Elastic model of DNA supercoiling in the infinite-length limit

Abstract

The energies of plectonemic and toroidal supercoiled DNA are calculated by treating DNA as an elastic rod with a finite radius. End effects are ignored and all extensive quantities (e.g., writhe, bend energy) are treated as linear densities (writhe per unit length, bend energy per unit length). Minimum energy configurations are found. For plectonemic DNA, the superhelical pitch angle cz is in the range 45" < ag90". For low values of specific linking difference, most superhelicity is in writhe. As specific linking difference increases, a greater proportion of superhelicity is in twist. Under physiological conditions, roughly 8X% of superhelicity is in writhe. Ionic strength effects are discussed, and it is found that variation of excluded volume with ionic strength has a large effect, resulting in significantly greater torsional stress in supercoiled DNA at low ionic strength. For biologically relevant values of specific linking difference, the plectonemic conformation is energetically favored over toroidal conformations. Results are compared with electron microscopy data. The application of the model to DNA conformational transitions is discussed. strength.45A8 J. Chem. Phys. 95 (12), 15 December 1991

DNA in a liquid-crystalline environment: Tight bends, rings, supercoils

“…A classic example of the latter is supercoiled DNA which has routinely been studied by neglecting the entropy altogether. [2][3][4][5][6][7][8][9][10][11][12][13][14] Often, this may be a very good approximation. Still, in certain experiments, the undulations of the DNA helix within supercoils do play a significant role.…”

Transcription of genetic information in the framework of quantum information theory

“…It is noted that the von Neumann entropy for an entangled spin system in a pure state is reduced to the entanglement of formation given by concurrence in a mixed state. 25 Thus the above expression (30) represents the entanglement entropy of the spin system. Now we consider that the supercoiled stiff polymer (DNA) is confined inside a narrow tube of radius r .…”

The nonlinear dynamics of elastic tubes conveying a fluid

“…They have been applied to the study of problems as diverse as the super-coiling of DNA strands (Benham, 1979(Benham, , 1983Tanaka and Takahashi, 1985;Benham, 1989;Hunt and Hearst, 1991;Coleman et al, 1995b;Manning et al, 1996;Westcott et al, 1997;Tobias et al, 2000;Thompson et al, 2002;Hoffman et al, 2003;Hoffman, 2004) and the buckling of ocean cables (Zajac, 1962;Coyne, 1990;Costello, 1990;Neukirch and van der Heijden, 2002) -both of which, despite their enormous disparities in scale and mechanical properties, exhibit the same fundamental twist-towrithe instability, namely the looping that occurs when a critical twist threshold is reached.…”