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  • 1
    Electronic Resource
    Electronic Resource
    Intrinsic viscosity and rotational diffusion of bead models for rigid macromolecules and bioparticles (1998)
    Springer
    European biophysics journal 27 (1998), S. 549-557 
    Details
    ISSN: 1432-1017
    Keywords: Key words Intrinsic viscosity ; Rotational diffusion ; Rigid macromolecules ; Friction tensors ; Hydrodynamic theory
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The conventional Kirkwood-Riseman (K-R) treatment of the intrinsic viscosity of macromolecular bead models shows a deficiency when it is applied to models with few beads, whose sizes are not much smaller than of the modelled particle. We present a complete derivation of the intrinsic viscosity up to first order in interbead distances (Oseen-type hydrodynamic interaction), finding that a term that belongs to the zeroth-order contribution is missing in the usual description. This term is simply proportional to the total volume of the bead model. The nature of this correction for viscosity is similar to a previously described correction for rotational coefficients. We discuss the performance of these corrections for various simple models, including ellipsoids as well as oligomeric structures in rodlike, chainlike and polyhedral conformations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002490050165
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Improved hydrodynamic interaction in macromolecular bead models (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 4817-4826 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The calculation of hydrodynamic properties of macromolecules in terms of bead models requires an adequate description of the hydrodynamic interaction between the spherical elements. For this purpose, the original or modified Oseen tensor are customarily used, although it has been shown that this simple description may lead to erroneous results, particularly for rotational coefficients. In this paper we study several more elaborate theories for multisphere systems. We apply those treatments to our problem of rigid bead models, implementing them in computer programs, and making calculations for various test structures. The comparison of the results from the various theories, and from other, presumably very accurate procedures, allow us to give some guidelines to improve the treatment of hydrodynamic interactions in macromolecular bead models. These advances are introduced in new versions of our public-domain computer software. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.479743
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  • 3
    Electronic Resource
    Electronic Resource
    Deformation, scattering, and birefringence of flexible polymer chains under external forces or electric fields (1997)
    Bognor Regis [u.a.] : Wiley-Blackwell
    Journal of Polymer Science Part B: Polymer Physics 35 (1997), S. 689-697 
    Details
    ISSN: 0887-6266
    Keywords: tensile force ; electric field ; chain conformation ; birefringence ; scattering ; Physics ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: The effect of a tensile stress or an electric field on the conformation of a flexible polymer chain has been studied by combining theory with numerical simulation. In the presence of such external agents, the macromolecule experiences the action of two opposite forces at the chain ends. Two models are considered: the Gaussian bead-and-spring chain, and the freely jointed chain with segments of fixed length. From simulated Brownian trajectories we calculate steady-state properties of the polymer under the continuing action of the external forces. Thus, we compute the chain deformation and expansion, measured by the square radius of gyration, and analyze the influence of the external force on low-angle scattering of radiation. The effect of the link orientation in the optical anisotropy or birefringence is also analyzed. From existing theories, we predict very simple relationships between expansion, low-angle scattering, and birefringence, valid for Gaussian chains of any length, and for long freely jointed chains. The simulation results confirm those relationships. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys, 35: 689-697, 1997
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 4
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    Bacillus subtilis RecU protein cleaves Holliday junctions and anneals single-stranded DNA (2003)
    National Academy of Sciences
    Details
    Publication Date: 2003-12-30
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 5
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    Genetic and morphological characterization of the endangered Austral papaya Vasconcellea chilensis (Planch. ex A. DC.) Solms (2014)
    Springer
    Details
    Publication Date: 2014-07-09
    Print ISSN: 0925-9864
    Electronic ISSN: 1573-5109
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Springer
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  • 6
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    Chromosomal transformation in Bacillus subtilis is a non-polar recombination reaction (2016)
    Oxford University Press
    Details
    Publication Date: 2016-04-08
    Description: Natural chromosomal transformation is one of the primary driving forces of bacterial evolution. This reaction involves the recombination of the internalized linear single-stranded (ss) DNA with the homologous resident duplex via RecA-mediated integration in concert with SsbA and DprA or RecO. We show that sequence divergence prevents Bacillus subtilis chromosomal transformation in a log-linear fashion, but it exerts a minor effect when the divergence is localized at a discrete end. In the nucleotide bound form, RecA shows no apparent preference to initiate recombination at the 3'- or 5'-complementary end of the linear duplex with circular ssDNA, but nucleotide hydrolysis is required when heterology is present at both ends. RecA·dATP initiates pairing of the linear 5' and 3' complementary ends, but only initiation at the 5'-end remains stably paired in the absence of SsbA. Our results suggest that during gene transfer RecA·ATP, in concert with SsbA and DprA or RecO, shows a moderate preference for the 3'-end of the duplex. We show that RecA-mediated recombination initiated at the 3'- or 5'-complementary end might have significant implication on the ecological diversification of bacterial species with natural transformation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Bacillus subtilis RecO and SsbA are crucial for RecA-mediated recombinational DNA repair (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-12
