Supercoils, DNA

G. Ramachandran and T. Schlick. Solvent effects on supercoiled DNA dynamics explored by Langevin dynamics simulations. Phys. Rev. E, 51 6188-6203, 1995. 

G. Ramachandran and T. Schlick. Beyond optimization Simulating the dynamics of supercoiled DNA by a macroscopic model. In P. M. Pardalos, D. Shal-loway, and G. Xue, editors. Global Minimization of Nonconvex Energy Functions Molecular Conformation and Protein Folding, volume 23 of DIM ACS Series in Discrete Mathematics and Theoretical Computer Science, pages 215-231, Providence, Rhode Island, 1996. American Mathematical Society. 

T. Schlick and W. K. Olson. Trefoil knotting revealed by molecular dynamics simulations of supercoiled DNA. Science, 257 1110-1115, 1992. 

Electron micrographs of supercoiled DNA m vitro demonstrate that supercoiled molecules have a stmcture intermediate between Figures 4c and 4d, where changes in the linking number are accompanied by approximately a 75% change in Wr and a 25% change in Tw. This conformation is called plectonemic supercoiling. 

The basic parameter characterizing supercoiled DNA is the linking number (L). This is the number of times the two strands are intertwined, and, provided both strands remain covalently intact, L cannot change. In a relaxed circular... 

Negatively supercoiled DNA can arrange into a toroidal state (Figure 12.26). The toroidal state of negatively supercoiled DNA is stabilized by wrapping around proteins which serve as spools for the DNA ribbon. This toroidal con-... 

Bentin T., Nielsen P. E. Enhanced peptide nucleic acid binding to supercoiled DNA possible implications for DNA breathing dynamics. Biochemistry 1996 35 8863-8869. 

Stellwagen, NC, Effect of Pulsed and Reversing Electric Eields on the Orientation of Linear and Supercoiled DNA Molecules in Agarose Gels, Biochemistry 27, 6417, 1988. 

Garon, C. F. and Peterson, L. L., An improved method for the isolation of supercoiled DNA molecules using ion-exchange column chromatography, Gene Anal. Technol., 4, 5, 1987. 

An extract from Lactuca indica showed significant free radical scavenging activity, and protected phixl74 supercoiled DNA against strand cleavage and reduced oxidative stress in human promyelocytic leukemia HL-60 cells. On account of protocatechulic acid, methyl p-hydroxybenzoate, caffeic acid, 3,5-dicaffeoylquinic acid, luteolin 7-O-fT glucopyranoside, and quercetin 3-0-(3-g 1 ucopyranoside are the major antioxidative constituents (111). 

Alkynyl-3-methoxy-4-hydroxycyclobutenones [31] have also been shown to cleave supercoiled DNA, and DNA damage was believed to be mediated by diradicals (Fig. 9) arising from the thermal decomposition of cyclobutenones at 49 °C. 

In most DNA molecules the two ends of the DNA double helix are joined to form a closed circle. When this occurs the DNA then forms a supercoil by winding back on itself. Supercoiled DNA depends on the integrity of the closed circle. Any breaks in the circle will cause unwinding of the supercoil. 

Figure 13.7 Caesium chloride density gradient centrifugation for (a) the separation of DNA from RNA and protein and (b) the separation of linear DNA and supercoiled DNA.

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