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  • 1
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    Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics (2016)
    Oxford University Press
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    Publication Date: 2016-06-21
    Description: DNA loop formation on nucleosomes is strongly implicated in chromatin remodeling and occurs spontaneously in nucleosomes subjected to superhelical stress. The nature of such loops depends crucially on the balance between DNA deformation and DNA interaction with the nucleosome core. Currently, no high-resolution structural data on these loops exist. Although uniform rod models have been used to study loop size and shape, these models make assumptions concerning DNA mechanics and DNA–core binding. We present here atomic-scale molecular dynamics simulations for two different loop sizes. The results point to the key role of localized DNA kinking within the loops. Kinks enable the relaxation of DNA bending strain to be coupled with improved DNA–core interactions. Kinks lead to small, irregularly shaped loops that are asymmetrically positioned with respect to the nucleosome core. We also find that loop position can influence the dynamics of the DNA segments at the extremities of the nucleosome.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    DNA minicircles clarify the specific role of DNA structure on retroviral integration (2016)
    Oxford University Press
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    Publication Date: 2016-09-20
    Description: Chromatin regulates the selectivity of retroviral integration into the genome of infected cells. At the nucleosome level, both histones and DNA structure are involved in this regulation. We propose a strategy that allows to specifically study a single factor: the DNA distortion induced by the nucleosome. This strategy relies on mimicking this distortion using DNA minicircles (MCs) having a fixed rotational orientation of DNA curvature, coupled with atomic-resolution modeling. Contrasting MCs with linear DNA fragments having identical sequences enabled us to analyze the impact of DNA distortion on the efficiency and selectivity of integration. We observed a global enhancement of HIV-1 integration in MCs and an enrichment of integration sites in the outward-facing DNA major grooves. Both of these changes are favored by LEDGF/p75, revealing a new, histone-independent role of this integration cofactor. PFV integration is also enhanced in MCs, but is not associated with a periodic redistribution of integration sites, thus highlighting its distinct catalytic properties. MCs help to separate the roles of target DNA structure, histone modifications and integrase (IN) cofactors during retroviral integration and to reveal IN-specific regulation mechanisms.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Spinning in different directions: western rock lobster larval condition varies with eddy polarity, but does their diet? (2015)
    Oxford University Press
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    Publication Date: 2015-05-24
    Description: Larvae of the western rock lobster ( Panulirus cygnus ) that occur in the south-east Indian Ocean offshore of Western Australia have been found to be in poorer nutritional condition in anticyclonic compared with cyclonic mesoscale eddies. The reason for this is unknown, but culture-based experiments have shown that diet composition and water temperature are key determinants of phyllosoma health and survival. Whether differences in prey composition are the cause of poor phyllosoma condition in situ was tested in the present study by high-throughput sequencing of 18S rDNA amplified from the gut contents of 48 lobster larvae from two cyclonic and two anticyclonic eddies. We determined that phyllosoma prey composition did not vary significantly between anticyclonic and cyclonic eddies and that any variation was at the level of sample site (permutational multivariate analysis of variance F 2,35 = 5.12, P 〈 0.0001). We therefore reject the hypothesis that prey composition alone during the late larval phase determines larval condition. This indicates that the competing hypotheses are more likely: for example, that eddy water temperature is responsible for reducing the condition of phyllosomas directly, or indirectly by impoverishing the nutritional value of their foodweb.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Conservation of coastal stingrays: seasonal abundance and population structure of the short-tailed stingray Dasyatis brevicaudata at a Marine Protected Area (2012)
    Oxford University Press
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    Publication Date: 2012-08-22
    Description: Le Port, A., Lavery, S., and Montgomery, J. C. 2012. Conservation of coastal stingrays: seasonal abundance and population structure of the short-tailed stingray Dasyatis brevicaudata at a Marine Protected Area. – ICES Journal of Marine Science, 69: . Elasmobranch (shark, ray, and skate) populations around the world are in decline, and effective conservation measures are urgently needed. Marine Protected Areas (MPA) placed in locations important for key life-history stages may form part of an effective conservation strategy. In this context, we examined the seasonal abundance and population structure of the short-tailed stingray ( Dasyatis brevicaudata ) at an offshore MPA in northeastern New Zealand, and the reported use of this location as a mating ground. Diver surveys were conducted from 2004 to 2007 at the Poor Knights Islands Marine Reserve (PKIMR). During this time, we observed: (i) a substantial increase in adult and subadult numbers, particularly females during the suggested breeding season, and a corresponding increase in females bearing fresh mating scars; and (ii) large numbers of smaller (probably immature) D. brevicaudata individuals of both sexes from spring to autumn. These results suggest that the PKIMR acts as both a mating aggregation location and a nursery for this species. We suggest that for coastal stingrays such as D. brevicaudata , small MPAs may be effective at protecting key life-history stages, but that as movements outside of reserve boundaries also occur, additional management tools may also be necessary.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 5
