life Science, Biology
    Thema/Rubrik (Code) sg570
    Sprache Englisch
    Verlag Universitätsbibliothek der Ludwig-Maximilians-Universität
    Erscheinungsort München
    Dokumenttyp Buch ; Online ; Dissertation / Habilitation
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  10. Artikel ; Online: Dynamics of the Buckling Transition in Double-Stranded DNA and RNA.

    Ott, Katharina / Martini, Linda / Lipfert, Jan / Gerland, Ulrich

    Biophysical journal

    2020  Band 118, Heft 7, Seite(n) 1690–1701

    Abstract: DNA under torsional strain undergoes a buckling transition that is the fundamental step in plectoneme nucleation and supercoil dynamics, which are critical for the processing of genomic information. Despite its importance, quantitative models of the ... ...

    Abstract DNA under torsional strain undergoes a buckling transition that is the fundamental step in plectoneme nucleation and supercoil dynamics, which are critical for the processing of genomic information. Despite its importance, quantitative models of the buckling transition, in particular to also explain the surprising two-orders-of-magnitude difference between the buckling times for RNA and DNA revealed by single-molecule tweezers experiments, are currently lacking. Additionally, little is known about the configurations of the DNA during the buckling transition because they are not directly observable experimentally. Here, we use a discrete worm-like chain model and Brownian dynamics to simulate the DNA/RNA buckling transition. Our simulations are in good agreement with experimentally determined parameters of the buckling transition. The simulations show that the buckling time strongly and exponentially depends on the bending stiffness, which accounts for more than half the measured difference between DNA and RNA. Analyzing the microscopic conformations of the chain revealed by our simulations, we find clear evidence for a solenoid-shaped transition state and a curl intermediate. The curl intermediate features a single loop and becomes increasingly populated at low forces. Taken together, the simulations suggest that the worm-like chain model can account semiquantitatively for the buckling dynamics of both DNA and RNA.
    Mesh-Begriff(e) DNA/genetics ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; RNA/genetics
    Chemische Substanzen RNA (63231-63-0) ; DNA (9007-49-2)
    Sprache Englisch
    Erscheinungsdatum 2020-02-29
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2020.01.049
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