521 research outputs found

    The bend stiffness of S-DNA

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    We formulate and solve a two-state model for the elasticity of nicked, double-stranded DNA that borrows features from both the Worm Like Chain and the Bragg--Zimm model. Our model is computationally simple, and gives an excellent fit to recent experimental data through the entire overstretching transition. The fit gives the first value for the bending stiffness of the overstretched state as about 10 nm*kbt, a value quite different from either B-form or single-stranded DNA.Comment: 7 pages, 1 figur

    Detrital zircon records of Late Cretaceous syn-rift sedimentary sequences of New Caledonia: an Australian provenance questioned

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    International audienceThe Late Cretaceous clastic coastal sediments of New Caledonia are contemporaneous with the latest stages of the eastern Australian marginal rifting. As such, they record the erosion of basement terranes located on uplifted and tilted blocks and a contemporaneous volcanic activity. Detrital zircon populations contain two major components, the younger of which is Early Cretaceous, and the older Early Paleozoic and Precambrian. Following recent advances in the knowledge of detrital zircon content of basement terranes, and at variance with previous interpretations, that hypothesised a possible direct Australian provenance for Precambrian zircons, the detrital zircon record of these syn-rift sediments allows a local recycled provenance to be established. In consequence, this new evidence confirms that New Caledonia was already isolated from Australia as early as Coniacian time (ca. 89-85 Ma) a fact consistent with the development of faunal and floral endemism at that period. The prominent abundance of Early Cretaceous detrital zircons also establishes the importance of a previously unrecorded Early Cretaceous magmatism in the area

    Torsional Directed Walks, Entropic Elasticity, and DNA Twist Stiffness

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    DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional directed walk'. Motivated by a recent experiment on single lambda-DNA molecules [Strick et al., Science 271 (1996) 1835], we formulate the torsional directed walk problem and solve it analytically in the appropriate force regime. Our technique affords a direct physical determination of the microscopic twist stiffness C and twist-stretch coupling D relevant for DNA functionality. The theory quantitatively fits existing experimental data for relative extension as a function of overtwist over a wide range of applied force; fitting to the experimental data yields the numerical values C=120nm and D=50nm. Future experiments will refine these values. We also predict that the phenomenon of reduction of effective twist stiffness by bend fluctuations should be testable in future single-molecule experiments, and we give its analytic form.Comment: Plain TeX, harvmac, epsf; postscript available at http://dept.physics.upenn.edu/~nelson/index.shtm

    Discrete elastic model for stretching-induced flagellar polymorphs

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    Force-induced reversible transformations between coiled and normal polymorphs of bacterial flagella have been observed in recent optical-tweezer experiment. We introduce a discrete elastic rod model with two competing helical states governed by a fluctuating spin-like variable that represents the underlying conformational states of flagellin monomers. Using hybrid Brownian dynamics Monte-Carlo simulations, we show that a helix undergoes shape transitions dominated by domain wall nucleation and motion in response to externally applied uniaxial tension. A scaling argument for the critical force is presented in good agreement with experimental and simulation results. Stretching rate-dependent elasticity including a buckling instability are found, also consistent with the experiment

    Probing complex RNA structures by mechanical force

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    RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by solely invoking successive openings of native helices. Indeed, typical force-extension responses of complex RNA molecules are largely shaped by stretching-induced, long-lived intermediates including non-native helices. This is first shown for a set of generic structural motifs found in larger RNA structures, and then for Escherichia coli's 1540-base long 16S ribosomal RNA, which exhibits a surprisingly well-structured and reproducible unfolding pathway under mechanical stretching. Using out-of-equilibrium stochastic simulations, we demonstrate that these experimental results reflect the slow relaxation of RNA structural rearrangements. Hence, micromanipulations of single RNA molecules probe both their native structures and long-lived intermediates, so-called "kinetic traps", thereby capturing -at the single molecular level- the hallmark of RNA folding/unfolding dynamics.Comment: 9 pages, 9 figure
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