Closed circular DNA

Fig. 6. The envelope of the writhing number of closed circular DNA subject to torsional stress as a function of 7, as computed from Langevin trajectories. Data are from [31].

Fig. 7. Writhe distributions for closed circular DNA as obtained by LI (see Section 4.1) versus explicit integration of the Langevin equations. Data are from [36].

Dl A. Supercoiling. Supercoiling is a topological property of closed-circular DNA molecules. Circular DNA molecules can exist in various conformations differing in the number of times one strand of the helix crosses the other. These different isomeric conformations are called topoisomers and maybe characterized in terms of the linking number, Ek. A linear DNA molecule having Nbase pairs and h base pairs per turn of the helix, if joined end to end, has the following ... 

Fig. 4. Laboratory tubing model for supercoiling in closed-circular DNA (a) relaxed DNA, ALK = 0 (b) ALK = ATw -...

Knots nd Ca.tena.nes, Closed-circular DNA hehces can cross over one another three or more times to form topological knots. These stmctures are not common, but have been found to occur naturally in some bacteriophage DNAs. 

Catenanes are formed when two or more closed-circular DNAs are linked together to form a chain. Catenanes were first isolated in human mitochondrial DNA and have since been identified in a number of biological systems. These stmctures often occur as intermediates during the repHcation of circular DNA molecules. 

Double-stranded DNA (calf thymus) Single-stranded DNA Heat-denatured DNA Closed circular DNA Ribosomal RNA (rat liver)... 

Closed circuit voltage, 3 410 Closed-circular DNA, 27 611. See also Deoxyribonucleic acid (DNA) Closed-closed tubular reactors, 25 288 Closed-loop bioremediation defined, 3 759t... 

It is obvious that the single-molecule approaches can reveal features of the dynamics of chromatin assembly and its force dependence that could not be observed using the standard biochemical assays to study assembly following changes in superhelicity in closed circular DNA molecules, looking at changes in protection against enzymes like micrococcal nuclease, or the accessibility of restriction enzymes. 

Chracteristics of B. m terium s plasmid system have been summarized by Carlton (3p. The plasmids are typical in that they band as covalently closed circular DNA in ethidium bromide-cesium chloride gradients and they are resistant to irreversible alkaline denaturation (17). However, B. megaterium plasmids are atypical in that they exist in approximately 10 size classes and as many copies per cell ( ). In fact, for the smaller plasmids there are hundreds of copies per cell so that plasmid DNA may represent up to 40% of the total extractable DNA (31). This is unusual since for most plasmids there are usually no more than a few copies per cell. Also, hybridization studies suggest that there is extensive homology between three B. megaterium plasmids of different sizes and between these plasmids and the chromosomal DNA (31,33). Carlton (31) concludes that the most likely explanation of the origin of B. megaterium plasmids is that they are molecular hybrids between one or more plasmid elements and various portions of the chromosomal DNA. 

The underwound state can be maintained only if the DNA is a closed circle or if it is bound and stabilized by proteins so that the strands are not free to rotate about each other. If there is a break in one strand of an isolated, protein-free circular DNA, free rotation at that point will cause the underwound DNA to revert spontaneously to the relaxed state. In a closed-circular DNA molecule, however, the number of helical turns cannot be changed without at least transiently breaking one of the DNA strands. The number of helical turns in a DNA molecule therefore provides a precise description of supercoiling. 

We can now extend these ideas to a closed-circular DNA with 2,100 bp (Fig. 24-16a). When the molecule... 

FIGURE 24-16 Linking number applied to closed-circular DNA molecules. A 2,100 bp circular DNA is shown in three forms (a) relaxed, Lk = 200 (b) relaxed with a nick (break) in one strand, Lk undefined and (c) underwound by two turns, Lk = 198. The underwound molecule generally exists as a supercoiled molecule, but underwinding also facilitates the separation of DNA strands. 

Tw and Wr need not be integers. Twist and writhe are geometric rather than topological properties, because they may be changed by deformation of a closed-circular DNA molecule. 

FIGURE 24-28 Chromatin assembly, (a) Relaxed, closed-circular DNA. (b) Binding of a histone core to form a nucleosome induces one negative supercoil, in the absence of any strand breaks, a positive supercoil must form elsewhere in the DNA (ALk = 0). (c) Relaxation of this positive supercoil by a topoisomerase leaves one net negative supercoil (ALk = -1). 

HGURE 24-35 Model for the effect of condensins on DNA super-coiling. Binding of condensins to a closed-circular DNA in the presence of topoisomerase I leads to the production of positive supercoils (+). Wrapping of the DNA about the condensin introduces positive supercoils because it wraps in the opposite sense to a solenoidal supercoil (see Fig. 24-24).The compensating negative supercoils (—) that appear elsewhere in the DNA are then relaxed by topoisomerase I. In the chromosome, it is the wrapping of the DNA about condensin that may contribute to DNA condensation. 

Linking Number A closed-circular DNA molecule in its relaxed form has an Lk of 500. Approximately how many base pairs are in this DNA How is the linking number altered (increases, decreases, doesn t change, becomes undefined) when (a) a protein complex is bound to form a nucleosome,... 

Double-stranded DNA in solutions of low salt content usually assume the B-DNA conformation with 10.4-10.5 base pairs per turn. If the two ends are joined the resulting covalently closed circular DNA will be "relaxed." However, there are topoisomerases that act on this form of DNA by cutting both strands, holding the ends, and twisting the two chains (Chapter 27). 

In closed circular DNA the value of Wr is usually negative, the secondary structure being a fully formed Watson-Crick helix but with right-handed interwound superhelical turns or left-handed toroidal superhelical turns. The helix is said to be underwound (Lk < Tw). 

Agarose gel electrophoresis is able to resolve topoisomers of native, covalently closed, circular DNA that differ only in their degree of supercoiling. This technique has proved useful in the analysis and characterization of... 

W. Bauer and J. Vinograd,/. Mol. Biol. 33, 141-171 (1968). The Interaction of Closed Circular DNA with Intercalative Dyes. ... 

DNA that contained both closed, circular DNA and supercoiled DNA. Would you expect to see two bands in the sedimentation pattern Explain. 

Methods that cause selective precipitation of chromosomal DNA by various agents. These methods exploit the relative resistance of covalently closed circular DNA to extremes of pH, temperature, or other denaturing agents. 

The influence of molecular shape on electrophoretic mobility is not a critical factor to consider in the experiment. The action of restriction enzymes on both covalent closed circular DNA and linear DNA results in the formation of linear fragments. 

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