    Description: Genetic data have revealed that the absence of Bacillus subtilis RecO and one of the end-processing avenues (AddAB or RecJ) renders cells as sensitive to DNA damaging agents as the null recA , suggesting that both end-resection pathways require RecO for recombination. RecA, in the rATP·Mg 2+ bound form (RecA·ATP), is inactive to catalyze DNA recombination between linear double-stranded (ds) DNA and naked complementary circular single-stranded (ss) DNA. We showed that RecA·ATP could not nucleate and/or polymerize on SsbA·ssDNA or SsbB·ssDNA complexes. RecA·ATP nucleates and polymerizes on RecO·ssDNA·SsbA complexes more efficiently than on RecO·ssDNA·SsbB complexes. Limiting SsbA concentrations were sufficient to stimulate RecA·ATP assembly on the RecO·ssDNA·SsbB complexes. RecO and SsbA are necessary and sufficient to ‘activate’ RecA·ATP to catalyze DNA strand exchange, whereas the AddAB complex, RecO alone or in concert with SsbB was not sufficient. In presence of AddAB, RecO and SsbA are still necessary for efficient RecA·ATP-mediated three-strand exchange recombination. Based on genetic and biochemical data, we proposed that SsbA and RecO (or SsbA, RecO and RecR in vivo ) are crucial for RecA activation for both, AddAB and RecJ–RecQ (RecS) recombinational repair pathways.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Identification of a conserved 5'-dRP lyase activity in bacterial DNA repair ligase D and its potential role in base excision repair (2016)
    Oxford University Press
    Details
    Publication Date: 2016-03-01
    Description: Bacillus subtilis is one of the bacterial members provided with a nonhomologous end joining (NHEJ) system constituted by the DNA-binding Ku homodimer that recruits the ATP-dependent DNA Ligase D ( Bsu LigD) to the double-stranded DNA breaks (DSBs) ends. Bsu LigD has inherent polymerization and ligase activities that allow it to fill the short gaps that can arise after realignment of the broken ends and to seal the resulting nicks, contributing to genome stability during the stationary phase and germination of spores. Here we show that Bsu LigD also has an intrinsic 5'-2-deoxyribose-5-phosphate (dRP) lyase activity located at the N-terminal ligase domain that in coordination with the polymerization and ligase activities allows efficient repairing of 2'-deoxyuridine-containing DNA in an in vitro reconstituted Base Excision Repair (BER) reaction. The requirement of a polymerization, a dRP removal and a final sealing step in BER, together with the joint participation of Bsu LigD with the spore specific AP endonuclease in conferring spore resistance to ultrahigh vacuum desiccation suggest that Bsu LigD could actively participate in this pathway. We demonstrate the presence of the dRP lyase activity also in the homolog protein from the distantly related bacterium Pseudomonas aeruginosa , allowing us to expand our results to other bacterial LigDs.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Genetic recombination in Bacillus subtilis: a division of labor between two single-strand DNA-binding proteins (2012)
    Oxford University Press
    Details
    Publication Date: 2012-06-28
    Description: We have investigated the structural, biochemical and cellular roles of the two single-stranded (ss) DNA-binding proteins from Bacillus subtilis , SsbA and SsbB. During transformation, SsbB localizes at the DNA entry pole where it binds and protects internalized ssDNA. The 2.8-Å resolution structure of SsbB bound to ssDNA reveals a similar overall protein architecture and ssDNA-binding surface to that of Escherichia coli SSB. SsbA, which binds ssDNA with higher affinity than SsbB, co-assembles onto SsbB-coated ssDNA and the two proteins inhibit ssDNA binding by the recombinase RecA. During chromosomal transformation, the RecA mediators RecO and DprA provide RecA access to ssDNA. Interestingly, RecO interaction with ssDNA-bound SsbA helps to dislodge both SsbA and SsbB from the DNA more efficiently than if the DNA is coated only with SsbA. Once RecA is nucleated onto the ssDNA, RecA filament elongation displaces SsbA and SsbB and enables RecA-mediated DNA strand exchange. During plasmid transformation, RecO localizes to the entry pole and catalyzes annealing of SsbA- or SsbA/SsbB-coated complementary ssDNAs to form duplex DNA with ssDNA tails. Our results provide a mechanistic framework for rationalizing the coordinated events modulated by SsbA, SsbB and RecO that are crucial for RecA-dependent chromosomal transformation and RecA-independent plasmid transformation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Bacillus subtilis RecA and its accessory factors, RecF, RecO, RecR and RecX, are required for spore resistance to DNA double-strand break (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-28
    Description: Bacillus subtilis RecA is important for spore resistance to DNA damage, even though spores contain a single non-replicating genome. We report that inactivation of RecA or its accessory factors, RecF, RecO, RecR and RecX, drastically reduce survival of mature dormant spores to ultrahigh vacuum desiccation and ionizing radiation that induce single strand (ss) DNA nicks and double-strand breaks (DSBs). The presence of non-cleavable LexA renders spores less sensitive to DSBs, and spores impaired in DSB recognition or end-processing show sensitivities to X-rays similar to wild-type. In vitro RecA cannot compete with SsbA for nucleation onto ssDNA in the presence of ATP. RecO is sufficient, at least in vitro , to overcome SsbA inhibition and stimulate RecA polymerization on SsbA-coated ssDNA. In the presence of SsbA, RecA slightly affects DNA replication in vitro , but addition of RecO facilitates RecA-mediated inhibition of DNA synthesis. We propose that repairing of the DNA lesions generates a replication stress to germinating spores, and the RecA·ssDNA filament might act by preventing potentially dangerous forms of DNA repair occurring during replication. RecA might stabilize a stalled fork or prevent or promote dissolution of reversed forks rather than its cleavage that should require end-processing.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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