Topology in Molecular Biology
2 Topology in Biology: From DNA Mechanics to Enzymology 7 Intrinsically straight wormlike chains, those whose minimum-energy con ...
8 S.D. Levene Fig. 2.3.Several conformations of an intrinsically straight wormlike chain with contour length,L, equal to the per ...
2 Topology in Biology: From DNA Mechanics to Enzymology 9 static value of the persistence length,Ps. For DNA fragments that repr ...
10 S.D. Levene Fig. 2.4.Topology of closed circular DNA. (a) Sign convention for DNA crossings in closed-circular DNA. The conve ...
2 Topology in Biology: From DNA Mechanics to Enzymology 11 Fig. 2.5.Interconversion of idealized branched and unbranched plecton ...
12 S.D. Levene Fig. 2.6.(a) The set of all prime topologies containing up to nine irreducible knot crossings and dimeric catenan ...
2 Topology in Biology: From DNA Mechanics to Enzymology 13 kb-laddersupercolled plasmidknotted plasmidlinear plasmidknotted plas ...
14 S.D. Levene information in a cell nucleus that is of order 5–10μm in diameter. In the case of the human genome, there is abou ...
2 Topology in Biology: From DNA Mechanics to Enzymology 15 Fig. 2.8.Equilibrium between interwound (plectonemic) and toroidal su ...
16 S.D. Levene complex is responsible for carrying out specific cleavage, strand exchange, and ligation steps that result in the ...
2 Topology in Biology: From DNA Mechanics to Enzymology 17 Fig. 2.9.Two representations of the structure of a DNA Holliday junct ...
18 S.D. Levene Fig. 2.10.Topology of products generated by recombination of circular DNA mole- cules mediated by theλ-int superf ...
2 Topology in Biology: From DNA Mechanics to Enzymology 19 Fig. 2.11.(a) Linear DNA recombination substrates consisting of minim ...
20 S.D. Levene be significant bending of the DNA arms that emerge from the junction. In the latter case at least 90 degrees of D ...
2 Topology in Biology: From DNA Mechanics to Enzymology 21 D.M. Crothers, J. Drak, J.D. Kahn, S.D. Levene, Methods Enzymol. 212 ...
3 Monte Carlo Simulation of DNA Topological Properties A. Vologodskii Summary.In the scale of hundreds and thousands of base pai ...
24 A. Vologodskii are homogeneous, thin, and long. They can be easy converted from linear to circular form. Circular DNA molecul ...
3 Monte Carlo Simulation of DNA Topological Properties 25 the torus class. The quantitative description of such links is calledt ...
26 A. Vologodskii Fig. 3.2.A typical conformation of supercoiled DNA. Thedouble helixis presented here by the flexible rod. The ...
3 Monte Carlo Simulation of DNA Topological Properties 27 Fig. 3.3.Probing conformational properties of supercoiled DNA by forma ...
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