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  1. Book: Biophysics of DNA

    Vologodskij, Aleksandr Vadimovič

    2015  

    Author's details Alexander Vologodskii
    Keywords DNA. ; Biophysics
    Subject code 572.86
    Language English
    Size VI, 254 S., [8] Bl. : Ill., graph. Darst., 25 cm
    Publisher Cambridge Univ. Press
    Publishing place Cambridge u.a.
    Publishing country Great Britain
    Document type Book
    Note Formerly CIP. ; Includes bibliographical references and index
    HBZ-ID HT018594473
    ISBN 978-1-107-03493-8 ; 1-107-03493-0
    Database Catalogue ZB MED Medicine, Health

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    Shelf markLoan statusLocation
    2015 A 1178 available for loan (reading room) Lesesaal EG

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  2. Article ; Online: When Computer Simulation Excels Experiment.

    Vologodskii, Alexander

    Biophysical journal

    2016  Volume 110, Issue 10, Page(s) 2136–2137

    Language English
    Publishing date 2016--24
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2016.04.016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Type II topoisomerases: Experimental studies, theoretical models, and logic: Reply to comments on "Disentangling DNA molecules".

    Vologodskii, Alexander

    Physics of life reviews

    2016  Volume 18, Page(s) 165–167

    MeSH term(s) DNA ; DNA Topoisomerases, Type II/metabolism ; Logic ; Models, Theoretical ; Nucleic Acid Conformation
    Chemical Substances DNA (9007-49-2) ; DNA Topoisomerases, Type II (EC 5.99.1.3)
    Language English
    Publishing date 2016
    Publishing country Netherlands
    Document type Journal Article ; Comment
    ZDB-ID 2148883-6
    ISSN 1873-1457 ; 1571-0645
    ISSN (online) 1873-1457
    ISSN 1571-0645
    DOI 10.1016/j.plrev.2016.09.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Disentangling DNA molecules.

    Vologodskii, Alexander

    Physics of life reviews

    2016  Volume 18, Page(s) 118–134

    Abstract: The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they ... ...

    Abstract The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.
    MeSH term(s) DNA/chemistry ; DNA/metabolism ; DNA Topoisomerases, Type II ; Models, Molecular
    Chemical Substances DNA (9007-49-2) ; DNA Topoisomerases, Type II (EC 5.99.1.3)
    Language English
    Publishing date 2016
    Publishing country Netherlands
    Document type Review ; Journal Article
    ZDB-ID 2148883-6
    ISSN 1873-1457 ; 1571-0645
    ISSN (online) 1873-1457
    ISSN 1571-0645
    DOI 10.1016/j.plrev.2016.05.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Unlinking of supercoiled DNA catenanes by type IIA topoisomerases.

    Vologodskii, Alexander

    Biophysical journal

    2011  Volume 101, Issue 6, Page(s) 1403–1411

    Abstract: It was found recently that DNA catenanes, formed during replication of circular plasmids, become positively (+) supercoiled, and the unlinking of such catenanes by type IIA topoisomerases proceeds much more efficiently than the unlinking of negatively (-) ...

    Abstract It was found recently that DNA catenanes, formed during replication of circular plasmids, become positively (+) supercoiled, and the unlinking of such catenanes by type IIA topoisomerases proceeds much more efficiently than the unlinking of negatively (-) supercoiled catenanes. In an attempt to explain this striking finding we studied, by computer simulation, conformational properties of supercoiled DNA catenanes. Although the simulation showed that conformational properties of (+) and (-) supercoiled replication catenanes are very different, these properties per se do not give any advantage to (+) supercoiled over (-) supercoiled DNA catenanes for unlinking. An advantage became evident, however, when we took into account the established features of the enzymatic reaction catalyzed by the topoisomerases. The enzymes create a sharp DNA bend in the first bound DNA segment and allow for the transport of the second segment only from inside the bend to its outside. We showed that in (-) supercoiled DNA catenanes this protein-bound bent segment becomes nearly inaccessible for segments of the other linked DNA molecule, inhibiting the unlinking.
    MeSH term(s) Antigens, Neoplasm/metabolism ; DNA Topoisomerases, Type II/metabolism ; DNA, Superhelical/chemistry ; DNA, Superhelical/metabolism ; DNA-Binding Proteins/metabolism ; Models, Molecular ; Nucleic Acid Conformation
    Chemical Substances Antigens, Neoplasm ; DNA, Superhelical ; DNA-Binding Proteins ; DNA Topoisomerases, Type II (EC 5.99.1.3)
    Language English
    Publishing date 2011-09-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2011.08.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: DNA-ligand binding and the force-extension experiments. Comment on "Biophysical characterization of DNA binding from single molecule force measurements" by Chaurasiya et al.

    Vologodskii, Alexander

    Physics of life reviews

    2010  Volume 7, Issue 3, Page(s) 346–7; discussion 358–61

    MeSH term(s) Bacterial Proteins/metabolism ; Base Sequence/genetics ; Base Sequence/physiology ; Binding Sites/genetics ; Binding Sites/physiology ; Biophysical Phenomena ; DNA/chemistry ; DNA/metabolism ; DNA/ultrastructure ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; Elasticity ; High Mobility Group Proteins/metabolism ; Ligands ; Pliability
    Chemical Substances Bacterial Proteins ; DNA-Binding Proteins ; High Mobility Group Proteins ; Ligands ; histone-like protein HU, bacteria ; DNA (9007-49-2)
    Language English
    Publishing date 2010-09
    Publishing country Netherlands
    Document type Comment ; Journal Article
    ZDB-ID 2148883-6
    ISSN 1873-1457 ; 1571-0645
    ISSN (online) 1873-1457
    ISSN 1571-0645
    DOI 10.1016/j.plrev.2010.06.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Theoretical models of DNA topology simplification by type IIA DNA topoisomerases.

