Competition between curls and plectonemes near the buckling transition of stretched supercoiled DNA

Marko, John F.; Neukirch, Sébastien

doi:10.1103/physreve.85.011908

Cited by 81 publications

(181 citation statements)

References 44 publications

(110 reference statements)

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“…6). This actually is line with theoretical [26,29] and experimental [11,12,13] trends for single molecule twisting; the size of the extension drop reduces and goes away with decreasing salt concentration. Therefore, perhaps this feature is indeed the hallmark of the formation of end loop of a super plectoneme structure, in which the braid axis traces out a plectoneme.…”

Section: Discussion and Outlooksupporting

confidence: 87%

“…[33] and [34], also implied in the calculations of Refs. [17,25,26,27]. This self-consistent calculation is akin to the approach used by Ref.…”

Section: Discussion and Outlookmentioning

confidence: 99%

“…a.) Electronic Mail: domolee@hotmail.com To describe single molecule twisting experiments and plectoneme supercoiling a considerable amount of theoretical work has been performed [17,18,19,20,21,22,23,24,25,26,27,28,29,30]. However, little work has been done on the statistical mechanics of dual molecular braiding [31,32].…”

Section: Introductionmentioning

confidence: 99%

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Self-consistent treatment of electrostatics in molecular DNA braiding through external forces

Lee

2014

Phys. Rev. E

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In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the braid. The system is subjected to an external pulling force, and a moment that induces the braiding. In a model, developed for understanding such a system, we assume that each molecule can be divided into a braided and unbraided section. We also suppose that the DNA is nicked so that there is no constraint of the individual linking numbers of the molecules. Included in the model are steric and electrostatic interactions, thermal fluctuations of the braided and unbraided sections of the molecule, as well as the constraint on the braid linking (catenation) number. We compare two approximations used in estimating the free energy of the braided section. One is where the amplitude of undulations of one molecule with respect to the other is determined only by steric interactions. The other is a self-consistent determination of the mean squared amplitude of these undulations. In this second approximation electrostatics should play an important role in determining this quantity, as suggested by physical arguments. We see that if the electrostatic interaction is sufficiently large there are indeed notable differences between the two approximations. We go on to test the self-consistent approximation, included in the full model, against experimental data, for such a system, and we find good agreement. However, there seems to by a slight left/right handed braid asymmetry in some of the experimental results. We discuss what might be the origin of this small asymmetry

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Section: Discussion and Outlooksupporting

confidence: 87%

“…[33] and [34], also implied in the calculations of Refs. [17,25,26,27]. This self-consistent calculation is akin to the approach used by Ref.…”

Section: Discussion and Outlookmentioning

confidence: 99%

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Self-consistent treatment of electrostatics in molecular DNA braiding through external forces

Lee

2014

Phys. Rev. E

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“…3 A and 4 A and the values g exp and b exp derived by fitting the experimental measurements to a power-law fitting function, the predicted n b -versus-F behavior is reasonably confirmed (g exp x0:6), but the theoretical relationship between dL e =dn t and F has not been adequately established (b exp x À 0:25). However, quantitative discrepancies between theory and experiment have been observed for bare DNA several times in past research (29,(57)(58)(59), and more sophisticated models have been presented (60)(61)(62)(63)(64) to describe the experimental findings with better accuracy. Here, we focus on the dependence of g exp and b exp on the binding of the evaluated platinum-based drugs.…”

Section: Discussionmentioning

confidence: 99%

Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements

Salerno

Beretta

Zanchetta

et al. 2016

Biophysical Journal

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Platinum-containing molecules are widely used as anticancer drugs. These molecules exert cytotoxic effects by binding to DNA through various mechanisms. The binding between DNA and platinum-based drugs hinders the opening of DNA, and therefore, DNA duplication and transcription are severely hampered. Overall, impeding the above-mentioned important DNA mechanisms results in irreversible DNA damage and the induction of apoptosis. Several molecules, including multinuclear platinum compounds, belong to the family of platinum drugs, and there is a body of research devoted to developing more efficient and less toxic versions of these compounds. In this study, we combined different biophysical methods, including single-molecule assays (magnetic tweezers) and bulk experiments (ultraviolet absorption for thermal denaturation) to analyze the differential stability of double-stranded DNA in complex with either cisplatin or multinuclear platinum agents. Specifically, we analyzed how the binding of BBR3005 and BBR3464, two representative multinuclear platinum-based compounds, to DNA affects its stability as compared with cisplatin binding. Our results suggest that single-molecule approaches can provide insights into the drug-DNA interactions that underlie drug potency and provide information that is complementary to that generated from bulk analysis; thus, single-molecule approaches have the potential to facilitate the selection and design of optimized drug compounds. In particular, relevant differences in DNA stability at the single-molecule level are demonstrated by analyzing nanomechanically induced DNA denaturation. On the basis of the comparison between the single-molecule and bulk analyses, we suggest that transplatinated drugs are able to locally destabilize small portions of the DNA chain, whereas other regions are stabilized.

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“…4). Several theoretical models have been able to reproduce with good accuracy the mean extension of these molecules (2,(13)(14)(15). Nevertheless, predictions differ in the numbers of plectonemes and in the types of structures that are able to form (14,15).…”

Section: Introductionmentioning

confidence: 95%

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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Competition between curls and plectonemes near the buckling transition of stretched supercoiled DNA

Cited by 81 publications

References 44 publications

Self-consistent treatment of electrostatics in molecular DNA braiding through external forces

Self-consistent treatment of electrostatics in molecular DNA braiding through external forces

Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements

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

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