DNA linear

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 ... 

Exonucleases. Like the endonucleases they are restriction enzymes which act at the 3 or 5 ends of linear DNA by hydrolysing off the nucleotides. Although they are highly specific for hydrolysing nucleotides at the 3 or 5 ends of linear DNA, the number of nucleotides cleaved are time dependent and usually have to be estimated from the time allocated for cleavage. Commercially available exonucleases are used without further purification. 

The processes of meiosis and mitosis involve many motile events, from the separation of the daughter chromosomes to the final act of cell separation at cytokinesis (Wadsworth, 1993). DNA replication itself may be considered as a motile event, because the polymerase complex moves along the linear DNA. One of the most obvious motile events is the separation of the chromosomes along the mitotic spindle at anaphase. Details of the structure and polarity of microtubules in the spindle apparatus in meiosis and mitosis are known through electron and light microscopy, but it is not yet clear whether the chromosomes are pushed, pulled or... 

Schwinefus, J.J., Hammond, R.W., Oana, H., Wang, S.-C., De Carmejane, O., Bonadio, ]., and Morris, M.M., Comparative conformational dynamics of su-percoiled plasmids and linear DNA during capillary electrophoresis, Macromolecules, 32, 4625, 1999. 

Single-cell eukaryotes Linear DNA Organelle DNA (RNA) As above Ca2+ gradients (external store)... 

There are some features of the genetic apparatus which are often lost from sight while concentration is engaged on one essential feature, the linear DNA that codes the proteins of the cell. The other features are ... 

We routinely use a mix of five mRNAs that are derived from the lys (ATCC no. 87482), trp (ATCC no. 87485), dap (ATCC no. 87486), thr (ATCC no. 87484), andphe (ATCC no. 87483) clones from the bacterium Bacillus subtilis cloned into a vector that contains a stretch of As. These RNAs are generated by in vitro transcription using a T3 in vitro transcription kit (e.g., MEGAscript from Ambion) of the linearized DNA template with the appropriate restriction enzyme. 

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.

Similar sequences of accurate analytical approximations to Cn(t) have been presented for circular DNAs(82) and linear DNAs with both ends clamped,(29,63) but are not reproduced here. At present, no complete sequence of accurate analytical approximations is available for linear DNAs with only one end clamped. 

Table 4.1. Lower-Bound and Upper-Bound Torsion Constants between Base Pairs for Various Linear DNAs at 20°C ...

Figure 4.13, Torsion constant a. versus NaCl concentration for linear DNAs. O, Linear pBR322 , calf thymus DNA x, 3300-bp Hindi fragment of pBR322.

Equation (4.68) with a = 0 applies for linear or nicked circular DNAs. When r = r, the (initially) supercoiled DNA is predicted to experience no deformational strain, as it is fully relaxed, and to bind the same amount of dye as its linear counterpart with the same concentration of free dye. Under these conditions, the supercoiled and linear DNA/chloroquine complexes are expected to exhibit identical local structures, rigidities, and deformational dynamics. This important corollary to the standard model was untested till recently.(53)... 

In the absence of chloroquine, the apparent torsion constants for supercoiled pBR322 DNAs with normal (allosteric transitions in secondary structure, so the secondary structures of supercoiled and linear DNAs might not be identical, despite their similar torsion constants. 

At binding ratios r > 0.27, both linear and supercoiled DNAs show evidence of a marked structural change. A component with intermediate lifetime (t 5 ns) appears in the ethidium fluorescence decay, which may represent a partially intercalated species. The apparent torsion constants become highly nonuniform and exhibit considerably altered values. The long-range torsion constant increases appreciably for the linear DNA, but decreases for the supercoiled DNAs, which are substantially positively supercoiled at that point.(53)... 

Up to r = 0.10, intercalated ethidium has no significant effect on the torsion constant of linear DNAs, as indicated in Figure 4.17.(223) Together... 

Figure 4.18. Torsion constant a of supercoiled pJMS2 DNA versus ethidium/base pair, denoted by EB/BP. The lilted symbols are torsion constants obtained after correcting for the effects of energy transfer. The open symbols are the apparent torsion constants obtained from FPA data without taking excitation transfer into account. Even after correcting for excitation transfer, the torsion constant of this supercoiled DNA decreases appreciably with increasing intercalated ethidium, in contrast to linear DNAs.

---