    Vologodskii, Alexander

    Nucleic acids research

    2009  Volume 37, Issue 10, Page(s) 3125–3133

    Abstract: It was discovered 12 years ago that type IIA topoisomerases can simplify DNA topology--the steady-state fractions of knots and links created by the enzymes are many times lower than the corresponding equilibrium fractions. Though this property of the ... ...

    Abstract It was discovered 12 years ago that type IIA topoisomerases can simplify DNA topology--the steady-state fractions of knots and links created by the enzymes are many times lower than the corresponding equilibrium fractions. Though this property of the enzymes made clear biological sense, it was not clear how small enzymes could selectively change the topology of very large DNA molecules, since topology is a global property and cannot be determined by a local DNA-protein interaction. A few models, suggested to explain the phenomenon, are analyzed in this review. We also consider experimental data that both support and contravene these models.
    MeSH term(s) Computer Simulation ; DNA/chemistry ; DNA Topoisomerases, Type II/chemistry ; Models, Chemical ; Models, Molecular ; Nucleic Acid Conformation
    Chemical Substances DNA (9007-49-2) ; DNA Topoisomerases, Type II (EC 5.99.1.3)
    Language English
    Publishing date 2009-04-21
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    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/gkp250
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  8. Article ; Online: Determining protein-induced DNA bending in force-extension experiments: theoretical analysis.

    Vologodskii, Alexander

    Biophysical journal

    2009  Volume 96, Issue 9, Page(s) 3591–3599

    Abstract: Computer simulations were used to investigate the possibility of determining protein-induced DNA bend angles by measuring the extension of a single DNA molecule. Analysis of the equilibrium sets of DNA conformations showed that shortening of DNA ... ...

    Abstract Computer simulations were used to investigate the possibility of determining protein-induced DNA bend angles by measuring the extension of a single DNA molecule. Analysis of the equilibrium sets of DNA conformations showed that shortening of DNA extension by a single protein-induced DNA bend can be as large as 35 nm. The shortening has a maximum value at the extending force of approximately 0.1 pN. At this force, the DNA extension experiences very large fluctuations that dramatically complicate the measurement. Using Brownian dynamics simulation of a DNA molecule extended by force, we were able to estimate the observation time needed to obtain the desired accuracy of the extension measurement. Also, the simulation revealed large fluctuations of the force, acting on the attached magnetic bead from the stretched DNA molecule.
    MeSH term(s) Algorithms ; Computer Simulation ; DNA/chemistry ; DNA/metabolism ; DNA-Binding Proteins/metabolism ; Models, Molecular ; Monte Carlo Method ; Nucleic Acid Conformation ; Thermodynamics ; Time Factors
    Chemical Substances DNA-Binding Proteins ; DNA (9007-49-2)
    Language English
    Publishing date 2009-01-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2009.02.022
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: DNA supercoiling helps to unlink sister duplexes after replication.

    Vologodskii, Alexander

    BioEssays : news and reviews in molecular, cellular and developmental biology

    2009  Volume 32, Issue 1, Page(s) 9–12

    Abstract: DNA supercoiling is one of the mechanisms that can help unlinking of newly replicated DNA molecules. Although DNA topoisomerases, which catalyze the strand passing of DNA segments through one another, make the unlinking problem solvable in principle, it ... ...

    Abstract DNA supercoiling is one of the mechanisms that can help unlinking of newly replicated DNA molecules. Although DNA topoisomerases, which catalyze the strand passing of DNA segments through one another, make the unlinking problem solvable in principle, it remains difficult to complete the process that enables the separation of the sister duplexes. A few different mechanisms were developed by nature to solve the problem. Some of the mechanisms are very intuitive while the others, like topology simplification by type II DNA topoisomerases and DNA supercoiling, are not so evident. A computer simulation and analysis of linked sister plasmids formed in Escherichia coli cells with suppressed topoisomerase IV suggests an insight into the latter mechanism.
    MeSH term(s) Computer Simulation ; DNA Replication ; DNA, Bacterial/chemistry ; DNA, Bacterial/metabolism ; DNA, Superhelical/chemistry ; DNA, Superhelical/metabolism ; Escherichia coli/metabolism ; Models, Biological ; Models, Molecular ; Nucleic Acid Conformation ; Plasmids/chemistry ; Plasmids/metabolism ; Thermodynamics
    Chemical Substances DNA, Bacterial ; DNA, Superhelical
    Language English
    Publishing date 2009-12-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.200900143
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Theoretical model, its parameters and predictions: Reply to comments on "DNA melting and energetics of the double helix".

    Vologodskii, Alexander / Frank-Kamenetskii, Maxim D

    Physics of life reviews

    2018  Volume 25, Page(s) 42–44

    MeSH term(s) DNA ; Models, Theoretical ; Nucleic Acid Conformation ; Nucleic Acid Denaturation ; Thermodynamics
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2018-05-02
    Publishing country Netherlands
    Document type Journal Article ; Comment
    ZDB-ID 2148883-6
    ISSN 1873-1457 ; 1571-0645
    ISSN (online) 1873-1457
    ISSN 1571-0645
    DOI 10.1016/j.plrev.2018.04.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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