Supercoiling and Denaturation of DNA Loops

Liverpool, Tanniemola B.; Harris, S B; Laughton, Charles A.

doi:10.1103/physrevlett.100.238103

Cited by 24 publications

(25 citation statements)

References 21 publications

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“…We observed a supercoiling (buckling) transition associated with the off-plane deformation instability of the minicircles for |σ| > |σ ± c (L)|, as predicted by analytical calculations on a simple elastic model [16,32] and recent full-atomistic simulations. [15] The transition is marked by a sudden increase in the writhe, while |σ c | decreases with L and practically disappears beyond L/l p ≈ 6 (σ ± c ∼ L −1 for elastic models).…”

Section: Discussionmentioning

confidence: 90%

“…DNA minicircles provide a convenient setting where mechanical properties, such as the asymmetry of the molecule under positive and negative supercoiling, the possibility of torsion-induced denaturation and kink formation can be studied both experimentally [7] and theoretically. [15,16,17] Despite steady progress in the field in recent decades, a full comprehension of these phenomena is still ahead of us. Analytical models have been successful in explaining many qualitative aspects of DNA mechanics, however, they are typically too simplistic to capture fine details, especially in the short chain limit.…”

Section: A Introductionmentioning

confidence: 99%

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Twist-writhe partitioning in a coarse-grained DNA minicircle model

2010

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Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion, therefore our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times.Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.

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Section: Discussionmentioning

confidence: 90%

Section: A Introductionmentioning

confidence: 99%

Twist-writhe partitioning in a coarse-grained DNA minicircle model

2010

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“…Finally, including in the algorithm other types of elementary motions, such as reptation moves (48), and in the model the possibility of denaturation (49), sequence heterogeneities (16), and the presence of bridging protein complexes (50) and independent topological microdomains (51) are avenues for future investigation.…”

Section: Discussionmentioning

confidence: 99%

Thermodynamics of Long Supercoiled Molecules: Insights from Highly Efficient Monte Carlo Simulations

Lepage

Képès

Junier

2015

Biophysical Journal

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Supercoiled DNA polymer models for which the torsional energy depends on the total twist of molecules (Tw) are a priori well suited for thermodynamic analysis of long molecules. So far, nevertheless, the exact determination of Tw in these models has been based on a computation of the writhe of the molecules (Wr) by exploiting the conservation of the linking number, Lk=Tw+Wr, which reflects topological constraints coming from the helical nature of DNA. Because Wr is equal to the number of times the main axis of a DNA molecule winds around itself, current Monte Carlo algorithms have a quadratic time complexity, O(L(2)), with respect to the contour length (L) of the molecules. Here, we present an efficient method to compute Tw exactly, leading in principle to algorithms with a linear complexity, which in practice is O(L(1.2)). Specifically, we use a discrete wormlike chain that includes the explicit double-helix structure of DNA and where the linking number is conserved by continuously preventing the generation of twist between any two consecutive cylinders of the discretized chain. As an application, we show that long (up to 21 kbp) linear molecules stretched by mechanical forces akin to magnetic tweezers contain, in the buckling regime, multiple and branched plectonemes that often coexist with curls and helices, and whose length and number are in good agreement with experiments. By attaching the ends of the molecules to a reservoir of twists with which these can exchange helix turns, we also show how to compute the torques in these models. As an example, we report values that are in good agreement with experiments and that concern the longest molecules that have been studied so far (16 kbp).

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“…Refinements to the classical elastic models that incorporate the findings from studies of DNA mechanics at the atomistic level such as sequence-dependent flexibility (Czapla et al . 2006), denaturation, and non-linear elasticity (Liverpool et al . 2008), provide a more accurate description of DNA mechanics and help bridge the gap between coarse-grained and atomistic models.…”

Section: Understanding Supercoiled Dna At the Molecular Level By Cmentioning

confidence: 99%

“…(2005) and Wiggins et al . (2005) modified traditional DNA bending theory to allow for `rare' transient appearances of sharp DNA kinks, while others proposed a role for spontaneous melting of base pairs (Liverpool et al . 2008; Yan & Marko, 2004; Yan et al .…”

Section: Understanding Supercoiled Dna At the Molecular Level By Cmentioning

confidence: 99%

Bullied no more: when and how DNA shoves proteins around

Fogg

Randall

Pettitt

et al. 2012

Quart. Rev. Biophys.

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The predominant protein-centric perspective in protein–DNA-binding studies assumes that the protein drives the interaction. Research focuses on protein structural motifs, electrostatic surfaces and contact potentials, while DNA is often ignored as a passive polymer to be manipulated. Recent studies of DNA topology, the supercoiling, knotting, and linking of the helices, have shown that DNA has the capability to be an active participant in its transactions. DNA topology-induced structural and geometric changes can drive, or at least strongly influence, the interactions between protein and DNA. Deformations of the B-form structure arise from both the considerable elastic energy arising from supercoiling and from the electrostatic energy. Here, we discuss how these energies are harnessed for topology-driven, sequence-specific deformations that can allow DNA to direct its own metabolism.

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Supercoiling and Denaturation of DNA Loops

Cited by 24 publications

References 21 publications

Twist-writhe partitioning in a coarse-grained DNA minicircle model

Twist-writhe partitioning in a coarse-grained DNA minicircle model

Thermodynamics of Long Supercoiled Molecules: Insights from Highly Efficient Monte Carlo Simulations

Bullied no more: when and how DNA shoves proteins around

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