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    Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction (2016)
    Oxford University Press
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    Publication Date: 2016-02-20
    Description: Molecular dynamics simulations of the Caenorhabditis elegans transcription factor SKN-1 bound to its cognate DNA site show that the protein–DNA interface undergoes significant dynamics on the microsecond timescale. A detailed analysis of the simulation shows that movements of two key arginine side chains between the major groove and the backbone of DNA generate distinct conformational sub-states that each recognize only part of the consensus binding sequence of SKN-1, while the experimentally observed binding specificity results from a time-averaged view of the dynamic recognition occurring within this complex.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Mitochondrial DNA population structure of the scalloped lobster Panulirus homarus (Linnaeus 1758) from the West Indian Ocean (2013)
    Oxford University Press
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    Publication Date: 2013-10-15
    Description: Farhadi, A., Farhamand, H., Nematollahi, M. A., Jeffs, A., and Lavery, S. D. 2013. Mitochondrial DNA population structure of the scalloped lobster Panulirus homarus (Linnaeus 1758) from the West Indian Ocean. – ICES Journal of Marine Science, 70: . The scalloped spiny lobster Panulirus homarus (Linnaeus, 1758) is a highly valuable species with a widespread global distribution, ranging from South Africa around the Persian Gulf, and across the Indo-Pacific as far as Japan and French Polynesia. Throughout its range, the species is an important fisheries species with global annual landings in the order of 3000 t. Mitochondrial control region DNA sequences (625 bp) were used to investigate the population genetic structure of this species in the West Indian Ocean (WIO), using 137 individuals collected from four sites, including two locations along the south coast of Iran, and sites along the coast of the Sultanate of Oman in the Arab Sea, as well as Tanzania in eastern Africa. High levels of haplotype diversity ( H = 0.997) were observed in all populations, although nucleotide diversity was relatively low (pi = 0.035). The hypothesis of a single stock in this region was rejected, with highly significant genetic differentiation revealed between Tanzania and the remaining locations (overall ST = 0.039, p 〈 0.00001), as well as slight genetic structure in the Arabian Sea region. Historical population expansion was inferred from Tajima's D and Fu's F tests. The results reveal at least two distinct genetic stocks in WIO and may have major implications for fisheries management.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 7
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    Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA (2014)
    Oxford University Press
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    Publication Date: 2014-10-10
    Description: We have made a detailed study of one of the most surprising sources of polymorphism in B-DNA: the high twist/low twist (HT/LT) conformational change in the d(CpG) base pair step. Using extensive computations, complemented with database analysis, we were able to characterize the twist polymorphism in the d(CpG) step in all the possible tetranucleotide environment. We found that twist polymorphism is coupled with BI/BII transitions, and, quite surprisingly, with slide polymorphism in the neighboring step. Unexpectedly, the penetration of cations into the minor groove of the d(CpG) step seems to be the key element in promoting twist transitions. The tetranucleotide environment also plays an important role in the sequence-dependent d(CpG) polymorphism. In this connection, we have detected a previously unexplored intramolecular C-H···O hydrogen bond interaction that stabilizes the low twist state when 3'-purines flank the d(CpG) step. This work explains a coupled mechanism involving several apparently uncorrelated conformational transitions that has only been partially inferred by earlier experimental or theoretical studies. Our results provide a complete description of twist polymorphism in d(CpG) steps and a detailed picture of the molecular choreography associated with this conformational change.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    {mu}ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA (2014)
    Oxford University Press
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    Publication Date: 2014-11-07
    Description: We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequence effects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Long-timescale dynamics of the Drew-Dickerson dodecamer (2016)
    Oxford University Press
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    Publication Date: 2016-05-20
    Description: We present a systematic study of the long-timescale dynamics of the Drew–Dickerson dodecamer (DDD: d(CGCGAATTGCGC) 2 ) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na + Cl – or K + Cl – . The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10 μs) simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 μs of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Analyzing ion distributions around DNA (2014)
    Oxford University Press
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    Publication Date: 2014-07-04
    Description: We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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